U.S. patent application number 16/400257 was filed with the patent office on 2019-08-22 for protein biomarker panels for detecting colorectal cancer and advanced adenoma.
The applicant listed for this patent is DiscernDx, Inc.. Invention is credited to Ryan Benz, John Blume, Lisa Croner, Roslyn Dillon, Jeffrey Jones, Athit Kao, Bruce Wilcox, Jia You.
Application Number | 20190257835 16/400257 |
Document ID | / |
Family ID | 55795201 |
Filed Date | 2019-08-22 |
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United States Patent
Application |
20190257835 |
Kind Code |
A1 |
Blume; John ; et
al. |
August 22, 2019 |
PROTEIN BIOMARKER PANELS FOR DETECTING COLORECTAL CANCER AND
ADVANCED ADENOMA
Abstract
Disclosed herein are panels related to the diagnosis or
recognition of colon and colorectal cancer in a subject. The
disclosed panels and related methods are used to predict or assess
colon tumor status in a patient. They can be used to determine
nature of tumor, recurrence, or patient response to treatments.
Some embodiments of the methods include generating a report for
clinical management.
Inventors: |
Blume; John; (Bellingham,
WA) ; Jones; Jeffrey; (Glendale, CA) ; Benz;
Ryan; (Huntington Beach, CA) ; Kao; Athit;
(San Marcos, CA) ; Croner; Lisa; (San Diego,
CA) ; Dillon; Roslyn; (Cardiff, CA) ; You;
Jia; (San Diego, CA) ; Wilcox; Bruce;
(Harrisonburg, VA) |
|
Applicant: |
Name |
City |
State |
Country |
Type |
DiscernDx, Inc. |
Palo Alto |
CA |
US |
|
|
Family ID: |
55795201 |
Appl. No.: |
16/400257 |
Filed: |
May 1, 2019 |
Related U.S. Patent Documents
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Application
Number |
Filing Date |
Patent Number |
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15629593 |
Jun 21, 2017 |
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16400257 |
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15094767 |
Apr 8, 2016 |
9689874 |
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15629593 |
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62146158 |
Apr 10, 2015 |
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62160560 |
May 12, 2015 |
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62165846 |
May 22, 2015 |
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62196889 |
Jul 24, 2015 |
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62239771 |
Oct 9, 2015 |
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Current U.S.
Class: |
1/1 |
Current CPC
Class: |
G01N 2333/70564
20130101; G01N 2333/99 20130101; G01N 33/57419 20130101; G01N
2333/70596 20130101; G01N 2333/47 20130101 |
International
Class: |
G01N 33/574 20060101
G01N033/574 |
Claims
1. A method of assessing a colorectal cancer risk status in an
individual, comprising the steps of obtaining a circulating blood
sample from the individual; obtaining a biomarker panel level for a
biomarker panel comprising a list of proteins in the sample
comprising AACT, CO3, CO9, MIF, and PSGL to comprise panel
information from said individual; comparing said panel information
from said individual to a reference panel information set
corresponding to a known colorectal cancer status; and categorizing
said individual as having said colorectal cancer risk status if
said individual's reference panel information does not differ
significantly from said reference panel information set.
2. The method of claim 1, wherein obtaining a circulating blood
sample comprises drawing blood from a vein or artery of the
individual
3. The method of claim 1, wherein the panel information comprises
age information for the individual.
4. The method of claim 1, wherein the list of proteins comprises
AACT, CO3, CO9, MIF, PSGL, CATD, CEA and SEPR.
5. The method of claim 1, wherein the categorizing has a
sensitivity of at least 81% and a specificity of at least 78%.
6. The method of claim 1, comprising transmitting a report of
results of said categorizing to a health practitioner.
7. The method of claim 6, wherein the report recommends that a
colonoscopy be performed.
8. The method of claim 1, wherein the individual undergoes a
colonoscopy.
9. The method of claim 1, wherein no parameter of said individual's
reference panel information in isolation is indicative of said
colorectal cancer status in said individual at a sensitivity of
greater than 65% or a specificity of greater than 65%.
10. The method of claim 1, wherein the obtaining protein levels
comprises contacting a fraction of the circulating blood sample to
a set of antibodies, wherein the set of antibodies comprises
antibodies specific to AACT, CO3, CO9, MIF, and PSGL.
11. A method of monitoring efficacy of a colorectal cancer
treatment regimen in an individual, comprising the steps of
obtaining a first sample comprising circulating blood from the
individual at a first time point; administering the treatment
regimen to the individual; obtaining a second sample comprising
circulating blood from the individual at a second time point;
obtaining a first panel level comprising protein levels for a list
of proteins in the first sample and a second panel level comprising
protein levels for a list of proteins in the second sample, said
list comprising AACT, CO3, CO9, MIF, and PSGL to comprise panel
information for said first sample and said second sample; wherein a
change in protein levels indicates efficacy of the colorectal
cancer treatment.
12. The method of claim 11, wherein obtaining the first sample
comprises drawing blood from a vein or artery of the
individual.
13. The method of claim 11, wherein the treatment regimen comprises
a colonoscopy.
14. The method of claim 11, wherein the list of proteins comprises
AACT, CO3, CO9, MIF, PSGL, CATD, CEA and SEPR.
15. The method of claim 11, comprising changing the treatment
regimen if no efficacy is indicated.
16. The method of claim 11, comprising repeating the treatment
regimen if no efficacy is indicated.
17. The method of claim 11, comprising discontinuing the treatment
regimen if efficacy is indicated.
18. A method of assessing an advanced adenoma risk status in an
individual, comprising the steps of obtaining a circulating blood
sample from the individual; obtaining protein levels for a list of
proteins relevant to advanced adenoma in the sample comprising at
least three of CATD, CLUS, GDF15 and SAA1 to comprise biomarker
panel information from said individual; comparing said panel
information from said individual to a reference panel information
set corresponding to a known advanced adenoma status; and
categorizing said individual as having said advanced adenoma risk
status if said individual's reference panel information does not
differ significantly from said reference panel information set.
19. The method of claim 18, wherein obtaining a circulating blood
sample comprises drawing blood from a vein or artery of the
individual
20. The method of claim 18, wherein the panel information comprises
age information for the individual.
21. The method of claim 18, comprising transmitting a report of
results of said categorizing to a healthcare professional.
22. The method of claim 18, wherein the individual undergoes a
colonoscopy.
23. A method of assessing a colorectal health risk status in an
individual, comprising the steps of obtaining a circulating blood
sample from the individual; obtaining a biomarker panel level for a
biomarker panel comprising a list of proteins in the sample
comprising AACT, CO3, CO9, MIF, PSGL, SEPR, CEA, CATD, CLUS, GDF15
and SAA1, and obtaining an age for the individual, wherein AACT,
CO3, CO9, MIF, PSGL, SEPR, CEA, CATD, and age comprise colorectal
cancer panel information from said individual; and wherein CATD,
CLUS, GDF15 and SAA1 comprise advanced adenoma panel information
from said individual; comparing said colorectal cancer panel
information from said individual to a reference colorectal cancer
panel information set corresponding to a known colorectal cancer
status; comparing said advanced adenoma panel information from said
individual to a reference advanced adenoma panel information set
corresponding to a known advanced adenoma status; and categorizing
said individual as having a colorectal health risk if either of
said colorectal cancer panel or said advanced adenoma panel does
not differ significantly from a reference panel positive for a
colorectal health risk.
24. The method of claim 23, wherein obtaining a circulating blood
sample comprises drawing blood from a vein or artery of the
individual.
25. The method of claim 23, wherein the list of proteins comprises
no more than 20 proteins.
26. The method of claim 23, comprising transmitting a report of
results of said categorizing to a health practitioner.
27. The method of claim 26, wherein the report recommends that a
colonoscopy be performed.
28. The method of claim 23, wherein the individual undergoes a
colonoscopy.
29. The method of claim 26, wherein the individual undergoes a
stool cancer assay.
30. The method of claim 26, wherein the obtaining protein levels
comprises contacting a fraction of the circulating blood sample to
a set of antibodies, wherein the set of antibodies comprises
antibodies specific to AACT, CO3, CO9, MIF, PSGL, SEPR, CEA, CATD,
CLUS, GDF15 and SAA1.
Description
RELATED APPLICATIONS
[0001] The present application is a continuation of U.S.
application Ser. No. 15/629,593, filed Jun. 21, 2017, which is a
continuation of U.S. application Ser. No. 15/094,767, filed Apr. 8,
2016, now U.S. Pat. No. 9,689,874, which claims the benefit of U.S.
Provisional Application Ser. No. 62/146,158, filed Apr. 10, 2015,
U.S. Provisional Application Ser. No. 62/160,560, filed May 12,
2015, U.S. Provisional Application Ser. No. 62/165,846, filed May
22, 2015, U.S. Provisional Application Ser. No. 62/196,889, filed
Jul. 24, 2015, and U.S. Provisional Application Ser. No.
62/239,771, filed Oct. 9, 2015, which are all hereby incorporated
by reference in their entirety.
SEQUENCE LISTING
[0002] The instant application contains a Sequence Listing which
has been submitted electronically in ASCII format and is hereby
incorporated by reference in its entirety. Said ASCII copy, created
May 1, 2019, is named 53897-738-302-SL.txt and is 106 KB in
size.
BACKGROUND OF THE INVENTION
[0003] Colorectal cancer (CRC) can result from uncontrolled cell
growth in the colon or rectum (parts of the large intestine), or in
the appendix. CRC can develop from a colon polyp. A colon polyp
typically comprises a benign clump of cells that forms on the
lining of the large intestine or rectum. While many colon polyps
are non-malignant, a polyp can develop into an adenoma. Colorectal
adenomas can then grow into advanced colorectal adenomas, which can
then develop into CRC.
[0004] Colorectal cancer is a leading cause of cancer-related
deaths in the United States with over 142, 820 diagnosed cases and
over 50,000 deaths in 2013. According to a 2011 study, there are an
estimated 1.2 million diagnoses per year and 600,000 deaths
worldwide. CRC is one of the most preventable cancers given its
typically slow progression from early stages to metastatic disease
and available tools for its diagnosis, but it is one of the least
prevented cancers. This is at least partly due to the poor
compliance with available screening by patients due to the invasive
or unpleasant nature of the current screening tests.
[0005] The risk of developing CRC increases with age. Ninety
percent of new cases and 93% of deaths occur in people age 50 and
older. During their 60s, men have a 10-fold increased risk of
developing CRC compared to their 40s. Regular screening allows for
the removal of advanced colorectal adenomas or precancerous polyps
and detection of early stage cancer, which is the key factor in the
effective treatment of the disease.
[0006] The survival rate for patients diagnosed with CRC is highly
dependent on when it is caught. CRC usually progresses through four
stages, defined as Stage I through Stage IV. Stages I and II are
local stages, during which aberrant cell growth is confined to the
colon or rectum. Stage III is a regional stage, meaning the cancer
has spread to the surrounding tissue but remains local. Stage IV is
distal and indicates that the cancer has spread throughout the
other organs of the body, most commonly the liver or lungs. It is
estimated that the five-year survival rate is over 90% for those
patients who were diagnosed with Stage I CRC, compared to 13% for a
Stage IV diagnosis. If caught early, CRC is typically treated by
surgical removal of the cancer. After the cancer spreads, surgical
removal of the cancer is typically followed by chemotherapy
[0007] Colonoscopy and sigmoidoscopy remain the gold standard for
detecting colon cancer. However, the highly invasive nature and the
expense of these exams contribute to low acceptance from the
population. Furthermore, such highly invasive procedures expose
subjects to risk of complications such as infection.
[0008] The most common non-invasive test for colorectal cancer is
the fecal occult blood test ("FOBT"). Unfortunately, in addition to
its high false-positive rate, the sensitivity of the FOBT remains
around 50% and may have less sensitivity for detection of early
stage CRC. Numerous serum markers, such as carcinoembryonic antigen
("CEA"), carbohydrate antigen 19-9, and lipid-associated sialic
acid, have been investigated in colorectal cancer. However, their
low sensitivity has induced the American Society of Clinical
Oncology to state that none can be recommended for screening and
diagnosis, and that their use should be limited to post-surgery
surveillance.
[0009] Because of the significantly increased chance of survival if
CRC is detected early in the disease progression, CRC is one of
three cancers for which the American Cancer Society, or ACS,
recommends routine screening (breast and cervical cancer are the
others). In the United States, screening for CRC is currently
recommended by the ACS and the U.S. Preventative Services Task
Force, or USPSTF, for all men and women aged 50-75 using fecal
occult blood testing, or FOBT, which is a fecal test, or one of two
procedures: colonoscopy or sigmoidoscopy. Despite the benefits of
routine screening on improving five-year survival rates if CRC is
diagnosed early, the rate of screening compliance is low due in
part to the limitations of existing solutions.
SUMMARY OF THE INVENTION
[0010] Provided herein are methods of assessing a colorectal cancer
status in an individual. Also provided herein are methods of
assessing a colorectal cancer risk status in a blood sample of an
individual. Some such methods comprise the steps of obtaining a
circulating blood sample from the individual; obtaining a biomarker
panel level for a biomarker panel comprising a list of proteins in
the sample comprising AACT, CO3, CO9, MIF, and PSGL to comprise
panel information from said individual; comparing said panel
information from said individual to a reference panel information
set corresponding to a known colorectal cancer status; and
categorizing said individual as having said colorectal cancer
status if said individual's reference panel information does not
differ significantly from said reference panel information set.
Various aspects of these methods are recited below, contemplated as
distinct or in combination. Methods are also contemplated to
include methods wherein obtaining a circulating blood sample
comprises drawing blood from a vein or artery of the individual.
Methods are also contemplated to include methods wherein the panel
information comprises age information for the individual.
Optionally, the list of proteins comprises AACT, CO3, CO9, MIF,
PSGL, CATD, CEA and SEPR. Optionally, the list of proteins
comprises no more than 15 proteins. In some cases the list
comprises more than 8 proteins, where in a CRC signal is derived
from the list of proteins comprising AACT, CO3, CO9, MIF, PSGL,
CATD, CEA and SEPR. Optionally, the list of proteins comprises no
more than 8 proteins. In some cases, the list of proteins comprises
AACT, CO3, CO9, MIF, PSGL, CATD, CEA and SEPR. Optionally, the
categorizing has a sensitivity of at least 81% and a specificity of
at least 78%. Methods are also contemplated to comprise
transmitting a report of results of said categorizing a health
practitioner. Optionally, the report indicates a sensitivity of at
least 81%. Optionally, the report indicates a specificity of at
least 78%. Optionally, the report recommends that a colonoscopy be
performed. Optionally, the individual undergoes a colonoscopy.
Optionally, the report recommends an independent surgical
intervention. Optionally, the individual undergoes an independent
surgical intervention. Optionally, the report recommends undergoing
an independent cancer assay. Optionally, the individual undergoes
an independent cancer assay. Optionally, the report recommends
undergoing a stool cancer assay. Optionally, the individual
undergoes a stool cancer assay. Optionally, the report recommends
administering an anticancer composition. Optionally, an anticancer
composition is administered to the individual. Optionally, the
report recommends continued monitoring. Optionally, at least one
biomarker level of said individual's panel information differs
significantly from a corresponding value from said reference panel,
and wherein said individual's panel level as a whole does not
differ significantly from said reference panel level. Also
contemplated herein are methods wherein no parameter of said
individual's reference panel information in isolation is indicative
of said colorectal cancer status in said individual at a
sensitivity of greater than 65% or a specificity of greater than
65%. Optionally, the obtaining protein levels comprises contacting
a fraction of the circulating blood sample to a set of antibodies,
wherein the set of antibodies comprises antibodies specific to
AACT, CO3, CO9, MIF, and PSGL. Optionally, the obtaining protein
levels comprises subjecting a fraction of the circulating blood
sample to a mass spectrometric analysis. Optionally, at least one
of said comparing and said categorizing is performed on a computer
configured to analyze reference panel information. Optionally, said
reference panel information set corresponding to a known colorectal
cancer status comprises a product of a machine learning model.
Optionally, the machine learning model is trained using at least
100 biomarker panels corresponding to known colorectal health
status. Panels disclosed herein distinguish samples having a CRC
signal not only from samples from healthy individuals but also from
samples from individuals having other types cancer or other cell
cycle or cell proliferation aliments, as indicated in FIG. 4.
[0011] Also provided herein are methods of monitoring efficacy of a
colorectal cancer treatment regimen in an individual. Some such
methods comprise the steps of obtaining a first sample comprising
circulating blood from the individual at a first time point;
administering the treatment regimen to the individual; obtaining a
second sample comprising circulating blood from the individual at a
second time point; obtaining a first panel level comprising protein
levels for a list of proteins in the first sample and a second
panel level comprising protein levels for a list of proteins in the
second sample, said list comprising AACT, CO3, CO9, MIF, and PSGL
to comprise panel information for said first sample and said second
sample; wherein a change in protein levels indicates efficacy of
the colorectal cancer treatment. Also provided herein are ex vivo
methods of monitoring efficacy of a colorectal cancer treatment in
an individual. Some such methods comprise the steps of obtaining a
first sample comprising circulating blood from the individual at a
first time point; obtaining a second sample comprising circulating
blood from the same individual receiving a colorectal cancer
treatment at a second time point; obtaining a first panel level
comprising protein levels for a list of proteins in the first
sample and a second panel level comprising protein levels for a
list of proteins in the second sample, said list comprising AACT,
CO3, CO9, MIF, and PSGL to comprise panel information for said
first sample and said second sample; wherein a change in protein
levels indicates efficacy of the colorectal cancer treatment.
Various aspects of these methods are recited below, contemplated as
distinct or in combination. Methods are contemplated to include
obtaining the first sample comprises drawing blood from a vein or
artery of the individual. Optionally, the colorectal cancer
treatment or treatment regimen comprises administration of a
pharmaceutical composition. Optionally, the colorectal cancer
treatment or treatment regimen comprises administration of a
chemotherapeutic agent. Optionally, the colorectal cancer treatment
or treatment regimen comprises a colonoscopy. Optionally, the
colorectal cancer treatment or treatment regimen comprises a
polypectomy. Optionally, the colorectal cancer treatment or
treatment regimen comprises radiotherapy. Methods are also
contemplated to include methods comprising comparing said first
sample panel level and said second panel level to at least one
panel level of a healthy reference, wherein the second sample panel
level being more similar to the panel level of the healthy
reference indicates efficacy of the colorectal cancer treatment.
Optionally, methods comprise said first sample panel level and said
second panel level to at least one panel level of a healthy
reference, wherein the first sample panel level being more similar
to the panel level of the colorectal cancer reference indicates
efficacy of the colorectal cancer treatment. Optionally, the list
of proteins comprises AACT, CO3, CO9, MIF, PSGL, CATD, CEA and
SEPR. Optionally, the list of proteins comprises no more than 15
proteins. Optionally, the list of proteins comprises no more than 8
proteins. Optionally, the list of proteins comprises AACT, CO3,
CO9, MIF, PSGL, CATD, CEA and SEPR. Optionally, methods comprise
changing the colorectal cancer treatment or treatment regimen if no
efficacy is indicated. Optionally, methods comprise repeating
colorectal cancer treatment or the treatment regimen if no efficacy
is indicated. Optionally, methods comprise continuing the
colorectal cancer treatment or treatment regimen if no efficacy is
indicated. Optionally, methods comprise discontinuing the
colorectal cancer treatment or treatment regimen if efficacy is
indicated.
[0012] Also provided herein are panels of proteins indicative of an
individual's colorectal cancer status. Some such panels comprise at
least 5 proteins selected from the list consisting of AACT, CO3,
CO9, MIF, PSGL, CATD, CEA and SEPR, wherein measurement of the
panel at a level that does not differ significantly from a
reference panel from circulating blood of an individual is
indicative of the individual's colorectal cancer status
corresponding to a reference panel colorectal cancer status at a
sensitivity of at least 81% and a specificity of at least 78%; and
wherein no constituent protein level of said panel is indicative of
the individual's colorectal cancer status at a sensitivity of
greater than 65% and a specificity of greater than 65%. Various
aspects of these panels are recited below, contemplated as distinct
and in combination. Panels are contemplated to comprise at least 6
proteins selected from the list consisting of AACT, CO3, CO9, MIF,
PSGL, CATD, CEA and SEPR. Optionally, panels comprise no more than
12 proteins, of which at least 4 proteins selected from the list
consisting of AACT, CO3, CO9, MIF, PSGL, CATD, CEA and SEPR.
Optionally, panels comprise no more than 12 proteins, wherein the
panel of proteins comprises AACT, CO3, CO9, MIF, PSGL, CATD, CEA
and SEPR. Optionally, panels consist of AACT, CO3, CO9, MIF, PSGL,
CATD, CEA and SEPR. Also contemplated herein are any of the
abovementioned panels of proteins for use in assessing a colorectal
cancer status according to any of the above methods or monitoring
efficacy of a colorectal cancer treatment according to any of the
above methods.
[0013] Also provided herein are kits comprising an antibody panel,
said antibody panel comprising antibodies that identify at least 5
proteins selected from the list consisting of AACT, CO3, CO9, MIF,
PSGL, CATD, CEA and SEPR. Various aspects of these kits are recited
below, contemplated as distinct or in combination. Kits are
contemplated to comprise an antibody that binds to a control
protein. Optionally, kits comprise no more than 15 antibodies.
Optionally, kits comprise no more than 12 antibodies. Optionally,
said antibody panel comprises antibodies that identify all of AACT,
CO3, CO9, MIF, PSGL, CATD, CEA and SEPR. Optionally kits comprise
instructions functionally related to use of the kit to assess a
patient colorectal cancer status. Also contemplated herein are any
of the abovementioned kits for use in assessing a colorectal cancer
status according to any of the above methods or monitoring efficacy
of a colorectal cancer treatment according to any of the above
methods.
[0014] Also contemplated herein are computer systems configured to
assess a colorectal cancer risk in an individual. Some such
computer systems comprise a memory unit for receiving data
comprising measurement of a panel of proteins comprising at least 5
proteins selected from the list consisting of AACT, CO3, CO9, MIF,
PSGL, CATD, CEA and SEPR from a biological sample comprising
circulating blood, computer-executable instructions for assessing a
colorectal cancer risk associated with said measurement of said
panel of proteins, an output unit for delivering a report assessing
said colorectal cancer risk associated with said measurement of
said panel of proteins. Optionally, said panel comprises at least 6
proteins selected from the list consisting of AACT, CO3, CO9, MIF,
PSGL, CATD, CEA and SEPR. Optionally, said panel comprises no more
than 12 proteins, of which at least 5 proteins selected from the
list consisting of AACT, CO3, CO9, MIF, PSGL, CATD, CEA and SEPR.
Optionally, said panel comprises no more than 12 proteins, wherein
the panel of proteins comprises AACT, CO3, CO9, MIF, PSGL, CATD,
CEA and SEPR. Optionally, said panel consists of AACT, CO3, CO9,
MIF, PSGL, CATD, CEA and SEPR. Optionally, the memory unit is
configured for receiving data comprising measurement of a second
panel of proteins. Optionally, said data comprising measurement of
a panel of proteins comprises ELISA data. Optionally, said data
comprising measurement of a panel of proteins comprises mass
spectrometry data. Optionally, assessing a colorectal cancer risk
comprises comparing said data to a reference panel associated with
a known colorectal cancer status. Optionally, said individual is
assigned said known colorectal cancer status when said data does
not differ significantly from said reference panel. Optionally,
said reference panel indicates presence of colorectal cancer.
Optionally, said reference panel indicates absence of colorectal
cancer. Optionally, assessing a colorectal cancer risk is performed
on a computer configured to analyze reference panel information.
Optionally, said memory unit comprises at least one reference panel
information set corresponding to a known colorectal cancer status.
Optionally, the at least one reference panel information set
comprises a machine learning model. Computer systems are also
contemplated wherein the machine learning model is trained using at
least 100 biomarker panels corresponding to known colorectal health
status. Optionally, said report indicates a sensitivity of at least
81% and a specificity of at least 78%. Optionally, said report
indicates a sensitivity of at least 81%. Optionally, said report
indicates a specificity of at least 78%. Optionally, said report
recommends that a colonoscopy be performed. Optionally, said report
recommends an independent surgical intervention. Optionally, said
report recommends undergoing an independent cancer assay.
Optionally, said report recommends undergoing a stool cancer assay.
Optionally, said report recommends administering an anticancer
composition. Optionally, said report recommends continued
monitoring. Computer systems herein are also contemplated wherein
at least one parameter of said individual's reference panel
information differs significantly from a corresponding value from
said reference panel information set, and wherein said individual's
reference panel information does not differ significantly from said
reference panel information set. Optionally, no single protein of
said panel indicates the individual's colorectal cancer status at a
specificity of greater than 65% or a sensitivity of greater than
65%. Optionally, the memory unit is configured to receive age
information from said individual. Optionally, the
computer-executable instructions factor in age of the individual
when assessing said colorectal cancer risk associated with said
measurement of said panel of proteins.
[0015] Also provided herein are methods of assessing an advanced
adenoma risk status in an individual. Also provided herein are
methods of assessing an advanced adenoma risk status in a blood
sample of an individual. Some such methods include comprising the
steps of obtaining a circulating blood sample from the individual;
obtaining protein levels for a list of proteins relevant to
advanced adenoma in the sample comprising at least three of CATD,
CLUS, GDF15 and SAA1 to comprise biomarker panel information from
said individual; comparing said panel information from said
individual to a reference panel information set corresponding to a
known advanced adenoma status; and categorizing said individual as
having said advanced adenoma risk status if said individual's
reference panel information does not differ significantly from said
reference panel information set. Various aspects of these methods
are recited below, contemplated as distinct or in combination.
Methods herein are contemplated to include obtaining a circulating
blood sample comprises drawing blood from a vein or artery of the
individual. Optionally, the panel information comprises age
information for the individual. Optionally, the list of proteins
comprises no more than 15 proteins. Optionally, the list of
proteins comprises no more than 5 proteins. Optionally, list of
proteins comprises CATD, CLUS, GDF15 and SAA1. Optionally, the
categorizing has a sensitivity of at least 50% and a specificity of
at least 80%. Optionally, the categorizing has a sensitivity of at
least 47% and a specificity of at least 83%. Optionally, the
categorizing has a sensitivity of at least 47% and a specificity of
at least 80%. Optionally, methods herein comprise transmitting a
report of results of said categorizing to a healthcare
professional. Optionally, the report indicates a sensitivity of at
least 47%. Optionally, the report indicates a sensitivity of at
least 50%. Optionally, the report indicates a specificity of at
least 80%. Optionally, the report recommends that a colonoscopy be
performed. Optionally, the individual undergoes a colonoscopy.
Optionally, the report recommends an independent surgical
intervention. Optionally, the individual undergoes an independent
surgical intervention. Optionally, the report recommends undergoing
an independent cancer assay. Optionally, the individual undergoes
an independent cancer assay. Optionally, the report recommends
undergoing a stool cancer assay. Optionally, the individual
undergoes a stool cancer assay. Optionally, the report recommends
administering an anticancer composition. Optionally, an anticancer
composition is administered to the individual. Optionally, the
report recommends continued monitoring. Methods are also
contemplated herein wherein at least one parameter of said
individual's reference panel differs significantly from a
corresponding value from said reference panel set, and wherein said
individual's reference panel information as a whole does not differ
significantly from said reference panel information set.
Optionally, methods are contemplated wherein no parameter of said
individual's reference panel information in isolation is indicative
of said advanced adenoma status in said individual at a sensitivity
of greater than 65% or a specificity of greater than 65%.
Optionally, the obtaining protein levels comprises contacting a
fraction of the circulating blood sample to a set of antibodies,
wherein the set of antibodies comprises antibodies specific to
CATD, CLUS, GDF15 and SAA1. Optionally, the obtaining protein
levels comprises subjecting a fraction of the circulating blood
sample to a mass spectrometric analysis. Optionally, the obtaining
protein levels comprises contacting the sample to protein binding
DNA aptamers. Optionally, the obtaining protein levels comprises
contacting the sample to an antibody array. Optionally, at least
one of said comparing and said categorizing is performed on a
computer configured to analyze reference panel information.
Optionally, said reference panel information set corresponding to a
known advanced adenoma status comprises is a product of a machine
learning model. Optionally, the machine learning model is trained
using at least 100 biomarker panels corresponding to known
colorectal health status.
[0016] Also provided herein are methods of monitoring efficacy of
an advanced adenoma treatment regimen in an individual. Some such
methods comprise the steps of obtaining a first sample comprising
circulating blood from the individual at a first time point;
administering the treatment regimen to the individual; obtaining a
second sample comprising circulating blood from the individual at a
second time point; obtaining a first panel level protein levels for
a list of proteins relevant to advanced adenoma assessment in the
first sample and a second panel level protein levels for a list of
proteins relevant to advanced adenoma assessment in the second
sample, said list comprising CATD, CLUS, GDF15 and SAA1 to comprise
panel information for said first sample and said second sample;
wherein a change in protein levels indicates efficacy of the
advanced adenoma treatment. Also provided herein are ex vivo
methods of monitoring efficacy of an advanced adenoma treatment in
an individual. Some such methods comprise the steps of obtaining a
first sample comprising circulating blood from the individual at a
first time point; obtaining a second sample comprising circulating
blood from the same individual receiving an advanced adenoma
treatment at a second time point; obtaining a first panel level
comprising protein levels for a list of proteins in the first
sample and a second panel level comprising protein levels for a
list of proteins in the second sample, said list comprising CATD,
CLUS, GDF15 and SAA1 to comprise panel information for said first
sample and said second sample; wherein a change in protein levels
indicates efficacy of the colorectal cancer treatment. Various
aspects of these methods are recited below, contemplated as
distinct or in combination. Methods are also included wherein
obtaining the first sample comprises drawing blood from a vein or
artery of the individual. Optionally, the advanced adenoma
treatment or treatment regimen comprises administration of a
pharmaceutical composition. Optionally, the advanced adenoma
treatment or treatment regimen comprises administration of a
chemotherapeutic agent. Optionally, the advanced adenoma treatment
or treatment regimen comprises a colonoscopy. Optionally, the
advanced adenoma treatment or treatment regimen comprises a
polypectomy. Optionally, the advanced adenoma treatment or
treatment regimen comprises radiotherapy. Methods are also
contemplated comprising comparing said first sample protein levels
and said second panel protein levels to protein levels of a healthy
reference, wherein the second sample levels being more similar to
the protein levels of the healthy reference indicates efficacy of
the advanced adenoma treatment. Optionally, comparing said first
sample protein levels and said second panel protein levels to
protein levels of an advanced adenoma reference, wherein the first
sample levels being more similar to the protein levels of the
advanced adenoma reference indicates efficacy of the advanced
adenoma treatment. Optionally, the list of proteins relevant to
advanced adenoma assessment comprises CATD, CLUS, GDF15 and SAA1.
Optionally, the list of proteins relevant to advanced adenoma
assessment comprises no more than 12 proteins. Optionally, the list
of proteins relevant to advanced adenoma assessment comprises no
more than 8 proteins. Optionally, the list of proteins relevant to
advanced adenoma assessment consists of CATD, CLUS, GDF15 and SAA1.
Optionally, methods herein comprise changing the advanced adenoma
treatment or treatment regimen if no efficacy is indicated. Also
contemplated herein are methods comprising repeating the advanced
adenoma treatment or treatment regimen if no efficacy is indicated.
Optionally, methods are contemplated to comprise continuing the
advanced adenoma treatment or treatment regimen if no efficacy is
indicated. Optionally, methods are contemplated to comprise
discontinuing the advanced adenoma treatment or treatment regimen
if efficacy is indicated.
[0017] Also provided herein are panels of proteins indicative of an
individual's advanced adenoma status. Some such panels are
contemplated to comprise at least 3 proteins relevant to advanced
adenoma assessment selected from the list consisting of CATD, CLUS,
GDF15 and SAA1, wherein measurement of the panel at a level that
does not differ significantly from a reference panel from
circulating blood of an individual is indicative of the
individual's advanced adenoma status corresponding to a reference
panel advanced adenoma status at a sensitivity of at least 50% and
a specificity of at least 80%; and wherein no constituent protein
level of said panel is indicative of the individual's advanced
adenoma status at a sensitivity of greater than 65% and a
specificity of greater than 65%. Panels are contemplated to
comprise proteins relevant to advanced adenoma assessment CATD,
CLUS, GDF15 and SAA1.
[0018] Also provided herein are kits comprising an antibody panel,
said antibody panel comprising antibodies that identify at least 3
proteins advanced adenoma assessment selected from the list
consisting of CATD, CLUS, GDF15 and SAA1. Various aspects of these
kits are recited below, contemplated as distinct or in combination.
Kits are contemplated to comprise an antibody that binds to a
control protein. Optionally, kits comprise no more than 15
antibodies. Optionally, kits comprise no more than 12 antibodies.
Optionally, said antibody panel comprises antibodies that identify
all of CATD, CLUS, GDF15 and SAA1. Optionally kits comprise
instructions functionally related to use of the kit to assess a
patient advanced adenoma status. Also contemplated herein are any
of the abovementioned panels of proteins for use in assessing a
colorectal cancer status according to any of the above methods or
monitoring efficacy of a colorectal cancer treatment according to
any of the above methods. Also contemplated herein are any of the
abovementioned kits for use in assessing a colorectal cancer status
according to any of the above methods or monitoring efficacy of a
colorectal cancer treatment according to any of the above
methods.
[0019] Also contemplated herein are computer systems configured to
assess advanced adenoma risk in an individual. Some such computer
systems comprise a memory unit for receiving data comprising
measurement of a panel of proteins comprising at least 3 proteins
selected from the list consisting of CATD, CLUS, GDF15 and SAA1
from a biological sample comprising circulating blood,
computer-executable instructions for assessing advanced adenoma
risk associated with said measurement of said panel of proteins, an
output unit for delivering a report assessing said advanced adenoma
risk associated with said measurement of said panel of proteins.
Optionally, said panel comprises CATD, CLUS, GDF15 and SAA1.
Optionally, said panel comprises no more than 12 proteins, of which
at least 5 proteins selected from the list consisting of AACT, CO3,
CO9, MIF, PSGL, CATD, CEA and SEPR. Optionally, said panel
comprises no more than 12 proteins, wherein the panel of proteins
comprises CATD, CLUS, GDF15 and SAA1. Optionally, said panel
consists of CATD, CLUS, GDF15 and SAA1. Optionally, the memory unit
is configured for receiving data comprising measurement of a second
panel of proteins. Optionally, said data comprising measurement of
a panel of proteins comprises ELISA data. Optionally, said data
comprising measurement of a panel of proteins comprises mass
spectrometry data. Optionally, assessing a advanced adenoma risk
comprises comparing said data to a reference panel associated with
a known advanced adenoma status. Optionally, said individual is
assigned said known advanced adenoma status when said data does not
differ significantly from said reference panel. Optionally, said
reference panel indicates presence of advanced adenoma. Optionally,
said reference panel indicates absence of advanced adenoma.
Optionally, assessing a advanced adenoma risk is performed on a
computer configured to analyze reference panel information.
Optionally, said memory unit comprises at least one reference panel
information set corresponding to a known advanced adenoma status.
Optionally, the at least one reference panel information set
comprises a machine learning model. Computer systems are also
contemplated wherein the machine learning model is trained using at
least 100 biomarker panels corresponding to known colorectal health
status. Optionally, said report indicates a sensitivity of at least
50% and a specificity of at least 80%. Optionally, said report
indicates a sensitivity of at least 50%. Optionally, said report
indicates a specificity of at least 80%. Optionally, said report
recommends that a colonoscopy be performed. Optionally, said report
recommends an independent surgical intervention. Optionally, said
report recommends undergoing an independent cancer assay.
Optionally, said report recommends undergoing a stool cancer assay.
Optionally, said report recommends administering an anticancer
composition. Optionally, said report recommends continued
monitoring. Computer systems herein are also contemplated wherein
at least one parameter of said individual's reference panel
information differs significantly from a corresponding value from
said reference panel information set, and wherein said individual's
reference panel information does not differ significantly from said
reference panel information set. Optionally, no single protein of
said panel indicates the individual's advanced adenoma status at a
specificity of greater than 65% or a sensitivity of greater than
65%. Optionally, the memory unit is configured to receive age
information from said individual. Optionally, the
computer-executable instructions factor in age of the individual
when assessing said advanced adenoma risk associated with said
measurement of said panel of proteins.
[0020] Also provided herein are methods of assessing a colorectal
health risk status in an individual. Also provided herein are ex
vivo methods of assessing a colorectal health risk status in a
blood sample of an individual. Some such methods comprise the steps
of obtaining a circulating blood sample from the individual;
obtaining a biomarker panel level for a biomarker panel comprising
a list of proteins in the sample comprising AACT, CO3, CO9, MIF,
PSGL, SEPR, CEA, CATD, CLUS, GDF15 and SAA1, and obtaining an age
for the individual, wherein AACT, CO3, CO9, MIF, PSGL, SEPR, CEA,
CATD, and age comprise colorectal cancer panel information from
said individual; and wherein CATD, CLUS, GDF15 and SAA1 comprise
advanced adenoma panel information from said individual; comparing
said colorectal cancer panel information from said individual to a
reference colorectal cancer panel information set corresponding to
a known colorectal cancer status; comparing said advanced adenoma
panel information from said individual to a reference advanced
adenoma panel information set corresponding to a known advanced
adenoma status; and categorizing said individual as having a
colorectal health risk if either of said colorectal cancer panel or
said advanced adenoma panel does not differ significantly from a
reference panel positive for a colorectal health risk. Various
aspects of these methods are recited below, contemplated as
distinct or in combination. Methods herein are contemplated to
include obtaining a circulating blood sample comprises drawing
blood from a vein or artery of the individual. Optionally, the
panel information comprises age information for the individual.
Optionally, the list of proteins comprises no more than 20
proteins. Optionally, the list of proteins comprises no more than
11 proteins. Optionally, the categorizing has a sensitivity of at
least 80% and a specificity of at least 50%. Optionally, the
categorizing has a sensitivity of at least 80% and a specificity of
at least 47%. Optionally, the categorizing has a sensitivity of at
least 83% and a specificity of at least 47%. Optionally, methods
herein comprise transmitting a report of results of said
categorizing to a healthcare professional. Optionally, the report
indicates a sensitivity of at least 8%. Optionally, the report
indicates a specificity of at least 50%. Optionally, the report
recommends that a colonoscopy be performed. Optionally, the
individual undergoes a colonoscopy. Optionally, the report
recommends an independent surgical intervention. Optionally, the
individual undergoes an independent surgical intervention.
Optionally, the report recommends undergoing an independent cancer
assay. Optionally, the individual undergoes an independent cancer
assay. Optionally, the report recommends undergoing a stool cancer
assay. Optionally, the individual undergoes a stool cancer assay.
Optionally, the report recommends administering an anticancer
composition. Optionally, an anticancer composition is administered
to the individual. Optionally, the report recommends continued
monitoring. Methods are also contemplated herein wherein at least
one parameter of said individual's reference panel differs
significantly from a corresponding value from said reference panel
set, and wherein said individual's reference panel information as a
whole does not differ significantly from said reference panel
information set. Optionally, methods are contemplated wherein no
parameter of said individual's reference panel information in
isolation is indicative of said advanced adenoma status in said
individual at a sensitivity of greater than 65% or a specificity of
greater than 65%. Optionally, the obtaining protein levels
comprises contacting a fraction of the circulating blood sample to
a set of antibodies, wherein the set of antibodies comprises
antibodies specific to AACT, CO3, CO9, MIF, PSGL, SEPR, CEA, CATD,
CLUS, GDF15 and SAA1. Optionally, the obtaining protein levels
comprises subjecting a fraction of the circulating blood sample to
a mass spectrometric analysis. Optionally, the obtaining protein
levels comprises contacting the sample to protein binding DNA
aptamers. Optionally, the obtaining protein levels comprises
contacting the sample to an antibody array. Optionally, at least
one of said comparing and said categorizing is performed on a
computer configured to analyze reference panel information.
Optionally, said reference panel information set corresponding to a
known advanced adenoma status comprises is a product of a machine
learning model. Optionally, the machine learning model is trained
using at least 100 biomarker panels corresponding to known
colorectal health status.
[0021] Provided herein are methods, compositions, kits, computer
readable media, and systems for the diagnosis and/or treatment of
at least one of advanced colorectal adenoma and colorectal cancer.
Through the methods and compositions provided herein, a sample is
taken from an individual such as an individual at risk of advanced
colorectal adenoma or colorectal cancer. The sample is assayed to
determine the accumulation levels of a panel of markers such as
proteins, for example a panel of markers comprising or consisting
of the markers in panels disclosed herein. In many cases the panels
comprise proteins that individually are known to play a role in
indicating the presence of advanced colorectal adenoma or
colorectal cancer, while in other cases the panels comprise a
protein or proteins not know to correlate with advanced colorectal
adenoma or colorectal cancer. However, in all cases the
identification and accumulation of markers into a panel results in
a level of specificity, sensitivity or specificity and sensitivity
that substantially surpasses that of individual markers or smaller
or less accurate sets of markers.
[0022] Additionally, methods, panels and other tests disclosed
herein substantially surpass the sensitivity, specificity, or
sensitivity and specificity of currently available tests such as
currently available blood-based tests. Panel accumulation levels
are measured in a number of ways in various embodiments, for
example through an ELISA assay, through mass spectroscopy analysis
or through alternate approaches to protein accumulation level
quantification.
[0023] Panel accumulation levels are compared to a positive control
or negative control standard, or to a model of advanced colorectal
adenoma or colorectal cancer accumulation levels or of healthy
accumulation levels, such that a prediction is made regarding an
assayed individual's health status. In some cases, a panel assay
result is accompanied by a recommendation regarding an intervention
or an alternate verification of the panel assay results.
[0024] Provided herein are biomarker panels and assays useful for
the diagnosis and/or treatment of at least one of advanced
colorectal adenoma and colorectal cancer.
[0025] Also provided herein are kits, comprising a computer
readable medium described herein, and instructions for use of the
computer readable medium.
[0026] A number of treatment regimens are contemplated herein and
known to one of skill in the art, such as chemotherapy,
administration of a biologic therapeutic agent, and surgical
intervention such as low anterior resection or abdominoperineal
resection, or ostomy.
BRIEF DESCRIPTION OF THE DRAWINGS
[0027] The patent or application file contains at least one drawing
executed in color. Copies of this patent or patent application
publication with color drawing(s) will be provided by the Office
upon request and payment of the necessary fee.
[0028] FIG. 1 depicts a Biomarker Panel development pipeline.
[0029] FIG. 2 illustrates an AUC curve for a lead CRC panel.
[0030] FIG. 3 illustrates an AUC curve for a lead AA panel.
[0031] FIG. 4 presents validation data for a lead CRC panel.
[0032] FIG. 5 presents protein levels from biomarker proteins in
CRC and healthy control samples.
[0033] FIG. 6 presents protein levels from biomarker proteins in AA
and healthy control samples.
[0034] FIG. 7A illustrates a Discovery ROC AUC plot for CRC Model
1.
[0035] FIG. 7B illustrates a Validation ROC AUC plot for CRC Model
1.
[0036] FIG. 8A illustrates a Discovery ROC AUC plot for CRC Model
2.
[0037] FIG. 8B illustrates a Validation ROC AUC plot for CRC Model
2.
[0038] FIG. 9A illustrates a Discovery ROC AUC plot for CRC Model
3.
[0039] FIG. 9B illustrates a Validation ROC AUC plot for CRC Model
3.
[0040] FIG. 10A illustrates a Discovery ROC AUC plot for CRC Model
4.
[0041] FIG. 10B illustrates a Validation ROC AUC plot for CRC Model
4.
[0042] FIG. 11A illustrates a Discovery ROC AUC plot for CRC Model
5.
[0043] FIG. 11B illustrates a Validation ROC AUC plot for CRC Model
5.
[0044] FIG. 12A illustrates a Discovery ROC AUC plot for CRC Model
6.
[0045] FIG. 12B illustrates a Validation ROC AUC plot for CRC Model
6.
[0046] FIG. 13A illustrates a Discovery ROC AUC plot for CRC Model
7.
[0047] FIG. 13B illustrates a Validation ROC AUC plot for CRC Model
7.
[0048] FIG. 14A illustrates a Discovery ROC AUC plot for CRC Model
8.
[0049] FIG. 14B illustrates a Validation ROC AUC plot for CRC Model
8.
[0050] FIG. 15A illustrates a Discovery ROC AUC plot for CRC Model
9.
[0051] FIG. 15B illustrates a Validation ROC AUC plot for CRC Model
9.
[0052] FIG. 16A illustrates a Discovery ROC AUC plot for CRC Model
10.
[0053] FIG. 16B illustrates a Validation ROC AUC plot for CRC Model
10.
[0054] FIG. 17A illustrates a Discovery ROC AUC plot for CRC Model
5 with NOC.
[0055] FIG. 17B illustrates a Validation ROC AUC plot for CRC Model
5 with NOC.
[0056] FIG. 18 illustrates a Max Accuracy plot for CRC Models
1-10.
[0057] FIG. 19 depicts a Computer System architecture consistent
with the Methods, Compositions, Kits and Systems disclosed
herein.
[0058] FIG. 20 presents AUC values for randomly generated CRC
panels from a targeted-MS enriched biomarker population.
DETAILED DESCRIPTION
[0059] Provided herein are biomarker panels, methods, compositions,
kits, and systems for the non-invasive assessment of colorectal
health, for example through the detection of at least one of
advanced colorectal adenoma ("AA") and colorectal cancer ("CRC").
Biomarker panels, methods, compositions, kits, and systems
described herein are used to determine a likelihood that a subject
has a colorectal condition such as at least one of an advanced
colorectal adenoma and CRC through the noninvasive assay of a
sample taken from circulating blood circulating blood. Some such
biomarker panels are used noninvasively to detect a colorectal
health issue such as colorectal cancer with a sensitivity of as
much as 81% or greater, and a specificity of as much as 78% or
greater. An exemplary CRC biomarker panel comprises the markers
AACT, CATD, CEA, CO3, CO9, MIF, PSGL, and SEPR, and the non-protein
biomarker of age of the individual providing the sample. Some such
biomarker panels are used noninvasively to detect a colorectal
health issue such as an advanced adenoma with a sensitivity of as
much as 50% or greater, and a specificity of as much as 80% or
greater. An exemplary biomarker panel relevant to advanced adenoma
assessment comprises the markers CATD, CLUS, GDF15 and SAA1.
[0060] Biomarker panels as disclosed herein share a property that
sensitive, specific conclusions regarding an individual's
colorectal health are made using protein level information derived
from circulating blood, alone or in combination with other
information such as an individual's age, gender, health history or
other characteristics. A benefit of the present protein panels is
that they provide a sensitive, specific colorectal health
assessment using conveniently, noninvasively obtained samples.
There is no need to rely upon data obtained from an intrusive
abdominal assay such as a colonoscopy or a sigmoidoscopy, or from
stool sample material. As a result compliance rates are
substantially higher, and colorectal health issues are more easily
recognized early in their progression, so that they may be more
efficiently treated. Ultimately, the effect of this benefit is
measured in lives saved, and is substantial.
[0061] Biomarker panels as disclosed herein are selected such that
their predictive value as panels is substantially greater than the
predictive value of their individual members. Panel members
generally do not co-vary with one another, such that panel members
provide independent contributions to the panel's overall health
signal. Accordingly, a panel is able to substantially outperform
the performance of any individual constituent indicative of an
individual's colorectal health status, such that a commercially and
medicinally relevant degree of confidence (such as sensitivity,
specificity or sensitivity and specificity) is obtained. Thus, in
the panels as disclosed herein, multiple panel members indicative
of a health issue provide a much stronger signal than is found, for
example in a panel wherein two or more members rise or fall in
strict concert such that the signal derived therefrom is
effectively a single signal, repeated twice. Accordingly, panels as
disclosed herein are robust to variation in single constituent
measurements. For example because panel members vary independently
of one another, panels herein often indicate a health risk despite
the fact that one or more than one individual members of the panel
would not indicate that the health risk is present if measured
alone. In some cases, panels herein indicate a health risk at a
significant level of confidence despite the fact that no individual
panel member indicates the health risk at a significant level of
confidence on its own. In some cases, panels herein indicate a
health risk at a significant level of confidence despite the fact
that at least one individual member indicates at a significant
level of confidence that the health risk is not present.
[0062] Biomarkers consistent with the panels herein comprise
biological molecules that circulate in the bloodstream of an
individual, such as proteins. Readily available information such as
individual's age, gender, weight, height, body mass index or other
easily measured or obtained information is also eligible as a
marker in some cases. In particular, some panels herein rely upon
age, gender, or age and gender as biomarkers.
[0063] Common to many biomarkers herein is the ease with which they
are assayed in an individual. Biomarkers herein are readily
obtained by a blood draw from an artery or vein of an individual,
or are obtained via interview or by simple biometric analysis. A
benefit of the ease with which biomarkers herein are obtained is
that invasive assays such as colonoscopy or sigmoidoscopy are not
required for biomarker measurement. Similarly, stool samples are
not required for biomarker determination. As a result, panel
information as disclosed herein is often readily obtained through a
blood draw in combination with a visit to a doctor's office.
Compliance rates are accordingly substantially higher than are
compliance rates for colorectal health assays involving stool
samples or invasive procedures.
[0064] Exemplary panels disclosed herein comprise circulating
proteins or fragments thereof that are recognizably or uniquely
mapped to their parent protein, and in some cases comprise a
readily obtained biomarker such as an individual's age.
[0065] Characteristics of Panels Disclosed Herein relative to other
Biomarker Panels
[0066] Panels disclosed herein substantially outperform individual
markers or randomly generated panels. Although at least some
members of the panels herein are implicated in cancer, the panels
herein far outperform panels derived randomly from any art
teachings. This is illustrated by examination of panel performance
as compared to individual members, randomly generated panels, and
in light of the unpredictability of individual markers for any
individual health assessment.
[0067] Panels were constructed from an original candidate pool of
187 potential biomarkers selected from the literature. See FIG. 1.
Using a 274 member age and gender matched discovery sample set,
targeted mass spectroscopy was used to identify 28 biomarkers from
the original set that co-vary with health status of the 274 members
of the discovery sample set. This 28 member set is not a random
selection of the 187 member original candidate pool, and the 28
member set was not selected from the original 187 member candidate
pool based upon any teaching in the art.
[0068] The 28 member set was tested against a separate age and
gender matched 300 member sample set to come to CRC panels as
disclosed herein, such as the 8 member panel comprising AACT, CO3,
CO9, MIF, PSGL, CATD, CEA and SEPR. This and similar panels were
selected from an original 187 member candidate pool but are not
taught to be particularly effective in combination to the exclusion
of other candidate pool constituents. Rather, the panel is come to
through repeated analysis of independently derived samples in
combination with the inventor's own insights into panel
construction and health status prediction.
[0069] FIG. 2 depicts an AUC plot for a lead CRC panel derived
herein. The AUC plot clearly illustrates that the CRC panel
performs substantially better than random chance, as depicted by
the diagonal on this figure. FIG. 3 depicts an AUC plot for a lead
AA panel derived herein. The AUC plot clearly illustrates that the
AA panel performs substantially better than random chance, as
depicted by the diagonal on this figure.
[0070] Biomarker panels herein perform substantially better than
any random selection of biomarkers individually implicated in
cancer generally, such as those of the 187 member candidate pool.
That is, if one of skill in the art were to start with a list of
biomarkers available in the literature and randomly assemble, or
even assemble in light of teachings available to one of skill in
the art, a biomarker panel to use to assay for a colorectal health
issue such as colorectal cancer or advanced adenoma in an
individual, one does not come to a biomarker as disclosed herein.
Biomarker panels disclosed herein substantially outperform randomly
selected panels and panels selected in light of the art.
[0071] Biomarker panels herein perform substantially better than
any individual constituent marker individually implicated in cancer
generally, such as those of the 187 member candidate pool. Some
individual biomarkers indicate CRC or advanced adenoma, but with a
sensitivity and a specificity that is far below that of the
biomarker panels as disclosed herein. Use of individual biomarkers,
or combinations of biomarkers not recited or readily apparent to
one of skill in the art from the disclosure herein, is not
contemplated pursuant to this disclosure.
[0072] Reference is made to FIGS. 5 and 6. In these figures,
individual protein levels are compared between samples that are
positive or negative for CRC (FIG. 5) or AA (FIG. 6). Proteins
presented in these figures are not randomly selected, rather they
are chosen from the MS-enriched set of 28 proteins identified from
among the 187 protein list identified in the art as being
potentially of relevance to cancer health assessment. For each
paired boxplot, the healthy sample levels are at left or top, while
the CRC or AA positive protein levels are depicted at right or
bottom. For the vast majority of individual protein markers, there
is little difference between the condition positive and condition
negative protein levels. Levels are not identical, but the
difference in most cases does not look to one of skill in the art
to be significant, particularly at a level at which one would base
a colorectal health assessment. With a few exceptions, such as FIG.
5 CEA, CRP, or GARS levels, the listed protein levels are quite
similar between condition and no-condition samples. See, as
representative examples FIG. 5 A1AG1, A1AT, AACT, ANAX1, APOA1,
CAH1, CO9, GELS, HTP, OSTP or PSGL, among others. The situation for
FIG. 6 is quite similar, with individual protein levels rarely
differing very conspicuously between condition positive and
condition negative individuals.
[0073] It is clear from FIG. 5 and FIG. 6 that no individual
marker, even from this targeted-MS enriched set, is expected to
perform as well as the panels presented herein. Furthermore, there
is little suggestion from the protein levels presented in FIG. 5 or
FIG. 6 that combinations of protein levels may have a synergistic
effect so as to attain the performance of the panels as disclosed
herein.
[0074] Aggregation of protein markers alone does not accomplish the
level of performance of the panels disclosed herein. Reference is
made to Example 21, below. Random panels are generated from the
targeted MS-enriched set of 28 markers, and their performance is
compared to that of the panels herein. The enriched 28 member set
is already expected to yield panels that perform much better than
those generated from the unenriched parent 187 marker set. It is
observed that the panels herein, particularly the panels of 8-10
members, as shown, substantially outperform panels generated at
random from an already enriched set of protein markers. These
random panels do not represent panels that one would come to from
the art, as they are already enriched from the 187 member list as
mentioned in the art as being relevant to cancer detection. Thus,
even performance comparable to levels seen in the randomly
generated panels from the 28 marker set represents a substantial
improvement over more generally apparent panels. Panels herein,
however generally match (AA lead panel) or more often substantially
outperform (CRC panels) up to almost 100% of the randomly generated
panels from the enriched set of 28 markers. See again Example
21.
[0075] Biomarker panels herein yield results that are more
reliable, more sensitive and more specific than simply the
collection of their individual constituents. That is, in some cases
individual biomarkers are detected at levels that are individually
not informative with a degree of sensitivity and specificity to be
medically relevant, but the level of the biomarker panel
nonetheless provides a colorectal health assessment with a degree
of confidence that is medically actionable. In some cases no
individual biomarker of the panel is present at a level that is
individually indicative of a health issue warranting follow-up, but
the biomarker panel as a whole, assessed as indicated herein,
provides an assessment that is indicative of a health issue
warranting follow-up.
[0076] Biomarkers herein yield results that are in some cases
qualitatively different from those of their constituent biomarkers.
That is, in some cases one or more individual biomarkers of the
panel are present at a level that is individually indicative of a
colorectal health status that is contradictory to the health status
indicated by the level of the panel as a whole, including the
contradictory biomarker. In such cases, it is often found that
independent health assessment, for example by colonoscopy or by
stool sample analysis, supports the panel assessment rather than
the health status assessment provided by the contradictory
individual marker.
[0077] Reference is made to Example 22 below. In that example the
CRC biomarker panels provide predictions that are inconsistent with
the predictions that result from looking at constituent biomarker
levels in isolation. The protein CO3, in particular, is measured at
a level in the CRC-positive individual, patient 1, that is
intermediate between the CO3 levels observed for two CRC-negative
individuals. If one were scoring these biomarkers individually
rather than as parts of a panel, one would be unlikely to score
patient 1 as CRC positive and patients 2 and 3 as CRC negative in
light of patient 1's CO3 level falling between those of patient 2
and 3.
[0078] However, using the panel analysis as disclosed herein, one
comes to a result that is qualitatively different from the result
expected by examination of an individual panel biomarker in
isolation. This data as presented in Example 22, below, highlights
the fact that the panels herein are not simply quantitatively
better but are also in some cases qualitatively different from
their individual biomarker constituents.
[0079] Accordingly, biomarker panels disclosed herein are
understood to perform better than a random collection of candidate
markers as taught by the literature. Biomarker panels disclosed
herein are also understood to perform better statistically, and in
some cases qualitatively differently, than do their individual
biomarker constituents, such that a health assessment from the
biomarker panel as a whole is either more accurate or in some cases
provides a result that is qualitatively different from that of one
or more individual biomarker constituents.
Panel Constituents
[0080] Some biomarker panels comprise some or all of the protein
markers recited herein, subsets thereof or listed markers in
combination with additional markers or biological parameters. A
lead biomarker panel relevant to colorectal cancer assessment
comprises at least 4 markers, up to the full list, alone or in
combination with additional markers, said list selected from the
following: AACT, CATD, CEA, CO3, CO9, MIF, PSGL, SEPR, and also
including age as a biomarker. A lead biomarker panel relevant to
advanced adenoma assessment comprises markers selected from the
following: CATD, CLUS, GDF15 and SAA1. A lead biomarker panel, or a
combination of biomarker panels having combined colorectal cancer
and advanced adenoma assessment capabilities comprises biomarkers
such as AACT, CEA, CO3, CO9, MIF, PSGL, SEPR, CATD, CLUS, GDF15 and
SAA1, and age as a non-protein biomarker, or a subset thereof
optionally having at least one individual marker excluded or
replaced with one or more markers.
[0081] Often, it is convenient or efficient to combine a colorectal
cancer biomarker panel and an advanced adenoma panel into a single
kit or a single biomarker panel. In these cases, one sees a kit
comprising eleven biomarkers, or a subset or larger set thereof,
including AACT, CATD, CEA, CO3, CO9, MIF, PSGL, SEPR, CLUS, GDF15
and SAA1, of which AACT, CEA, CO3, CO9, MIF, PSGL, and SEPR or a
subset or larger group comprising these markers is informative as
to colorectal cancer status; CLUS, GDF15 and SAA1 or a subset or
larger group comprising these markers is informative as to advanced
adenoma status; and CATD, if included, is informative as to both
colorectal cancer status and advanced adenoma status.
[0082] Alternate colorectal cancer biomarker panels are listed
below. Much like the panel discussed above, these panels, or
subsets or additions, are used alone or in combination with the
above-mentioned advanced adenoma panel, optionally using markers
such as CATD, CLUS, GDF15 or SAA1 to be indicative of advanced
adenoma and colorectal cancer. An exemplary biomarker panel
comprises at least 4 markers, up to the full list, alone or in
combination with additional markers, said list selected from the
following: A1AG1, A1AT, CATD, CEA, CO9, OSTPxAge, SEPR, wherein
OSTPxAge refers to OSTP viewed in combination with individual age.
An exemplary biomarker panel comprises at least 4 markers, up to
the full list, alone or in combination with additional markers,
said list selected from the following: A1AG1, A1AT, APOA1, CATD,
CEA, CLUS, CO3, CO9, FGB, FIBG, GARS, GELS, MIF, PRDX1, PSGL, SBP1,
SEPR. An exemplary biomarker panel comprises at least 4 markers, up
to the full list, alone or in combination with additional markers,
said list selected from the following: A1AG1, A1AT, CATD, CEA, CO9,
GARS, SEPR. An exemplary biomarker panel comprises at least 4
markers, up to the full list, alone or in combination with
additional markers, said list selected from the following: A1AG1,
A1AT, AACT, CATD, CEA, CO9, CRP, AACT, CO9, CRP, CRP, CRP, CRP,
CRP, CRP, GELS, S10A8, S10A8, S10A8, S10A8, S10A9, S10A9, GARS,
SAA1, SEPR. An exemplary biomarker panel comprises at least 4
markers, up to the full list, alone or in combination with
additional markers, said list selected from the following: CATD,
CEA, CO3, CO9, GARS, GELS, SEPR, TFRC. An exemplary biomarker panel
comprises at least 4 markers, up to the full list, alone or in
combination with additional markers, said list selected from the
following: CATD, CEA, AACT, CO9, SEPR. An exemplary biomarker panel
comprises at least 4 markers, up to the full list, alone or in
combination with additional markers, said list selected from the
following: A1AT, C3218600, C387796, C597612, C979276, CATD, CEA,
GARS, GELS, SEPR. An exemplary biomarker panel comprises at least 4
markers, up to the full list, alone or in combination with
additional markers, said list selected from the following: A1AG1,
A1AT, CATD, CEA, CO9, SEPR, CATD/SEPR, CATD/GELS, CO9/SEPR,
A1AT/FIBG, wherein a "I" indicates that a biomarker comprises a
ratio of one protein or other biomarker level to a second protein
or other biomarker level. An exemplary biomarker panel comprises at
least 4 markers, up to the full list, alone or in combination with
additional markers, said list selected from the following: CATD,
CEA, CO3, CO9, S10A8, GELS, SEPR, TFRC. An exemplary biomarker
panel comprises at least 4 markers, up to the full list, alone or
in combination with additional markers, said list selected from the
following: A1AG1, CATD, CEA, CO3, CO9, GELS, SEPR. For biomarker
panels disclosed herein, variants having all but 1, 2, 3, or about
90%, 80%, 70%, 60%, or 50% of the biomarkers recited are also
contemplated, as are panels that comprise additional biomarkers or
control markers.
[0083] Biomarkers are measured through a number of approaches
consistent with the disclosure herein. In many cases biomarkers are
measured through an immunological interaction, such as that which
occurs in an ELISA assay through which proteins or protein
fragments in a blood sample from an individual are bound to
specific antibodies, and the extent of binding is quantified as a
measure of protein abundance in the sample. ELISA assays capable of
measuring biomarker panels as disclosed herein are contemplated as
embodiments of the present disclosure as kits.
[0084] Alternately or in combination, biomarkers are measured
through mass spectrometric methods such as MS, MS/MS, MALDI-TOF or
other mass spectrometric approaches as appropriate. Often, the MS
approach quantifies a fragment of a biomarker rather than the
full-length protein. However, such approaches are sufficient to
determine the protein level of the biomarker to an accuracy
sufficient for a colorectal health assessment as disclosed
herein.
[0085] Some details of panel performance is dependent upon assay
approach, such that some panels perform slightly better using an
immunological or a mass spectrometric approach. However, it is
observed that in many cases panel performance is largely
independent of assay method, such that a panel that performs
slightly better using an immunological assay is nonetheless
informative as to an individual's colorectal health status when
assayed using mass spectrometric analysis, or vice versa.
[0086] Once an expression level for a biomarker panel is
determined, a colorectal health assessment is available for the
individual from which the sample is obtained. A number of
approaches are available to one of skill in the art to generate or
come to a colorectal health assessment from an individual's
biomarker panel expression level.
[0087] Some assessments rely upon comparison of an individual's
biomarker panel level to a reference level, such as a reference
biomarker panel level from an individual known or independently
verified to be in good colorectal health, or from an individual
known or independently verified to be in poor colorectal health,
such as is the case for an individual having colorectal cancer or
at least one advanced adenoma. Alternately an individual's
biomarker panel level is compared to a reference level constructed
from a plurality of individuals of common known colorectal health
status. In some cases the reference is an average of known panel
levels from a plurality of individuals, or alternately is a range
defined by the range of panel levels observed in the reference
individuals. A range reference panel level is in some cases a
weighted range, such that outlier values among the individuals
having a common colorectal health status are given lower predictive
value than panel levels that are common to a plurality or majority
or all of the panel levels.
[0088] In more complex assessment approaches, an individual's
biomarker panel level is compared to a reference level constructed
from a larger number of individuals of common known colorectal
health status, such as at least 10, at least 50, at least 100, at
least 500, at least 1000 or more individuals. Often, the reference
individuals are evenly distributed in health status between
positive and negative for a colorectal health status such as
positive and negative for colorectal cancer, or positive and
negative for advanced adenoma. Assessment comprises in some cases
iterative or simultaneous comparison of an individual's biomarker
panel level to a plurality of references of known health
status.
[0089] Alternately or in combination, a plurality of known
reference biomarker panel levels are used to train a computational
assessment algorithm such as a machine learning model such that a
single comparison between an individual's biomarker panel level and
a reference provides an outcome that integrates or aggregates
information from a large number of individuals of common known
colorectal health status, such as at least 10, at least 50, at
least 100, at least 500, at least 1000 or more individuals.
Generation of such a reference often facilitates much faster
assessment of an individual's colorectal health status, or
assessment using much less computational power.
[0090] A reference is generated from a plurality of reference
individual biomarker levels through any of a number of
computational approaches known to one of skill in the art. Machine
learning models are readily constructed, for example, using any
number of statistical programming programming languages such as R,
scripting languages such as Python and associated machine learning
packages, data mining software such as Weka or Java, Mathematica,
Matlab or SAS.
[0091] An individual's biomarker panel level is compared to a
reference as generated above or otherwise by one of skill in the
art, and an output assessment is generated. A number of output
assessments are consistent with the disclosure herein. Output
assessments comprise a single assessment, often narrowed by a
sensitivity, specificity or sensitivity and specificity parameter,
indicating a colorectal health status assessment. Alternately or in
combination, additional parameters are provided, such as an odds
ratio indicative of the relative increase in chance of suffering
from a colorectal health issue in light of the individual's
biomarker panel level or biomarker panel level assessment.
[0092] Results are variously provided to the individual or to a
health care professional or other professional. Results are
optionally accompanied by a heath recommendation, such as a
recommendation to confirm or independently assess a colorectal
health status assessment, for example using a stool sample assay or
an invasive approach such as a colonoscopy, sigmoidoscopy or other
supplemental assay for colorectal health.
[0093] A recommendation optionally includes information relevant to
a treatment regimen, such as information indicating that a
treatment regimen such as a polypectomy, radiotherapy,
chemotherapy, antibody therapy, biosimilar treatment or other
treatment regimen, such as information indicative of success or
efficacy of the regimen. Efficacy of a regimen is assessed in some
cases by comparison of an individual's biomarker panel level at a
first time point, optionally prior to a treatment and a later
second time point, optionally subsequent to a treatment instance.
Biomarker panel levels are compared to one another, each to a
reference, or otherwise assessed so as to determine whether a
treatment regimen demonstrates efficacy such that it should be
continued, increased, replaced with an alternate regimen or
discontinued because of its success in addressing the colorectal
health issue such as colorectal cancer or advanced adenoma. Some
assessments rely upon comparison of an individual's biomarker panel
level at multiple time points, such as at least one time point
prior to a treatment and at least one time point following a
treatment. Biomarker panel levels are compared one to another or to
at least one reference biomarker panel level or both to one another
and to at least one reference biomarker panel level.
Health Assessment Assays
[0094] The biomarker panels, methods, compositions, and kits
described herein provide assays for at least one of advanced
colorectal adenoma and CRC based on detection or measurement of
biomarkers in a biological sample obtained from a subject. The
biological sample preferably is a blood sample drawn from an artery
or vein of an individual. The blood sample can be a whole blood
sample, a plasma sample, or a serum sample. The disclosure provided
herein detects at least one of advanced colorectal adenoma and CRC
from a sample such as a blood sample with a sensitivity and a
specificity that renders the outcome of the test reliable enough to
be medically actionable. Health assessment methods, systems, kits
and panels herein have at least one of a sensitivity of at least
70% and specificity of at least 70%. Such methods can have at least
one of a sensitivity of 70% or greater and specificity of at least
70% based on measurement of 15 or fewer biomarkers in the
biological sample. In some cases, a method provided herein detects
at least one of advanced colorectal adenoma and CRC. Such method
can have at least one of a sensitivity at least 70% and specificity
at least 70% based on measurement of no more than 4 biomarkers, 5
biomarkers, 6 biomarkers, 7, biomarkers, 8 biomarkers, 9
biomarkers, 10 biomarkers, 11, biomarkers, 12 biomarkers, 13
biomarkers, 14 biomarkers, or 15 biomarkers. Some preferred
embodiments allow one to assess colorectal cancer using a biomarker
panel of 8 markers. Some preferred embodiments allow one to assess
advanced adenoma using a panel of 4 biomarkers. Some biomarker
panels allow one to assess both colorectal cancer and advanced
adenoma using a combined panel of 11 biomarkers.
[0095] In some cases the biomarker panels, methods, compositions,
and kits described herein are useful to screen for individuals at
elevated risk for CRC or advanced adenoma. In some cases, a
positive detection of at least one of an advanced colorectal
adenoma and CRC based upon a method described herein is used to
identify patients for whom to recommend an additional diagnostic
method. For example, in some cases where a method herein yields a
positive result, such method is used to alert a caregiver to
perform an additional test such as a colonoscopy, a sigmoidoscopy,
an independent cancer assay, or a stool cancer assay.
[0096] The biomarker panels, methods, compositions, and kits
described herein are also useful as a quality control metric for a
colonoscopy, sigmoidoscopy, or colon tissue biopsy. For example, a
positive detection of at least one of an advanced colorectal
adenoma and CRC based upon a method described herein can be used to
validate a result of a colonoscopy, sigmoidoscopy, or colon tissue
biopsy. For example, in some cases wherein a colonoscopy,
sigmoidoscopy, or colon tissue biopsy yielded a negative result,
but a method described herein yielded a positive result, such
method can be used to alert a caregiver to perform another
colonoscopy, sigmoidoscopy, or colon tissue biopsy, or to initiate
a treatment regimen such as administration of a pharmaceutical
composition.
[0097] Some methods provided herein comprise (a) obtaining a
biological sample from a subject; (b) measuring a panel of
biomarkers in the biological sample of the subject; (c) detecting a
presence or absence of at least one of advanced colorectal adenoma
and CRC in the subject based upon the measuring; and (d) either (i)
treating the at least one of advanced colorectal adenoma CRC and in
the subject based upon the detecting, or (ii) recommending to the
subject a colonoscopy, sigmoidoscopy, or colorectal tissue biopsy
based upon the results of the detecting. For the purposes of one or
more methods described herein, "treating" comprises providing a
written report to the subject or to a caretaker of the subject
which includes a recommendation to initiate a treatment for the
CRC. For the purposes of one or more methods described herein,
"recommending to the subject a colonoscopy" comprises providing a
written report to the subject or to a caretaker of the subject
which includes a recommendation that the subject undergo a
colonoscopy, sigmoidoscopy, or tissue biopsy to confirm an
assessment of the CRC. In some cases, the colonoscopy,
sigmoidoscopy, or tissue biopsy can be used to remove the at least
one of advanced colorectal adenoma and CRC, thereby treating the at
least one of advanced colorectal adenoma and CRC.
[0098] Exemplary methods optionally comprise (a) obtaining data
comprising a measurement of a biomarker panel in a biological
sample obtained from a subject, (b) generating a subject-specific
profile of the biomarker panel based upon the measurement data, (c)
comparing the subject-specific profile of the biomarker panel to a
reference profile of the biomarker panel; and (d) determining a
likelihood of at least one of advanced colorectal adenoma and
colorectal cancer based upon (c).
[0099] Exemplary methods optionally comprise (a) measuring a
biomarker panel in a biological sample obtained from the subject;
(b) detecting a presence or absence of colorectal cancer and/or
advanced colorectal adenoma in the subject based upon the
measuring; and (c) treating the colorectal cancer in the subject
based upon the detecting.
[0100] Exemplary methods optionally comprise (a) obtaining data
comprising a measurement of a biomarker panel in a biological
sample obtained from a subject, (b) generating a subject-specific
profile of the biomarker panel based upon the measurement data, (c)
comparing the subject-specific profile of the biomarker panel to a
reference profile of the biomarker panel; and (d) determining a
likelihood of at least one of advanced colorectal adenoma and
colorectal cancer based upon (c). Some methods provided herein
comprise (a) measuring a biomarker panel in a biological sample
obtained from the subject; (b) detecting a presence or absence of
colorectal cancer and/or advanced colorectal adenoma in the subject
based upon the measuring; and (c) recommending to the subject at
least one of a colonoscopy, sigmoidoscopy, and tissue biopsy in the
subject based upon the detecting. Exemplary methods optionally
comprise diagnosis of colorectal cancer or monitoring colorectal
cancer, so as to establish a prognosis for the subject. The levels
of one or a combination of the proteins listed can over time be
linked to differential outcomes for cancer patients, possibly
depending on the treatment chosen. Exemplary methods optionally
comprise monitoring the progression of cancer in a subject by
comparing the accumulation levels of one or more biomarkers in a
sample from a subject to the accumulation levels of the one or more
biomarkers in a sample obtained from the subject at a subsequent
point in time, wherein a difference in the expression of said one
or more biomarkers diagnoses or aids in the diagnosis of the
progression of the cancer in the subject. Some exemplary methods
comprise monitoring the effectiveness of a treatment. In some
cases, a method for monitoring the effectiveness of a treatment
comprises comparing the accumulation levels of one or more
biomarkers in a sample from a subject prior to providing at least a
portion of a treatment to the accumulation levels of said one or
more biomarkers in a sample obtained from the subject after the
subject has received at least a portion of the treatment, and
wherein a difference in the accumulation levels of said one or more
biomarker diagnoses or aids in the diagnosis of the efficacy of the
treatment.
[0101] Biomarkers
[0102] In some cases, biomarker panels described herein comprise at
least two biomarkers. The biomarkers can be selected from the group
comprising A1AG1, A1AT, AACT, APOA1, CATD, CEA, CLUS, CO3, CO9,
CRP, FGB, FIBG, GARS, GELS, HPT, MIF, OSTP, PRDX1, PSGL, S10A8,
S10A9, SAA1, SBP1, SEPR, and TFRC, or fragments thereof. Any of the
biomarkers described herein can be protein biomarkers. Furthermore,
the group of biomarkers in this example can in some cases
additionally comprise polypeptides with the characteristics found
in Table 1.
[0103] Exemplary protein biomarkers and, when available, their
human amino acid sequences, are listed in Table 1, below. Protein
biomarkers comprise full length molecules of the polypeptide
sequences of Table 1, as well as uniquely identifiable fragments of
the polypeptide sequences of Table 1. Markers can be but do not
need to be full length to be informative. In many cases, so long as
a fragment is uniquely identifiable as being derived from or
representing a polypeptide of Table 1, it is informative for
purposes herein.
[0104] In some embodiments a panel of biomarkers may comprise a
panel of proteins Disclosed herein are panels of proteins suitable
for CRC or AA detection. In some cases, panels of proteins
described herein comprise at least two proteins. In some cases, the
proteins is selected from the group consisting of AACT, CATD, CEA,
CO3, CO9, MIF, PSGL, SEPR, CLUS, GDF15, and SAA1 or fragments
thereof. In some cases the panel is a CRC panel, and the proteins
tested comprise AACT, CATD, CEA, CO3, CO9, MIF, PSGL, and SEPR. In
some cases, the biomarker panel comprises AACT, CATD, CEA, CO3,
CO9, MIF, PSGL, and SEPR and the age of the subject. In some cases,
the ratio of one or more pairs of protein accumulation levels is
used to categorize a patients CRC status. For example, in some
cases the categorizing comprises comparing ratios of CATD/SEPR,
CATD/CO3, CO9/SEPR., and/or A.1AT/GDF15. In some cases, the
subject's age is included for evaluation in addition to the protein
accumulation levels. In some cases, the protein panel comprises
AACT, CATD, CEA, CO3, CO9, MIF, PSGL, and SEPR, and the sensitivity
for CRC detection is at least 50%, at least 55%, at least 60%, at
least 65%, at least 70%, at least 75%, at least 80%, at least 85%,
at least 90%, at least 95%, at least 96%, at least 97%, at least
98%, at least 99%, or about 100%.
[0105] In some cases, the protein panel comprises AACT, CATD, CE.A,
CO3, CO9, MIF, PSGL, and SEPR, and the sensitivity for CRC
detection is at least 81%. In some cases, the protein panel
comprises AACT, LAID, CEA, CO3, CO9, MIF, PSGL, and SEPR, and the
specificity for CRC detection is at least 50%, at least 55%, at
least 60%, at least 65%, at least 70%, at least 75%, at least 80%,
at least 85%, at least 90%, at least 95%, at least 96%, at least
97%, at least 98%, at least 99%, or about 100%. In some cases, the
protein panel comprises AACT, CATD, CEA, CO3, CO9, MIF, PSGL, and
SEPR, and the specificity for CRC detection is at least 78%. In
some cases, the protein panel comprises AACT, CATD, CEA, CO3, CO9,
MIF, PSGL, and SEPR, and the sensitivity for CRC detection is at
least 81% and the specificity is 78%. Furthermore, in some cases
the panel of proteins in these examples additionally comprises
polypeptides with the characteristics found in Table 1. In some
cases, the biomarker panel comprises AACT, CATD, CEA, CO3, CO9,
MIF, PSGL, and SEPR, and the age of the subject, and the
sensitivity for CRC detection is at least 50%, at least 55%, at
least 60%, at least 65%, at least 70%, at least 75%, at least 80%,
at least 85%, at least 90%, at least 95%, at least 96%, at least
97%, at least 98%, at least 99%, or about 100%. In some cases, the
biomarker panel comprises AACT, CATD, CEA, CO3, CO9, MIF, PSGL, and
SEPR, and the age of the subject, and the sensitivity for CRC
detection is at least 81%. In some cases, the biomarker panel
comprises AACT, CATD, CEA, CO3, CO9, MIF, PSGL, and SEPR, and the
age of the subject, and the specificity for CRC detection is at
least 50%, at least 55%, at least 60%, at least 65%, at least 70%,
at least 75%, at least 80%, at least 85%, at least 90%, at least
95%, at least 96%, at least 97%, at least 98%, at least 99%, or
about 100%. In some cases, the biomarker panel comprises AACT,
CATD, CEA, CO3, CO9, MIF, PSGL, and SEPR, and the age of the
subject, and the specificity for CR.0 detection is at least 78%. In
some cases, the biomarker panel comprises AACT, CATD, CEA, CO3,
CO9, MIF, PSGL, and SEPR, and the age of the subject, and the
sensitivity for CRC detection is at least 81% and the specificity
is 78%. In some cases, the protein panel comprises AACT, CATD, CEA,
CO3, CO9, MIF, PSGL, and SEPR, and the positive predictive value
for CRC detection is at least 50%, at least 55%, at least 60%, at
least 65%, at least 70%, at least 75%, at least 80%, at least 85%,
at least 90%, at least 95%, at least 96%, at least 97%, at least
98%, at least 99%, or about 100%. In some cases, the protein panel
comprises AACT, CATD, CEA, CO3, CO9, M PSGL, and SEPR, and positive
predictive value is 31%. In some cases, the protein panel comprises
AACT, CATD, CEA, CO3, CO9, MIF, PSGL, and SEPR, and the age of the
subject, and the positive predictive value for CR.0 detection is at
least 50%, at least 55%, at least 60%, at least 65%, at least 70%,
at least 75%, at least 80%, at least 85%, at least 90%, at least
95%, at least 96%, at least 97%, at least 98%, at least 99%, or
about 100%. In some cases, the protein panel comprises AACT, CATD,
CEA, CO3, CO9, MIF, PSGL, and SEPR, and the age of the subject, and
positive predictive value is 31%. In some cases, the biomarker
panel comprises AACT, CATD, CEA, CO3, CO9, MIF, PSGL, and SEPR, and
the age of the subject, and the sensitivity for CRC detection is at
least 81%, the specificity is 78%, and the positive predictive
value is 31%. In some cases, the biomarker panel comprises AACT,
LAID, CEA, CO3, CO9, MW, PSGL, and SEPR, and the sensitivity for
CRC detection is at least 81%, the specificity is 78%, and the
positive predictive value is 31%. Furthermore, in some cases the
panel of proteins in these examples additionally comprises
polypeptides with the characteristics found in Table 1.
TABLE-US-00001 TABLE 1 Biomarkers and corresponding protein
sequences Protein Name Symbol Sequence Alpha-1-acid A1AG1
MALSWVLTVLSLLPLLEAQIPLCANLVPVPITNATLDQITGKWFY glycoprotein 1
IASAFRNEEYNKSVQEIQATFFYFTPNKTEDTIFLREYQTRQDQCI
YNTTYLNVQRENGTISRYVGGQEHFAHLLILRDTKTYMLAFDVN
DEKNWGLSVYADKPETTKEQLGEFYEALDCLRIPKSDVVYTDW KKDKCEPLEKQHEKERKQEEGES
(SEQ ID NO: 1) Alpha-1 A1AT
MPSSVSWGILLLAGLCCLVPVSLAEDPQGDAAQKTDTSHHDQD Antitrypsin
HPTFNKITPNLAEFAFSLYRQLAHQSNSTNIFFSPVSIATAFAMLS
LGTKADTHDEILEGLNFNLTEIPEAQIHEGFQELLRTLNQPDSQLQ
LTTGNGLFLSEGLKLVDKFLEDVKKLYHSEAFTVNFGDTEEAKK
QINDYVEKGTQGKIVDLVKELDRDTVFALVNYIFFKGKWERPFE
VKDTEEEDFHVDQVTTVKVPMMKRLGMFNIQHCKKLSSWVLL
MKYLGNATAIFFLPDEGKLQHLENELTHDIITKFLENEDRRSASL
HLPKLSITGTYDLKSVLGQLGITKVFSNGADLSGVTEEAPLKLSK
AVHKAVLTIDEKGTEAAGAMFLEAIPMSIPPEVKFNKPFVFLMIE QNTKSPLFMGKVVNPTQK
(SEQ ID NO: 2) Alpha-1- AACT
MERMLPLLALGLLAAGFCPAVLCHPNSPLDEENLTQENQDRGT Antichymotrypsin
HVDLGLASANVDFAFSLYKQLVLKAPDKNVIFSPLSISTALAFLS
LGAHNTTLTEILKGLKFNLTETSEAEIHQSFQHLLRTLNQSSDELQ
LSMGNAMFVKEQLSLLDRFTEDAKRLYGSEAFATDFQDSAAAK
KLINDYVKNGTRGKITDLIKDLDSQTMMVLVNYIFFKAKWEMPF
DPQDTHQSRFYLSKKKWVMVPMMSLHHLTIPYFRDEELSCTVV
ELKYTGNASALFILPDQDKMEEVEAMLLPETLKRWRDSLEFREI
GELYLPKFSISRDYNLNDILLQLGIEEAFTSKADLSGITGARNLAV
SQVVHKAVLDVFEEGTEASAATAVKITLLSALVETRTIVRFNRPF
LMIIVPTDTQNIFFMSKVTNPKQA (SEQ ID NO: 3) Apolipoprotein APOA1
MKAAVLTLAVLFLTGSQARHFWQQDEPPQSPWDRVKDLATVY A-I
VDVLKDSGRDYVSQFEGSALGKQLNLKLLDNWDSVTSTFSKLR
EQLGPVTQEFWDNLEKETEGLRQEMSKDLEEVKAKVQPYLDDF
QKKWQEEMELYRQKVEPLRAELQEGARQKLHELQEKLSPLGEE
MRDRARAHVDALRTHLAPYSDELRQRLAARLEALKENGGARL
AEYHAKATEHLSTLSEKAKPALEDLRQGLLPVLESFKVSFLSALE EYTKKLNTQ (SEQ ID NO:
4) Cathepsin D CATD MQPSSLLPLALCLLAAPASALVRIPLHKFTSIRRTMSEVGGSVED
LIAKGPVSKYSQAVPAVTEGPIPEVLKNYMDAQYYGEIGIGTPPQ
CFTVVFDTGSSNLWVPSIHCKLLDIACWIHHKYNSDKSSTYVKN
GTSFDIHYGSGSLSGYLSQDTVSVPCQSASSASALGGVKVERQVF
GEATKQPGITFIAAKFDGILGMAYPRISVNNVLPVFDNLMQQKL
VDQNIFSFYLSRDPDAQPGGELMLGGTDSKYYKGSLSYLNVTRK
AYWQVHLDQVEVASGLTLCKEGCEAIVDTGTSLMVGPVDEVRE
LQKAIGAVPLIQGEYMIPCEKVSTLPAITLKLGGKGYKLSPEDYT
LKVSQAGKTLCLSGFMGMDIPPPSGPLWILGDVFIGRYYTVFDR DNNRVGFAEAARL (SEQ ID
NO: 5) Carcinoembryonic CEA
MGPPSASPHRECIPWQGLLLTASLLNFWNPPTTAKLTIESMPLSV antigen-
AEGKEVLLLVHNLPQHLFGYSWYKGERVDGNSLIVGYVIGTQQ related cell
ATPGAAYSGRETIYTNASLLIQNVTQNDIGFYTLQVIKSDLVNEE adhesion
ATGQFHVYQENAPGLPVGAVAGIVTGVLVGVALVAALVCFLLL molecule 3
AKTGRTSIQRDLKEQQPQALAPGRGPSHSSAFSMSPLSTAQAPLP
NPRTAASIYEELLKHDTNIYCRMDHKAEVAS (SEQ ID NO: 6) Clusterin CLUS
MMKTLLLFVGLLLTWESGQVLGDQTVSDNELQEMSNQGSKYV
NKEIQNAVNGVKQIKTLIEKTNEERKTLLSNLEEAKKKKEDALN
ETRESETKLKELPGVCNETMMALWEECKPCLKQTCMKFYARVC
RSGSGLVGRQLEEFLNQSSPFYFWMNGDRIDSLLENDRQQTHML
DVMQDHFSRASSIIDELFQDRFFTREPQDTYHYLPFSLPHRRPHFF
FPKSRIVRSLMPFSPYEPLNFHAMFQPFLEMIHEAQQAMDIHFHS
PAFQHPPTEFIREGDDDRTVCREIRHNSTGCLRMKDQCDKCREIL
SVDCSTNNPSQAKLRRELDESLQVAERLTRKYNELLKSYQWKM
LNTSSLLEQLNEQFNWVSRLANLTQGEDQYYLRVTTVASHTSDS
DVPSGVTEVVVKLFDSDPITVTVPVEVSRKNPKFMETVAEKALQ EYRKKHREE (SEQ ID NO:
7) Complement CO3 MGPTSGPSLLLLLLTHLPLALGSPMYSIITPNILRLESEETMVLEA C3
HDAQGDVPVTVTVHDFPGKKLVLSSEKTVLTPATNHMGNVTFTI
PANREFKSEKGRNKFVTVQATFGTQVVEKVVLVSLQSGYLFIQT
DKTIYTPGSTVLYRIFTVNHKLLPVGRTVMVNIENPEGIPVKQDS
LSSQNQLGVLPLSWDIPELVNMGQWKIRAYYENSPQQVFSTEFE
VKEYVLPSFEVIVEPTEKFYYIYNEKGLEVTITARFLYGKKVEGT
AFVIFGIQDGEQRISLPESLKRIPIEDGSGEVVLSRKVLLDGVQNP
RAEDLVGKSLYVSATVILHSGSDMVQAERSGIPIVTSPYQIHFTK
TPKYFKPGMPFDLMVFVTNPDGSPAYRVPVAVQGEDTVQSLTQ
GDGVAKLSINTHPSQKPLSITVRTKKQELSEAEQATRTMQALPYS
TVGNSNNYLHLSVLRTELRPGETLNVNFLLRMDRAHEAKIRYYT
YLIMNKGRLLKAGRQVREPGQDLVVLPLSITTDFIPSFRLVAYYT
LIGASGQREVVADSVWVDVKDSCVGSLVVKSGQSEDRQPVPGQ
QMTLKIEGDHGARVVLVAVDKGVFVLNKKNKLTQSKIWDVVE
KADIGCTPGSGKDYAGVFSDAGLTFTSSSGQQTAQRAELQCPQP
AARRRRSVQLTEKRMDKVGKYPKELRKCCEDGMRENPMRFSC
QRRTRFISLGEACKKVFLDCCNYITELRRQHARASHLGLARSNL
DEDIIAEENIVSRSEFPESWLWNVEDLKEPPKNGISTKLMNIFLKD
SITTWEILAVSMSDKKGICVADPFEVTVMQDFFIDLRLPYSVVRN
EQVEIRAVLYNYRQNQELKVRVELLHNPAFCSLATTKRRHQQT
VTIPPKSSLSVPYVIVPLKTGLQEVEVKAAVYHHFISDGVRKSLK
VVPEGIRMNKTVAVRTLDPERLGREGVQKEDIPPADLSDQVPDT
ESETRILLQGTPVAQMTEDAVDAERLKHLIVTPSGCGEQNMIGM
TPTVIAVHYLDETEQWEKFGLEKRQGALELIKKGYTQQLAFRQP
SSAFAAFVKRAPSTWLTAYVVKVFSLAVNLIAIDSQVLCGAVKW
LILEKQKPDGVFQEDAPVIHQEMIGGLRNNNEKDMALTAFVLISL
QEAKDICEEQVNSLPGSITKAGDFLEANYMNLQRSYTVAIAGYA
LAQMGRLKGPLLNKFLTTAKDKNRWEDPGKQLYNVEATSYAL
LALLQLKDFDFVPPVVRWLNEQRYYGGGYGSTQATFMVFQALA
QYQKDAPDHQELNLDVSLQLPSRSSKITHRIHWESASLLRSEETK
ENEGFTVTAEGKGQGTLSVVTMYHAKAKDQLTCNKFDLKVTIK
PAPETEKRPQDAKNTMILEICTRYRGDQDATMSILDISMMTGFAP
DTDDLKQLANGVDRYISKYELDKAFSDRNTLIIYLDKVSHSEDD
CLAFKVHQYFNVELIQPGAVKVYAYYNLEESCTRFYHPEKEDG
KLNKLCRDELCRCAEENCFIQKSDDKVTLEERLDKACEPGVDYV
YKTRLVKVQLSNDFDEYIMAIEQTIKSGSDEVQVGQQRTFISPIK
CREALKLEEKKHYLMWGLSSDFWGEKPNLSYIIGKDTWVEHWP
EEDECQDEENQKQCQDLGAFTESMVVFGCPN (SEQ ID NO: 8) Complement CO9
MSACRSFAVAICILEISILTAQYTTSYDPELTESSGSASHIDCRMSP C9
WSEWSQCDPCLRQMFRSRSIEVFGQFNGKRCTDAVGDRRQCVP
TEPCEDAEDDCGNDFQCSTGRCIKMRLRCNGDNDCGDFSDEDD
CESEPRPPCRDRVVEESELARTAGYGINILGMDPLSTPFDNEFYN
GLCNRDRDGNTLTYYRRPWNVASLIYETKGEKNFRTEHYEEQIE
AFKSIIQEKTSNFNAAISLKFTPTETNKAEQCCEETASSISLHGKGS
FRFSYSKNETYQLFLSYSSKKEKMFLHVKGEIHLGRFVMRNRDV
VLTTTFVDDIKALPTTYEKGEYFAFLETYGTHYSSSGSLGGLYEL
IYVLDKASMKRKGVELKDIKRCLGYHLDVSLAFSEISVGAEFNK
DDCVKRGEGRAVNITSENLIDDVVSLIRGGTRKYAFELKEKLLR
GTVIDVTDFVNWASSINDAPVLISQKLSPIYNLVPVKMKNAHLK
KQNLERAIEDYINEFSVRKCHTCQNGGTVILMDGKCLCACPFKF
EGIACEISKQKISEGLPALEFPNEK (SEQ ID NO: 9) C-reactive CRP
MEKLLCFLVLTSLSHAFGQTDMSRKAFVFPKESDTSYVSLKAPL protein
TKPLKAFTVCLHFYTELSSTRGYSIFSYATKRQDNEILIFWSKDIG
YSFTVGGSEILFEVPEVTVAPVHICTSWESASGIVEFWVDGKPRV
RKSLKKGYTVGAEASIILGQEQDSFGGNFEGSQSLVGDIGNVNM
WDFVLSPDEINTIYLGGPFSPNVLNWRALKYEVQGEVFTKPQLW P (SEQ ID NO: 10)
Fibrinogen FGB MKRMVSWSFHKLKTMKHLLLLLLCVFLVKSQGVNDNEEGFFSA beta
chain RGHRPLDKKREEAPSLRPAPPPISGGGYRARPAKAAATQKKVER
KAPDAGGCLHADPDLGVLCPTGCQLQEALLQQERPIRNSVDELN
NNVEAVSQTSSSSFQYMYLLKDLWQKRQKQVKDNENVVNEYS
SELEKHQLYIDETVNSNIPTNLRVLRSILENLRSKIQKLESDVSAQ
MEYCRTPCTVSCNIPVVSGKECEEIIRKGGETSEMYLIQPDSSVKP
YRVYCDMNTENGGWTVIQNRQDGSVDFGRKWDPYKQGFGNV
ATNTDGKNYCGLPGEYWLGNDKISQLTRMGPTELLIEMEDWKG
DKVKAHYGGFTVQNEANKYQISVNKYRGTAGNALMDGASQLM
GENRTMTIHNGMFFSTYDRDNDGWLTSDPRKQCSKEDGGGWW
YNRCHAANPNGRYYWGGQYTWDMAKHGTDDGVVWMNWKG SWYSMRKMSMKIRPFFPQQ (SEQ ID
NO: 11) Fibrinogen FIBG
MSWSLHPRNLILYFYALLFLSSTCVAYVATRDNCCILDERFGSYC gamma chain
PTTCGIADFLSTYQTKVDKDLQSLEDILHQVENKTSEVKQLIKAI
QLTYNPDESSKPNMIDAATLKSRKMLEEIMKYEASILTHDSSIRY
LQEIYNSNNQKIVNLKEKVAQLEAQCQEPCKDTVQIHDITGKDC
QDIANKGAKQSGLYFIKPLKANQQFLVYCEIDGSGNGWTVFQKR
LDGSVDFKKNWIQYKEGFGHLSPTGTTEFWLGNEKIHLISTQSAI
PYALRVELEDWNGRTSTADYAMFKVGPEADKYRLTYAYFAGG
DAGDAFDGFDFGDDPSDKFFTSHNGMQFSTWDNDNDKFEGNC
AEQDGSGWWMNKCHAGHLNGVYYQGGTYSKASTPNGYDNGII
WATWKTRWYSMKKTTMKIIPFNRLTIGEGQQHHLGGAKQVRPE HPAETEYDSLYPEDDL (SEQ
ID NO: 12) Glycine-tRNA GARS
MPSPRPVLLRGARAALLLLLPPRLLARPSLLLRRSLSAASCPPISL ligase
PAAASRSSMDGAGAEEVLAPLRLAVRQQGDLVRKLKEDKAPQV
DVDKAVAELKARKRVLEAKELALQPKDDIVDRAKMEDTLKRRF
FYDQAFAIYGGVSGLYDFGPVGCALKNNIIQTWRQHFIQEEQILE
IDCTMLTPEPVLKTSGHVDKFADFMVKDVKNGECFRADHLLKA
HLQKLMSDKKCSVEKKSEMESVLAQLDNYGQQELADLFVNYN
VKSPITGNDLSPPVSFNLMFKTFIGPGGNMPGYLRPETAQGIFLNF
KRLLEFNQGKLPFAAAQIGNSFRNEISPRSGLIRVREFTMAEIEHF
VDPSEKDHPKFQNVADLHLYLYSAKAQVSGQSARKMRLGDAV
EQGVINNTVLGYFIGRIYLYLTKVGISPDKLRFRQHMENEMAHY
ACDCWDAESKTSYGWIEIVGCADRSCYDLSCHARATKVPLVAE
KPLKEPKTVNVVQFEPSKGAIGKAYKKDAKLVMEYLAICDECYI
TEMEMLLNEKGEFTIETEGKTFQLTKDMINVKRFQKTLYVEEVV
PNVIEPSFGLGRIMYTVFEHTFHVREGDEQRTFFSFPAVVAPFKCS
VLPLSQNQEFMPFVKELSEALTRHGVSHKVDDSSGSIGRRYART
DEIGVAFGVTIDFDTVNKTPHTATLRDRDSMRQIRAEISELPSIVQ
DLANGNITWADVEARYPLFEGQETGKKETIEE (SEQ ID NO: 13) Gelsolin GELS
MAPHRPAPALLCALSLALCALSLPVRAATASRGASQAGAPQGR
VPEARPNSMVVEHPEFLKAGKEPGLQIWRVEKFDLVPVPTNLYG
DFFTGDAYVILKTVQLRNGNLQYDLHYWLGNECSQDESGAAAI
FTVQLDDYLNGRAVQHREVQGFESATFLGYFKSGLKYKKGGVA
SGFKHVVPNEVVVQRLFQVKGRRVVRATEVPVSWESFNNGDCF
ILDLGNNIHQWCGSNSNRYERLKATQVSKGIRDNERSGRARVHV
SEEGTEPEAMLQVLGPKPALPAGTEDTAKEDAANRKLAKLYKV
SNGAGTMSVSLVADENPFAQGALKSEDCFILDHGKDGKIFVWK
GKQANTEERKAALKTASDFITKMDYPKQTQVSVLPEGGETPLFK
QFFKNWRDPDQTDGLGLSYLSSHIANVERVPFDAATLHTSTAMA
AQHGMDDDGTGQKQIWRIEGSNKVPVDPATYGQFYGGDSYIIL
YNYRHGGRQGQIIYNWQGAQSTQDEVAASAILTAQLDEELGGT
PVQSRVVQGKEPAHLMSLFGGKPMIIYKGGTSREGGQTAPASTR
LFQVRANSAGATRAVEVLPKAGALNSNDAFVLKTPSAAYLWVG
TGASEAEKTGAQELLRVLRAQPVQVAEGSEPDGFWEALGGKAA
YRTSPRLKDKKMDAHPPRLFACSNKIGRFVIEEVPGELMQEDLA
TDDVMLLDTWDQVFVWVGKDSQEEEKTEALTSAKRYIETDPAN
RDRRTPITVVKQGFEPPSFVGWFLGWDDDYWSVDPLDRAMAEL AA (SEQ ID NO: 14)
Haptoglobin HPT MSALGAVIALLLWGQLFAVDSGNDVTDIADDGCPKPPEIAHGYV
EHSVRYQCKNYYKLRTEGDGVYTLNDKKQWINKAVGDKLPEC
EADDGCPKPPEIAHGYVEHSVRYQCKNYYKLRTEGDGVYTLNN
EKQWINKAVGDKLPECEAVCGKPKNPANPVQRILGGHLDAKGS
FPWQAKMVSHHNLTTGATLINEQWLLTTAKNLFLNHSENATAK
DIAPTLTLYVGKKQLVEIEKVVLHPNYSQVDIGLIKLKQKVSVNE
RVMPICLPSKDYAEVGRVGYVSGWGRNANFKFTDHLKYVMLP
VADQDQCIRHYEGSTVPEKKTPKSPVGVQPILNEHTFCAGMSKY
QEDTCYGDAGSAFAVHDLEEDTWYATGILSFDKSCAVAEYGVY VKVTSIQDWVQKTIAEN (SEQ
ID NO: 15) Macrophage MIF
MPMFIVNTNVPRASVPDGFLSELTQQLAQATGKPPQYIAVHVVP migration
DQLMAFGGSSEPCALCSLHSIGKIGGAQNRSYSKLLCGLLAERLR inhibitory
ISPDRVYINYYDMNAANVGWNNSTFA factor (SEQ ID NO: 16) Osteopontin OSTP
MRIAVICFCLLGITCAIPVKQADSGSSEEKQLYNKYPDAVATWL
NPDPSQKQNLLAPQNAVSSEETNDFKQETLPSKSNESHDHMDD
MDDEDDDDHVDSQDSIDSNDSDDVDDTDDSHQSDESHHSDESD
ELVTDFPTDLPATEVFTPVVPTVDTYDGRGDSVVYGLRSKSKKF
RRPDIQYPDATDEDITSHMESEELNGAYKAIPVAQDLNAPSDWD
SRGKDSYETSQLDDQSAETHSHKQSRLYKRKANDESNEHSDVID
SQELSKVSREFHSHEFHSHEDMLVVDPKSKEEDKHLKFRISHELD SASSEVN (SEQ ID NO:
17) Peroxiredoxin-1 PRDX1
MSSGNAKIGHPAPNFKATAVMPDGQFKDISLSDYKGKYVVFFFY
PLDFTFVCPTEIIAFSDRAEEFKKLNCQVIGASVDSHFCHLAWVN
TPKKQGGLGPMNIPLVSDPKRTIAQDYGVLKADEGISFRGLFIID
DKGILRQITVNDLPVGRSVDETLRLVQAFQFTDKHGEVCPAGWK PGSDTIKPDVQKSKEYFSKQK
(SEQ ID NO: 18) P-Selectin PSGL
MPLQLLLLLILLGPGNSLQLWDTWADEAEKALGPLLARDRRQA glycoprotein
TEYEYLDYDFLPETEPPEMLRNSTDTTPLTGPGTPESTTVEPAAR ligand 1
RSTGLDAGGAVTELTTELANMGNLSTDSAAMEIQTTQPAATEA
QTTQPVPTEAQTTPLAATEAQTTRLTATEAQTTPLAATEAQTTPP
AATEAQTTQPTGLEAQTTAPAAMEAQTTAPAAMEAQTTPPAAM
EAQTTQTTAMEAQTTAPEATEAQTTQPTATEAQTTPLAAMEALS
TEPSATEALSMEPTTKRGLFIPFSVSSVTHKGIPMAASNLSVNYPV
GAPDHISVKQCLLAILILALVATIFFVCTVVLAVRLSRKGHMYPV
RNYSPTEMVCISSLLPDGGEGPSATANGGLSKAKSPGLTPEPRED REGDDLTLHSFLP (SEQ ID
NO: 19) S100A8 S10A8 MLTELEKALNSIIDVYHKYSLIKGNFHAVYRDDLKKLLETECPQ
YIRKKGADVWFKELDINTDGAVNFQEFLILVIKMGVAAHKKSHE ESHKE (SEQ ID NO: 20)
S100A9 S10A9 MTCKMSQLERNIETIINTFHQYSVKLGHPDTLNQGEFKELVRKD
LQNFLKKENKNEKVIEHIMEDLDTNADKQLSFEEFIMLMARLTW
ASHEKMHEGDEGPGHHHKPGLGEGTP (SEQ ID NO: 21) Serum SAA1
MKLLTGLVFCSLVLGVSSRSFFSFLGEAFDGARDMWRAYSDMR amyloid A-1
EANYIGSDKYFHARGNYDAAKRGPGGVWAAEAISDARENIQRF protein
FGHGAEDSLADQAANEWGRSGKDPNHFRPAGLPEKY (SEQ ID NO: 22) Selenium- SBP1
MATKCGNCGPGYSTPLEAMKGPREEIVYLPCIYRNTGTEAPDYL binding
ATVDVDPKSPQYCQVIHRLPMPNLKDELHHSGWNTCSSCFGDST protein 1
KSRTKLVLPSLISSRIYVVDVGSEPRAPKLHKVIEPKDIHAKCELA
FLHTSHCLASGEVMISSLGDVKGNGKGGFVLLDGETFEVKGTW
ERPGGAAPLGYDFWYQPRHNVMISTEWAAPNVLRDGFNPADVE
AGLYGSHLYVWDWQRHEIVQTLSLKDGLIPLEIRFLHNPDAAQG
FVGCALSSTIQRFYKNEGGTWSVEKVIQVPPKKVKGWLLPEMPG
LITDILLSLDDRFLYFSNWLHGDLRQYDISDPQRPRLTGQLFLGG
SIVKGGPVQVLEDEELKSQPEPLVVKGKRVAGGPQMIQLSLDGK
RLYITTSLYSAWDKQFYPDLIREGSVMLQVDVDTVKGGLKLNPN
FLVDFGKEPLGPALAHELRYPGGDCSSDIWI (SEQ ID NO: 23) Seprase SEPR
MKTWVKIVFGVATSAVLALLVMCIVLRPSRVHNSEENTMRALT
LKDILNGTFSYKTFFPNWISGQEYLHQSADNNIVLYNIETGQSYTI
LSNRTMKSVNASNYGLSPDRQFVYLESDYSKLWRYSYTATYYI
YDLSNGEFVRGNELPRPIQYLCWSPVGSKLAYVYQNNIYLKQRP
GDPPFQITFNGRENKIFNGIPDWVYEEEMLATKYALWWSPNGKF
LAYAEFNDTDIPVIAYSYYGDEQYPRTINIPYPKAGAKNPVVRIFI
IDTTYPAYVGPQEVPVPAMIASSDYYFSWLTWVTDERVCLQWL
KRVQNVSVLSICDFREDWQTWDCPKTQEHIEESRTGWAGGFFVS
TPVFSYDAISYYKIFSDKDGYKHIHYIKDTVENAIQITSGKWEAIN
IFRVTQDSLFYSSNEFEEYPGRRNIYRISIGSYPPSKKCVTCHLRKE
RCQYYTASFSDYAKYYALVCYGPGIPISTLHDGRTDQEIKILEEN
KELENALKNIQLPKEEIKKLEVDEITLWYKMILPPQFDRSKKYPL
LIQVYGGPCSQSVRSVFAVNWISYLASKEGMVIALVDGRGTAFQ
GDKLLYAVYRKLGVYEVEDQITAVRKFIEMGFIDEKRIAIWGWS
YGGYVSSLALASGTGLFKCGIAVAPVSSWEYYASVYTERFMGLP
TKDDNLEHYKNSTVMARAEYFRNVDYLLIHGTADDNVHFQNSA
QIAKALVNAQVDFQAMWYSDQNHGLSGLSTNHLYTHMTHFLK QCFSLSD (SEQ ID NO: 24)
Transferrin TFRC MMDQARSAFSNLFGGEPLSYTRFSLARQVDGDNSHVEMKLAVD
Receptor EEENADNNTKANVTKPKRCSGSICYGTIAVIVFFLIGFMIGYLGY Protein 1
CKGVEPKTECERLAGTESPVREEPGEDFPAARRLYWDDLKRKLS
EKLDSTDFTGTIKLLNENSYVPREAGSQKDENLALYVENQFREF
KLSKVWRDQHFVKIQVKDSAQNSVIIVDKNGRLVYLVENPGGY
VAYSKAATVTGKLVHANFGTKKDFEDLYTPVNGSIVIVRAGKIT
FAEKVANAESLNAIGVLIYMDQTKFPIVNAELSFFGHAHLGTGDP
YTPGFPSFNHTQFPPSRSSGLPNIPVQTISRAAAEKLFGNMEGDCP
SDWKTDSTCRMVTSESKNVKLTVSNVLKEIKILNIFGVIKGFVEP
DHYVVVGAQRDAWGPGAAKSGVGTALLLKLAQMFSDMVLKD
GFQPSRSIIFASWSAGDFGSVGATEWLEGYLSSLHLKAFTYINLD
KAVLGTSNFKVSASPLLYTLIEKTMQNVKHPVTGQFLYQDSNW
ASKVEKLTLDNAAFPFLAYSGIPAVSFCFCEDTDYPYLGTTMDT
YKELIERIPELNKVARAAAEVAGQFVIKLTHDVELNLDYERYNS
QLLSFVRDLNQYRADIKEMGLSLQWLYSARGDFFRATSRLTTDF
GNAEKTDRFVMKKLNDRVMRVEYHFLSPYVSPKESPFRHVFWG
SGSHTLPALLENLKLRKQNNGAFNETLFRNQLALATWTIQGAAN ALSGDVWDIDNEF (SEQ ID
NO: 25) Growth / GDF15 MPGQELRTVNGSQMLLVLLVLSWLPHGGALSLAEASRASFPGPS
differentiation ELHSEDSRFRELRKRYEDLLTRLRANQSWEDSNTDLVPAPAVRI factor
15 LTPEVRLGSGGHLHLRISRAALPEGLPEASRLHRALFRLSPTASRS
WDVTRPLRRQLSLARPQAPALHLRLSPPPSQSDQLLAESSSARPQ
LELHLRPQAARGRRRARARNGDHCPLGPGRCCRLHTVRASLED
LGWADWVLSPREVQVTMCIGACPSQFRAANMHAQIKTSLHRLK
PDTVPAPCCVPASYNPMVLIQKTDTGVSLQTYDDLLAKDCHCI (SEQ ID NO: 26)
[0106] Biomarkers contemplated herein also include polypeptides
having an amino acid sequence identical to a listed marker of Table
1 over a span of 8 residues, 9, residues, 10 residues, 20 residues,
50 residues, or alternately 5%, 10%, 20%, 30%, 40%, 50%, 60%, 70%
80% 90%, 95% or grater than 95% of the sequence of the biomarker.
Variant or alternative forms of the biomarker include for example
polypeptides encoded by any splice-variants of transcripts encoding
the disclosed biomarkers. In certain cases the modified forms,
fragments, or their corresponding RNA or DNA, may exhibit better
discriminatory power in diagnosis than the full-length protein.
[0107] Biomarkers contemplated herein also include truncated forms
or polypeptide fragments of any of the proteins described herein.
Truncated forms or polypeptide fragments of a protein can include
N-terminally deleted or truncated forms and C-terminally deleted or
truncated forms. Truncated forms or fragments of a protein can
include fragments arising by any mechanism, such as, without
limitation, by alternative translation, exo- and/or
endo-proteolysis and/or degradation, for example, by physical,
chemical and/or enzymatic proteolysis. Without limitation, a
biomarker may comprise a truncated or fragment of a protein,
polypeptide or peptide may represent about 1%, 2%, 3%, 4%, 5%, 6%,
7%, 8%, 9%, 10%, 11%, 12%, 13%, 14%, 15%, 16%, 17%, 18%, 19%, 20%,
25%, 30%, 35%, 40%, 45%, 50%, 55%, 60%, 65%, 70%, 75%, 80%, 85%,
90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100% of the
amino acid sequence of the protein.
[0108] Without limitation, a truncated or fragment of a protein may
include a sequence of about 5-20 consecutive amino acids, or about
10-50 consecutive amino acids, or about 20-100 consecutive amino
acids, or about 30-150 consecutive amino acids, or about 50-500
consecutive amino acid residues of the corresponding full length
protein.
[0109] In some instances, a fragment is N-terminally and/or
C-terminally truncated by between 1 and about 20 amino acids, such
as, for example, by between 1 and about 15 amino acids, or by
between 1 and about 10 amino acids, or by between 1 and about 5
amino acids, compared to the corresponding mature, full-length
protein or its soluble or plasma circulating form.
[0110] Any protein biomarker of the present disclosure such as a
peptide, polypeptide or protein and fragments thereof may also
encompass modified forms of said marker, peptide, polypeptide or
protein and fragments such as bearing post-expression modifications
including but not limited to, modifications such as
phosphorylation, glycosylation, lipidation, methylation,
selenocystine modification, cysteinylation, sulphonation,
glutathionylation, acetylation, oxidation of methionine to
methionine sulphoxide or methionine sulphone, and the like.
[0111] In some instances, a fragmented protein is N-terminally
and/or C-terminally truncated. Such fragmented protein can comprise
one or more, or all transitional ions of the N-terminally (a, b,
c-ion) and/or C-terminally (x, y, z-ion) truncated protein or
peptide. Exemplary human markers, nucleic acids, proteins or
polypeptides as taught herein are as annotated under NCBI Genbank
(accessible at the website ncbi.nlm.nih.gov) or Swissprot/Uniprot
(accessible at the website uniprot.org) accession numbers. In some
instances said sequences are of precursors (for example,
preproteins) of the of markers, nucleic acids, proteins or
polypeptides as taught herein and may include parts which are
processed away from mature molecules. In some instances although
only one or more isoforms is disclosed, all isoforms of the
sequences are intended.
[0112] Antibodies for the detection of the biomarkers listed herein
are commercially available. A partial list of sources for reagents
useful for the assay of biomarkers herein is presented in Table 2
below.
TABLE-US-00002 TABLE 2 Reagent Sources ELISA Assay Reference Plasma
Abbrev. Kit Vendor Reference Vendor Dilution A1AT Genway Biotech,
San Diego, CA Native protein MyBiosource, San Diego, CA 1:240,000
A1AG1 R&D Systems, Minneapolis, MN Native protein BioVendor,
Asheville, NC 1:20,000 AACT Genway Biotech, San Diego, CA Native
protein MyBiosource, San Diego, CA 1:10,000 ANXA1 Cloud Clone,
Wuhan, PRC Recombinant protein Origene, Rockville, MD 1:8,000 APOA1
Cusabio, Wuhan, PRC Native protein MyBiosource, San Diego, CA 1:800
CRP BioVendor, Asheville, NC Recombinant protein R&D Systems,
Minneapolis, MN 1:1,000 CAH1 Cloud Clone, Wuhan, PRC Recombinant
protein MyBiosource, San Diego, CA 1:32 CEA IBL International,
Toronto, ON Native protein Origene, Rockville, MD 1:1 CATD AbCam,
Cambridge, MA Native protein Novus Biologicals, Littleton, CA 1:250
CLUS BioVendor, Asheville, NC Native protein MyBiosource, San
Diego, CA 1:3,000 CO3 Abnova, Taipei, Taiwan Native protein
MyBiosource, San Diego, CA 1:250 CO9 AssayPro, St. Charles, MO
Native protein MyBiosource, San Diego, CA 1:20,000 DPP4 Cloud
Clone, Wuhan, PRC Native protein BioVendor, Asheville, NC 1:2,000
FGB Cloud Clone, Wuhan, PRC Recombinant protein Antibodies Online,
Atlanta, GA 1:8,000 FIBG Cloud Clone, Wuhan, PRC Native protein
MyBiosource, San Diego, CA 1:8,000 GELS Cloud Clone, Wuhan, PRC
Recombinant protein Origene, Rockville, MD 1:100 GARS Cloud Clone,
Wuhan, PRC Recombinant protein Novus Biologicals, Littleton, CA
1:40 GDF15 R&D Systems, Minneapolis, MN Native protein AbCam,
Cambridge, MA 1:8 HPT AssayPro, St. Charles, MO Recombinant protein
Origene, Rockville, MD 1:2,000 MIF R&D Systems, Minneapolis, MN
Recombinant protein MyBiosource, San Diego, CA 1:10 OSTP R&D
Systems, Minneapolis, MN Recombinant protein Origene, Rockville, MD
1:20 PSGL IBL America, Minneapolis, MN Recombinant protein Life
Technologies, Camarillo, CA 1:30 PRDX1 Cloud Clone, Wuhan, PRC
Recombinant protein MyBiosource, San Diego, CA 1:100 SBP1 Cloud
Clone, Wuhan, PRC Recombinant protein Origene, Rockville, MD 1:16
SEPR R&D Systems, Minneapolis, MN Recombinant protein Origene,
Rockville, MD 1:40 SAA1 Life Technologies, Camarillo, CA
Recombinant protein Origene, Rockville, MD 1:240 TIMP1 R&D
Systems, Minneapolis, MN Recombinant protein Life Technologies,
Camarillo, CA 1:100 TFRC Cloud Clone, Wuhan, PRC Native protein
MyBiosource, San Diego, CA 1:250 TFF3 R&D Systems, Minneapolis,
MN Recombinant protein R&D Systems, Minneapolis, MN 1:50 PKM2
ScheBo, Giessen, GER Recombinant protein Origene, Rockville, MD
1:100
[0113] For a given biomarker panel recited herein, variant
biomarker panels differing in one or more than one constituent are
also contemplated. Thus, turning to a lead CRC panel AACT, CATD,
CEA, CO3, CO9, MIF, PSGL, and SEPR as an example, a number of
related panels are disclosed. For this and other panels disclosed
herein, variants are contemplated comprising at least 8, at least
7, at least 6, at least 5, at least 4, at least 3, or at least 2 of
the biomarker constituents of a recited biomarker panel. Thus,
turning to a lead biomarker panel AACT, CATD, CEA, CO3, CO9, MIF,
PSGL, and SEPR, one sees the variant panels as listed in Table 3.
Age is optionally included as a non-protein feature for any of the
panel variants listed herein
TABLE-US-00003 TABLE 3 CRC Panel Embodiments Protein Nonprotein No.
Features Panel feature 1 8 AACT, CATD, CEA, CO3, +/-Age CO9, MIF,
PSGL, SEPR 2 7 AACT, CATD, CEA, CO3, CO9, MIF, PSGL +/-Age 3 7
AACT, CATD, CEA, CO3, CO9, MIF, SEPR +/-Age 4 7 AACT, CATD, CEA,
CO3, CO9, PSGL, SEPR +/-Age 5 7 AACT, CATD, CEA, CO3, MIF, PSGL,
SEPR +/-Age 6 7 AACT, CATD, CEA, CO9, MIF, PSGL, SEPR +/-Age 7 7
AACT, CATD, CO3, CO9, MIF, PSGL, SEPR +/-Age 8 7 AACT, CEA, CO3,
CO9, MIF, PSGL, SEPR +/-Age 9 7 CATD, CEA, CO3, CO9, MIF, PSGL,
SEPR +/-Age 10 6 AACT, CATD, CEA, CO3, CO9, MIF +/-Age 11 6 AACT,
CATD, CEA, CO3, CO9, PSGL +/-Age 12 6 AACT, CATD, CEA, CO3, CO9,
SEPR +/-Age 13 6 AACT, CATD, CEA, CO3, MIF, PSGL +/-Age 14 6 AACT,
CATD, CEA, CO3, MIF, SEPR +/-Age 15 6 AACT, CATD, CEA, CO3, PSGL,
SEPR +/-Age 16 6 AACT, CATD, CEA, CO9, MIF, PSGL +/-Age 17 6 AACT,
CATD, CEA, CO9, MIF, SEPR +/-Age 18 6 AACT, CATD, CEA, CO9, PSGL,
SEPR +/-Age 19 6 AACT, CATD, CEA, MIF, PSGL, SEPR +/-Age 20 6 AACT,
CATD, CO3, CO9, MIF, PSGL +/-Age 21 6 AACT, CATD, CO3, CO9, MIF,
SEPR +/-Age 22 6 AACT, CATD, CO3, CO9, PSGL, SEPR +/-Age 23 6 AACT,
CATD, CO3, MIF, PSGL, SEPR +/-Age 24 6 AACT, CATD, CO9, MIF, PSGL,
SEPR +/-Age 25 6 AACT, CEA, CO3, CO9, MIF, PSGL +/-Age 26 6 AACT,
CEA, CO3, CO9, MIF, SEPR +/-Age 27 6 AACT, CEA, CO3, CO9, PSGL,
SEPR +/-Age 28 6 AACT, CEA, CO3, MIF, PSGL, SEPR +/-Age 29 6 AACT,
CEA, CO9, MIF, PSGL, SEPR +/-Age 30 6 AACT, CO3, CO9, MIF, PSGL,
SEPR +/-Age 31 6 CATD, CEA, CO3, CO9, MIF, PSGL +/-Age 32 6 CATD,
CEA, CO3, CO9, MIF, SEPR +/-Age 33 6 CATD, CEA, CO3, CO9, PSGL,
SEPR +/-Age 34 6 CATD, CEA, CO3, MIF, PSGL, SEPR +/-Age 35 6 CATD,
CEA, CO9, MIF, PSGL, SEPR +/-Age 36 6 CATD, CO3, CO9, MIF, PSGL,
SEPR +/-Age 37 6 CEA, CO3, CO9, MIF, PSGL, SEPR +/-Age 38 5 AACT,
CATD, CEA, CO3, CO9 +/-Age 39 5 AACT, CATD, CEA, CO3, MIF +/-Age 40
5 AACT, CATD, CEA, CO3, PSGL +/-Age 41 5 AACT, CATD, CEA, CO3, SEPR
+/-Age 42 5 AACT, CATD, CEA, CO9, MIF +/-Age 43 5 AACT, CATD, CEA,
CO9, PSGL +/-Age 44 5 AACT, CATD, CEA, CO9, SEPR +/-Age 45 5 AACT,
CATD, CEA, MIF, PSGL +/-Age 46 5 AACT, CATD, CEA, MIF, SEPR +/-Age
47 5 AACT, CATD, CEA, PSGL, SEPR +/-Age 48 5 AACT, CATD, CO3, CO9,
MIF +/-Age 49 5 AACT, CATD, CO3, CO9, PSGL +/-Age 50 5 AACT, CATD,
CO3, CO9, SEPR +/-Age 51 5 AACT, CATD, CO3, MIF, PSGL +/-Age 52 5
AACT, CATD, CO3, MIF, SEPR +/-Age 53 5 AACT, CATD, CO3, PSGL, SEPR
+/-Age 54 5 AACT, CATD, CO9, MIF, PSGL +/-Age 55 5 AACT, CATD, CO9,
MIF, SEPR +/-Age 56 5 AACT, CATD, CO9, PSGL, SEPR +/-Age 57 5 AACT,
CATD, MIF, PSGL, SEPR +/-Age 58 5 AACT, CEA, CO3, CO9, MIF +/-Age
59 5 AACT, CEA, CO3, CO9, PSGL +/-Age 60 5 AACT, CEA, CO3, CO9,
SEPR +/-Age 61 5 AACT, CEA, CO3, MIF, PSGL +/-Age 62 5 AACT, CEA,
CO3, MIF, SEPR +/-Age 63 5 AACT, CEA, CO3, PSGL, SEPR +/-Age 64 5
AACT, CEA, CO9, MIF, PSGL +/-Age 65 5 AACT, CEA, CO9, MIF, SEPR
+/-Age 66 5 AACT, CEA, CO9, PSGL, SEPR +/-Age 67 5 AACT, CEA, MIF,
PSGL, SEPR +/-Age 68 5 AACT, CO3, CO9, MIF, PSGL +/-Age 69 5 AACT,
CO3, CO9, MIF, SEPR +/-Age 70 5 AACT, CO3, CO9, PSGL, SEPR +/-Age
71 5 AACT, CO3, MIF, PSGL, SEPR +/-Age 72 5 AACT, CO9, MIF, PSGL,
SEPR +/-Age 73 5 CATD, CEA, CO3, CO9, MIF +/-Age 74 5 CATD, CEA,
CO3, CO9, PSGL +/-Age 75 5 CATD, CEA, CO3, CO9, SEPR +/-Age 76 5
CATD, CEA, CO3, MIF, PSGL +/-Age 77 5 CATD, CEA, CO3, MIF, SEPR
+/-Age 78 5 CATD, CEA, CO3, PSGL, SEPR +/-Age 79 5 CATD, CEA, CO9,
MIF, PSGL +/-Age 80 5 CATD, CEA, CO9, MIF, SEPR +/-Age 81 5 CATD,
CEA, CO9, PSGL, SEPR +/-Age 82 5 CATD, CEA, MIF, PSGL, SEPR +/-Age
83 5 CATD, CO3, CO9, MIF, PSGL +/-Age 84 5 CATD, CO3, CO9, MIF,
SEPR +/-Age 85 5 CATD, CO3, CO9, PSGL, SEPR +/-Age 86 5 CATD, CO3,
MIF, PSGL, SEPR +/-Age 87 5 CATD, CO9, MIF, PSGL, SEPR +/-Age 88 5
CEA, CO3, CO9, MIF, PSGL +/-Age 89 5 CEA, CO3, CO9, MIF, SEPR
+/-Age 90 5 CEA, CO3, CO9, PSGL, SEPR +/-Age 91 5 CEA, CO3, MIF,
PSGL, SEPR +/-Age 92 5 CEA, CO9, MIF, PSGL, SEPR +/-Age 93 5 CO3,
CO9, MIF, PSGL, SEPR +/-Age 94 4 AACT, CATD, CEA, CO3 +/-Age 95 4
AACT, CATD, CEA, CO9 +/-Age 96 4 AACT, CATD, CEA, MIF +/-Age 97 4
AACT, CATD, CEA, PSGL +/-Age 98 4 AACT, CATD, CEA, SEPR +/-Age 99 4
AACT, CATD, CO3, CO9 +/-Age 100 4 AACT, CATD, CO3, MIF +/-Age 101 4
AACT, CATD, CO3, PSGL +/-Age 102 4 AACT, CATD, CO3, SEPR +/-Age 103
4 AACT, CATD, CO9, MIF +/-Age 104 4 AACT, CATD, CO9, PSGL +/-Age
105 4 AACT, CATD, CO9, SEPR +/-Age 106 4 AACT, CATD, MIF, PSGL
+/-Age 107 4 AACT, CATD, MIF, SEPR +/-Age 108 4 AACT, CATD, PSGL,
SEPR +/-Age 109 4 AACT, CEA, CO3, CO9 +/-Age 110 4 AACT, CEA, CO3,
MIF +/-Age 111 4 AACT, CEA, CO3, PSGL +/-Age 112 4 AACT, CEA, CO3,
SEPR +/-Age 113 4 AACT, CEA, CO9, MIF +/-Age 114 4 AACT, CEA, CO9,
PSGL +/-Age 115 4 AACT, CEA, CO9, SEPR +/-Age 116 4 AACT, CEA, MIF,
PSGL +/-Age 117 4 AACT, CEA, MIF, SEPR +/-Age 118 4 AACT, CEA,
PSGL, SEPR +/-Age 119 4 AACT, CO3, CO9, MIF +/-Age 120 4 AACT, CO3,
CO9, PSGL +/-Age 121 4 AACT, CO3, CO9, SEPR +/-Age 122 4 AACT, CO3,
MIF, PSGL +/-Age 123 4 AACT, CO3, MIF, SEPR +/-Age 124 4 AACT, CO3,
PSGL, SEPR +/-Age 125 4 AACT, CO9, MIF, PSGL +/-Age 126 4 AACT,
CO9, MIF, SEPR +/-Age 127 4 AACT, CO9, PSGL, SEPR +/-Age 128 4
AACT, MIF, PSGL, SEPR +/-Age 129 4 CATD, CEA, CO3, CO9 +/-Age 130 4
CATD, CEA, CO3, MIF +/-Age 131 4 CATD, CEA, CO3, PSGL +/-Age 132 4
CATD, CEA, CO3, SEPR +/-Age 133 4 CATD, CEA, CO9, MIF +/-Age 134 4
CATD, CEA, CO9, PSGL +/-Age 135 4 CATD, CEA, CO9, SEPR +/-Age 136 4
CATD, CEA, MIF, PSGL +/-Age 137 4 CATD, CEA, MIF, SEPR +/-Age 138 4
CATD, CEA, PSGL, SEPR +/-Age 139 4 CATD, CO3, CO9, MIF +/-Age 140 4
CATD, CO3, CO9, PSGL +/-Age 141 4 CATD, CO3, CO9, SEPR +/-Age 142 4
CATD, CO3, MIF, PSGL +/-Age 143 4 CATD, CO3, MIF, SEPR +/-Age 144 4
CATD, CO3, PSGL, SEPR +/-Age 145 4 CATD, CO9, MIF, PSGL +/-Age 146
4 CATD, CO9, MIF, SEPR +/-Age 147 4 CATD, CO9, PSGL, SEPR +/-Age
148 4 CATD, MIF, PSGL, SEPR +/-Age 149 4 CEA, CO3, CO9, MIF +/-Age
150 4 CEA, CO3, CO9, PSGL +/-Age 151 4 CEA, CO3, CO9, SEPR +/-Age
152 4 CEA, CO3, MIF, PSGL +/-Age 153 4 CEA, CO3, MIF, SEPR +/-Age
154 4 CEA, CO3, PSGL, SEPR +/-Age 155 4 CEA, CO9, MIF, PSGL +/-Age
156 4 CEA, CO9, MIF, SEPR +/-Age 157 4 CEA, CO9, PSGL, SEPR +/-Age
158 4 CEA, MIF, PSGL, SEPR +/-Age 159 4 CO3, CO9, MIF, PSGL +/-Age
160 4 CO3, CO9, MIF, SEPR +/-Age 161 4 CO3, CO9, PSGL, SEPR +/-Age
162 4 CO3, MIF, PSGL, SEPR +/-Age 163 4 CO9, MIF, PSGL, SEPR +/-Age
164 3 AACT, CATD, CEA +/-Age 165 3 AACT, CATD, CO3 +/-Age 166 3
AACT, CATD, CO9 +/-Age 167 3 AACT, CATD, MIF +/-Age 168 3 AACT,
CATD, PSGL +/-Age 169 3 AACT, CATD, SEPR +/-Age 170 3 AACT, CEA,
CO3 +/-Age 171 3 AACT, CEA, CO9 +/-Age 172 3 AACT, CEA, MIF +/-Age
173 3 AACT, CEA, PSGL +/-Age 174 3 AACT, CEA, SEPR +/-Age 175 3
AACT, CO3, CO9 +/-Age 176 3 AACT, CO3, MIF +/-Age 177 3 AACT, CO3,
PSGL +/-Age 178 3 AACT, CO3, SEPR +/-Age 179 3 AACT, CO9, MIF
+/-Age 180 3 AACT, CO9, PSGL +/-Age 181 3 AACT, CO9, SEPR +/-Age
182 3 AACT, MIF, PSGL +/-Age 183 3 AACT, MIF, SEPR +/-Age 184 3
AACT, PSGL, SEPR +/-Age 185 3 CATD, CEA, CO3 +/-Age 186 3 CATD,
CEA, CO9 +/-Age 187 3 CATD, CEA, MIF +/-Age 188 3 CATD, CEA, PSGL
+/-Age 189 3 CATD, CEA, SEPR +/-Age 190 3 CATD, CO3, CO9 +/-Age 191
3 CATD, CO3, MIF +/-Age 192 3 CATD, CO3, PSGL +/-Age 193 3 CATD,
CO3, SEPR +/-Age 194 3 CATD, CO9, MIF +/-Age 195 3 CATD, CO9, PSGL
+/-Age 196 3 CATD, CO9, SEPR +/-Age 197 3 CATD, MIF, PSGL +/-Age
198 3 CATD, MIF, SEPR +/-Age 199 3 CATD, PSGL, SEPR +/-Age 200 3
CEA, CO3, CO9 +/-Age 201 3 CEA, CO3, MIF +/-Age 202 3 CEA, CO3,
PSGL +/-Age 203 3 CEA, CO3, SEPR +/-Age 204 3 CEA, CO9, MIF +/-Age
205 3 CEA, CO9, PSGL +/-Age 206 3 CEA, CO9, SEPR +/-Age 207 3 CEA,
MIF, PSGL +/-Age 208 3 CEA, MIF, SEPR +/-Age 209 3 CEA, PSGL, SEPR
+/-Age 210 3 CO3, CO9, MIF +/-Age 211 3 CO3, CO9, PSGL +/-Age 212 3
CO3, CO9, SEPR +/-Age 213 3 CO3, MIF, PSGL +/-Age 214 3 CO3, MIF,
SEPR +/-Age 215 3 CO3, PSGL, SEPR +/-Age 216 3 CO9, MIF, PSGL
+/-Age 217 3 CO9, MIF, SEPR +/-Age 218 3 CO9, PSGL, SEPR +/-Age 219
3 MIF, PSGL, SEPR +/-Age 220 2 AACT, CATD +/-Age 221 2 AACT, CEA
+/-Age 222 2 AACT, CO3 +/-Age 223 2 AACT, CO9 +/-Age 224 2 AACT,
MIF +/-Age 225 2 AACT, PSGL +/-Age 226 2 AACT, SEPR +/-Age 227 2
CATD, CEA +/-Age 228 2 CATD, CO3 +/-Age 229 2 CATD, CO9 +/-Age 230
2 CATD, MIF +/-Age 231 2 CATD, PSGL +/-Age 232 2 CATD, SEPR +/-Age
233 2 CEA, CO3 +/-Age 234 2 CEA, CO9 +/-Age 235 2 CEA, MIF +/-Age
236 2 CEA, PSGL +/-Age 237 2 CEA, SEPR +/-Age 238 2 CO3, CO9 +/-Age
239 2 CO3, MIF +/-Age 240 2 CO3, PSGL +/-Age 241 2 CO3, SEPR +/-Age
242 2 CO9, MIF +/-Age 243 2 CO9, PSGL +/-Age
244 2 CO9, SEPR +/-Age 245 2 MIF, PSGL +/-Age 246 2 MIF, SEPR
+/-Age 247 2 PSGL, SEPR +/-Age
[0114] In some embodiments a biomarker comprises 8 or more
proteins, wherein 8 or more of the proteins comprise: AACT, CATD,
CEA, CO3, CO9, MIF, PSGL, and SEPR. In some embodiments a biomarker
panel comprises 7 or more proteins, wherein 7 of the proteins
comprises AACT, CATD, CEA, CO3, CO9, MIF, and PSGL. In some
embodiments a biomarker panel comprises 7 or more proteins, wherein
7 of the proteins comprises AACT, CATD, CEA, CO3, CO9, MIF, and
SEPR. In some embodiments a biomarker panel comprises 7 or more
proteins, wherein 7 of the proteins comprises AACT, CATD, CEA, CO3,
CO9, PSGL, and SEPR. In some embodiments a biomarker panel
comprises 7 or more proteins, wherein 7 of the proteins comprises
AACT, CATD, CEA, CO3, MIF, PSGL, and SEPR. In some embodiments a
biomarker panel comprises 7 or more proteins, wherein 7 of the
proteins comprises AACT, CATD, CEA, CO9, MIF, PSGL, and SEPR. In
some embodiments a biomarker panel comprises 7 or more proteins,
wherein 7 of the proteins comprises AACT, CATD, CO3, CO9, MIF,
PSGL, and SEPR. In some embodiments a biomarker panel comprises 7
or more proteins, wherein 7 of the proteins comprises AACT, CEA,
CO3, CO9, MIF, PSGL, and SEPR. In some embodiments a biomarker
panel comprises 7 or more proteins, wherein 7 of the proteins
comprises CATD, CEA, CO3, CO9, MIF, PSGL, and SEPR.
[0115] In some embodiments a biomarker panel comprises 6 or more
proteins, wherein 6 of the proteins comprises AACT, CATD, CEA, CO3,
CO9, and MIF. In some embodiments a biomarker panel comprises 6 or
more proteins, wherein 6 of the proteins comprises AACT, CATD, CEA,
CO3, CO9, and PSGL. In some embodiments a biomarker panel comprises
6 or more proteins, wherein 6 of the proteins comprises AACT, CATD,
CEA, CO3, CO9, and SEPR. In some embodiments a biomarker panel
comprises 6 or more proteins, wherein 6 of the proteins comprises
AACT, CATD, CEA, CO3, MIF, and PSGL. In some embodiments a
biomarker panel comprises 6 or more proteins, wherein 6 of the
proteins comprises AACT, CATD, CEA, CO3, MIF, and SEPR. In some
embodiments a biomarker panel comprises 6 or more proteins, wherein
6 of the proteins comprises AACT, CATD, CEA, CO3, PSGL, and SEPR.
In some embodiments a biomarker panel comprises 6 or more proteins,
wherein 6 of the proteins comprises AACT, CATD, CEA, CO9, MIF, and
PSGL. In some embodiments a biomarker panel comprises 6 or more
proteins, wherein 6 of the proteins comprises AACT, CATD, CEA, CO9,
MIF, and SEPR. In some embodiments a biomarker panel comprises 6 or
more proteins, wherein 6 of the proteins comprises AACT, CATD, CEA,
CO9, PSGL, and SEPR. In some embodiments a biomarker panel
comprises 6 or more proteins, wherein 6 of the proteins comprises
AACT, CATD, CEA, MIF, PSGL, and SEPR. In some embodiments a
biomarker panel comprises 6 or more proteins, wherein 6 of the
proteins comprises AACT, CATD, CO3, CO9, MIF, and PSGL. In some
embodiments a biomarker panel comprises 6 or more proteins, wherein
6 of the proteins comprises AACT, CATD, CO3, CO9, MIF, and SEPR. In
some embodiments a biomarker panel comprises 6 or more proteins,
wherein 6 of the proteins comprises AACT, CATD, CO3, CO9, PSGL, and
SEPR. In some embodiments a biomarker panel comprises 6 or more
proteins, wherein 6 of the proteins comprises AACT, CATD, CO3, MIF,
PSGL, and SEPR. In some embodiments a biomarker panel comprises 6
or more proteins, wherein 6 of the proteins comprises AACT, CATD,
CO9, MIF, and PSGL, and SEPR. In some embodiments a biomarker panel
comprises 6 or more proteins, wherein 6 of the proteins comprises
AACT, CEA, CO3, CO9, MIF, and PSGL. In some embodiments a biomarker
panel comprises 6 or more proteins, wherein 6 of the proteins
comprises AACT, CEA, CO3, CO9, MIF, and SEPR. In some embodiments a
biomarker panel comprises 6 or more proteins, wherein 6 of the
proteins comprises AACT, CEA, CO3, CO9, PSGL, and SEPR. In some
embodiments a biomarker panel comprises 6 or more proteins, wherein
6 of the proteins comprises AACT, CEA, CO3, MIF, PSGL, and SEPR. In
some embodiments a biomarker panel comprises 6 or more proteins,
wherein 6 of the proteins comprises AACT, CEA, CO9, MIF, PSGL, and
SEPR. In some embodiments a biomarker panel comprises 6 or more
proteins, wherein 6 of the proteins comprises AACT, CO3, CO9, MIF,
PSGL, and SEPR. In some embodiments a biomarker panel comprises 6
or more proteins, wherein 6 of the proteins comprises CATD, CEA,
CO3, CO9, MIF, and PSGL. In some embodiments a biomarker panel
comprises 6 or more proteins, wherein 6 of the proteins comprises
CATD, CEA, CO3, CO9, MIF, and SEPR. In some embodiments a biomarker
panel comprises 6 or more proteins, wherein 6 of the proteins
comprises CATD, CEA, CO3, CO9, PSGL, and SEPR. In some embodiments
a biomarker panel comprises 6 or more proteins, wherein 6 of the
proteins comprises CATD, CEA, CO3, MIF, PSGL, and SEPR. In some
embodiments a biomarker panel comprises 6 or more proteins, wherein
6 of the proteins comprises CATD, CEA, CO9, MIF, PSGL, and SEPR. In
some embodiments a biomarker panel comprises 6 or more proteins,
wherein 6 of the proteins comprises CATD, CO3, CO9, MIF, PSGL, and
SEPR. In some embodiments a biomarker panel comprises 6 or more
proteins, wherein 6 of the proteins comprises CEA, CO3, CO9, MIF,
PSGL, and SEPR.
[0116] In some embodiments a biomarker panel comprises 5 or more
proteins, wherein 5 of the proteins comprises AACT, CATD, CEA, CO3,
and CO9. In some embodiments a biomarker panel comprises 5 or more
proteins, wherein 5 of the proteins comprises AACT, CATD, CEA, CO3,
and MIF. In some embodiments a biomarker panel comprises 5 or more
proteins, wherein 5 of the proteins comprises AACT, CATD, CEA, CO3,
and PSGL. In some embodiments a biomarker panel comprises 5 or more
proteins, wherein 5 of the proteins comprises AACT, CATD, CEA, CO3,
and SEPR. In some embodiments a biomarker panel comprises 5 or more
proteins, wherein 5 of the proteins comprises AACT, CATD, CEA, CO9,
and MIF. In some embodiments a biomarker panel comprises 5 or more
proteins, wherein 5 of the proteins comprises AACT, CATD, CEA, CO9,
and PSGL. In some embodiments a biomarker panel comprises 5 or more
proteins, wherein 5 of the proteins comprises AACT, CATD, CEA, CO9,
and SEPR. In some embodiments a biomarker panel comprises 5 or more
proteins, wherein 5 of the proteins comprises AACT, CATD, CEA, MIF,
and PSGL. In some embodiments a biomarker panel comprises 5 or more
proteins, wherein 5 of the proteins comprises AACT, CATD, CEA, MIF,
and SEPR. In some embodiments a biomarker panel comprises 5 or more
proteins, wherein 5 of the proteins comprises AACT, CATD, CEA,
PSGL, and SEPR. In some embodiments a biomarker panel comprises 5
or more proteins, wherein 5 of the proteins comprises AACT, CATD,
CO3, CO9, and MIF. In some embodiments a biomarker panel comprises
5 or more proteins, wherein 5 of the proteins comprises AACT, CATD,
CO3, CO9, and PSGL. In some embodiments a biomarker panel comprises
5 or more proteins, wherein 5 of the proteins comprises AACT, CATD,
CO3, CO9, and SEPR. In some embodiments a biomarker panel comprises
5 or more proteins, wherein 5 of the proteins comprises AACT, CATD,
CO3, MIF, and PSGL. In some embodiments a biomarker panel comprises
5 or more proteins, wherein 5 of the proteins comprises AACT, CATD,
CO3, MIF, and SEPR. In some embodiments a biomarker panel comprises
5 or more proteins, wherein 5 of the proteins comprises AACT, CATD,
CO3, PSGL, and SEPR. In some embodiments a biomarker panel
comprises 5 or more proteins, wherein 5 of the proteins comprises
AACT, CATD, CO9, MIF, and PSGL. In some embodiments a biomarker
panel comprises 5 or more proteins, wherein 5 of the proteins
comprises AACT, CATD, CO9, MIF, and SEPR. In some embodiments a
biomarker panel comprises 5 or more proteins, wherein 5 of the
proteins comprises AACT, CATD, CO9, PSGL, and SEPR. In some
embodiments a biomarker panel comprises 5 or more proteins, wherein
5 of the proteins comprises AACT, CATD, MIF, PSGL, and SEPR. In
some embodiments a biomarker panel comprises 5 or more proteins,
wherein 5 of the proteins comprises AACT, CEA, CO3, CO9, and MIF.
In some embodiments a biomarker panel comprises 5 or more proteins,
wherein 5 of the proteins comprises AACT, CEA, CO3, CO9, and PSGL.
In some embodiments a biomarker panel comprises 5 or more proteins,
wherein 5 of the proteins comprises AACT, CEA, CO3, CO9, and SEPR.
In some embodiments a biomarker panel comprises 5 or more proteins,
wherein 5 of the proteins comprises AACT, CEA, CO3, MIF, and PSGL.
In some embodiments a biomarker panel comprises 5 or more proteins,
wherein 5 of the proteins comprises AACT, CEA, CO3, MIF, and SEPR.
In some embodiments a biomarker panel comprises 5 or more proteins,
wherein 5 of the proteins comprises AACT, CEA, CO3, PSGL, and SEPR.
In some embodiments a biomarker panel comprises 5 or more proteins,
wherein 5 of the proteins comprises AACT, CEA, CO9, MIF, and PSGL.
In some embodiments a biomarker panel comprises 5 or more proteins,
wherein 5 of the proteins comprises AACT, CEA, CO9, MIF, and SEPR.
In some embodiments a biomarker panel comprises 5 or more proteins,
wherein 5 of the proteins comprises AACT, CEA, CO9, PSGL, and SEPR.
In some embodiments a biomarker panel comprises 5 or more proteins,
wherein 5 of the proteins comprises AACT, CEA, MIF, PSGL, and SEPR.
In some embodiments a biomarker panel comprises 5 or more proteins,
wherein 5 of the proteins comprises AACT, CO3, CO9, MIF, and PSGL.
In some embodiments a biomarker panel comprises 5 or more proteins,
wherein 5 of the proteins comprises AACT, CO3, CO9, MIF, and SEPR.
In some embodiments a biomarker panel comprises 5 or more proteins,
wherein 5 of the proteins comprises AACT, CO3, CO9, PSGL, and SEPR.
In some embodiments a biomarker panel comprises 5 or more proteins,
wherein 5 of the proteins comprises AACT, CO3, MIF, PSGL, and SEPR.
In some embodiments a biomarker panel comprises 5 or more proteins,
wherein 5 of the proteins comprises AACT, CO9, MIF, PSGL, and SEPR.
In some embodiments a biomarker panel comprises 5 or more proteins,
wherein 5 of the proteins comprises CATD, CEA, CO3, CO9, and MIF.
In some embodiments a biomarker panel comprises 5 or more proteins,
wherein 5 of the proteins comprises CATD, CEA, CO3, CO9, and PSGL.
In some embodiments a biomarker panel comprises 5 or more proteins,
wherein 5 of the proteins comprises CATD, CEA, CO3, CO9, and SEPR.
In some embodiments a biomarker panel comprises 5 or more proteins,
wherein 5 of the proteins comprises CATD, CEA, CO3, MIF, and PSGL.
In some embodiments a biomarker panel comprises 5 or more proteins,
wherein 5 of the proteins comprises CATD, CEA, CO3, MIF, and SEPR.
In some embodiments a biomarker panel comprises 5 or more proteins,
wherein 5 of the proteins comprises CATD, CEA, CO3, PSGL, and SEPR.
In some embodiments a biomarker panel comprises 5 or more proteins,
wherein 5 of the proteins comprises CATD, CEA, CO9, MIF, and PSGL.
In some embodiments a biomarker panel comprises 5 or more proteins,
wherein 5 of the proteins comprises CATD, CEA, CO9, MIF, and SEPR.
In some embodiments a biomarker panel comprises 5 or more proteins,
wherein 5 of the proteins comprises CATD, CEA, CO9, PSGL, and SEPR.
In some embodiments a biomarker panel comprises 5 or more proteins,
wherein 5 of the proteins comprises CATD, CEA, MIF, PSGL, and SEPR.
In some embodiments a biomarker panel comprises 5 or more proteins,
wherein 5 of the proteins comprises CATD, CO3, CO9, MIF, and PSGL.
In some embodiments a biomarker panel comprises 5 or more proteins,
wherein 5 of the proteins comprises CATD, CO3, CO9, MIF, and SEPR.
In some embodiments a biomarker panel comprises 5 or more proteins,
wherein 5 of the proteins comprises CATD, CO3, CO9, PSGL, and SEPR.
In some embodiments a biomarker panel comprises 5 or more proteins,
wherein 5 of the proteins comprises CATD, CO3, MIF, PSGL, and SEPR.
In some embodiments a biomarker panel comprises 5 or more proteins,
wherein 5 of the proteins comprises CATD, CO9, MIF, PSGL, and SEPR.
In some embodiments a biomarker panel comprises 5 or more proteins,
wherein 5 of the proteins comprises CEA, CO3, CO9, MIF, and PSGL.
In some embodiments a biomarker panel comprises 5 or more proteins,
wherein 5 of the proteins comprises CEA, CO3, CO9, MIF, and SEPR.
In some embodiments a biomarker panel comprises 5 or more proteins,
wherein 5 of the proteins comprises CEA, CO3, CO9, PSGL, and SEPR.
In some embodiments a biomarker panel comprises 5 or more proteins,
wherein 5 of the proteins comprises CEA, CO3, MIF, PSGL, and SEPR.
In some embodiments a biomarker panel comprises 5 or more proteins,
wherein 5 of the proteins comprises CEA, CO9, MIF, PSGL, and SEPR.
In some embodiments a biomarker panel comprises 5 or more proteins,
wherein 5 of the proteins comprises CO3, CO9, MIF, PSGL, and
SEPR.
[0117] In some embodiments a biomarker panel comprises 4 or more
proteins, wherein 4 of the proteins comprises: AACT, CATD, CEA,
CO3; AACT, CATD, CEA, CO9; AACT, CATD, CEA, MIF; AACT, CATD, CEA,
PSGL; AACT, CATD, CEA, SEPR; AACT, CATD, CO3, CO9; AACT, CATD, CO3,
MIF; AACT, CATD, CO3, PSGL; AACT, CATD, CO3, SEPR; AACT, CATD, CO9,
MIF; AACT, CATD, CO9, PSGL; AACT, CATD, CO9, SEPR; AACT, CATD, MIF,
PSGL; AACT, CATD, MIF, SEPR; AACT, CATD, PSGL, SEPR; AACT, CEA,
CO3, CO9; AACT, CEA, CO3, MIF; AACT, CEA, CO3, PSGL; AACT, CEA,
CO3, SEPR; AACT, CEA, CO9, MIF; AACT, CEA, CO9, PSGL; AACT, CEA,
CO9, SEPR; AACT, CEA, MIF, PSGL; AACT, CEA, MIF, SEPR; AACT, CEA,
PSGL, SEPR; AACT, CO3, CO9, MIF; AACT, CO3, CO9, PSGL; AACT, CO3,
CO9, SEPR; AACT, CO3, MIF, PSGL; AACT, CO3, MIF, SEPR; AACT, CO3,
PSGL, SEPR; AACT, CO9, MIF, PSGL; AACT, CO9, MIF, SEPR; AACT, CO9,
PSGL, SEPR; AACT, MIF, PSGL, SEPR; CATD, CEA, CO3, CO9; CATD, CEA,
CO3, MIF; CATD, CEA, CO3, PSGL; CATD, CEA, CO3, SEPR; CATD, CEA,
CO9, MIF; CATD, CEA, CO9, PSGL; CATD, CEA, CO9, SEPR; CATD, CEA,
MIF, PSGL; CATD, CEA, MIF, SEPR; CATD, CEA, PSGL, SEPR; CATD, CO3,
CO9, MIF; CATD, CO3, CO9, PSGL; CATD, CO3, CO9, SEPR; CATD, CO3,
MIF, PSGL; CATD, CO3, MIF, SEPR; CATD, CO3, PSGL, SEPR; CATD, CO9,
MIF, PSGL; CATD, CO9, MIF, SEPR; CATD, CO9, PSGL, SEPR; CATD, MIF,
PSGL, SEPR; CEA, CO3, CO9, MIF; CEA, CO3, CO9, PSGL; CEA, CO3, CO9,
SEPR; CEA, CO3, MIF, PSGL; CEA, CO3, MIF, SEPR; CEA, CO3, PSGL,
SEPR; CEA, CO9, MIF, PSGL; CEA, CO9, MIF, SEPR; CEA, CO9, PSGL,
SEPR; CEA, MIF, PSGL, SEPR; CO3, CO9, MIF, PSGL; CO3, CO9, MIF,
SEPR; CO3, CO9, PSGL, SEPR; CO3, MIF, PSGL, SEPR; CO9, MIF, PSGL,
SEPR.
[0118] In some embodiments a bio-marker panel comprises 3 or more
proteins, wherein 3 of the proteins comprises: AACT, CATD, CEA;
AACT, CATD, CO3; AACT, CATD, CO9; AACT, CATD, MIF; AACT, CATD,
PSGL; AACT, CATD, SEPR; AACT, CEA, CO3; AACT, CEA, CO9; AACT, CEA,
MIF; AACT, CEA, PSGL; AACT, CEA, SEPR; AACT, CO3, CO9; AACT, CO3,
MIF; AACT, CO3, PSGL; AACT, CO3, SEPR; AACT, CO9, MIF; AACT, CO9,
PSGL; AACT, CO9, SEPR; AACT, MIF, PSGL; AACT, MIF, SEPR; AACT,
PSGL, SEPR; CATD, CEA, CO3; CATD, CEA, CO9; CATD, CEA, MIF; CATD,
CEA, PSGL; CATD, CEA, SEPR; CATD, CO3, CO9; CATD, CO3, MIF; CATD,
CO3, PSGL; CATD, CO3, SEPR; CATD, CO9, MIF; CATD, CO9, PSGL; CATD,
CO9, SEPR; CATD, MIF, PSGL; CATD, MIF, SEPR; CATD, PSGL, SEPR; CEA,
CO3, CO9; CEA, CO3, MIF; CEA, CO3, PSGL; CEA, CO3, SEPR; CEA, CO9,
MIF; CEA, CO9, PSGL; CEA, CO9, SEPR; CEA, MIF, PSGL; CEA, MIF,
SEPR; CEA, PSGL, SEPR; CO3, CO9, MIF; CO3, CO9, PSGL; CO3, CO9,
SEPR; CO3, MIF, PSGL; CO3, MIF, SEPR; CO3, PSGL, SEPR; CO9, MIF,
PSGL; CO9, MIF, SEPR; CO9, PSGL, SEPR; MIF, PSGL, SEPR.
[0119] In some embodiments a bio-marker panel comprises 2 or more
proteins, wherein 2 of the proteins comprises: AACT, CATD; AACT,
CEA; AACT, CO3; AACT, CO9; AACT, MIF; AACT, PSGL; AACT, SEPR; CATD,
CEA; CATD, CO3; CATD, CO9; CATD, MIF; CATD, PSGL; CATD, SEPR; CEA,
CO3; CEA, CO9; CEA, MIF; CEA, PSGL; CEA, SEPR; CO3, CO9; CO3, MIF;
CO3, PSGL; CO3, SEPR; CO9, MIF; CO9, PSGL; CO9, SEPR; MIF, PSGL;
MIF, SEPR; PSGL, SEPR.
[0120] The biomarker panels of Table 3 correspond to a number of
embodiments of the lead panel, as recited below. Similar variants
of other lead panels in the disclosure are contemplated and
apparent to one of skill in the art such that they do not warrant
redundant recitation.
[0121] In some embodiments, a diagnostic method provided herein
comprises measuring in the biological sample a biomarker panel
comprising at least 7, at least 6, at least 5, at least 4, at least
3, or at least 2 of: A1AG1, A1AT, CATD, CEA, CO9, OSTP, and SEPR.
In some embodiments, a diagnostic method provided herein comprises
measuring in the biological sample a biomarker panel comprising at
least 17, at least 16, at least 15, at least 14, at least 13, at
least 12, at least 11, at least 10, at least 9, at least 8, at
least 7, at least 6, at least 5, at least 4, at least 3, or at
least 2 of: A1AG1, A1AT, APOA1, CATD, CEA, CLUS, CO3, CO9, FGB,
FIBG, GARS, GELS, MIF, PRDX1, PSGL, SBP1, and SEPR. In some
embodiments, a diagnostic method provided herein comprises
measuring in the biological sample a biomarker panel consisting at
least 7, at least 6, at least 5, at least 4, at least 3, or at
least 2 of: A1AG1, A1AT, CATD, CEA, CO9, GARS, and SEPR. In some
embodiments, a diagnostic method provided herein comprises
measuring in the biological sample a biomarker panel comprising at
least 13, at least 12, at least 11, at least 10, at least 9, at
least 8, at least 7, at least 6, at least 5, at least 4, at least
3, or at least 2 of: A1AG1, A1AT, AACT, CATD, CEA, CO9, CRP, GARS,
GELS, S10A8, S10A9, SAA1, and SEPR. In some embodiments, a
diagnostic method provided herein comprises measuring in the
biological sample a biomarker panel comprising at least 8, at least
7, at least 6, at least 5, at least 4, at least 3, or at least 2
of: CATD, CEA, CO3, CO9, GARS, GELS, SEPR, and TFRC. In some
embodiments, a diagnostic method provided herein comprises
measuring in the biological sample a biomarker panel comprising at
least 5, at least 4, at least 3, or at least 2 of: CATD, CEA, AACT,
CO9, and SEPR. In some embodiments, a diagnostic method provided
herein comprises measuring in the biological sample a biomarker
panel comprising at least 6, at least 5, at least 4, at least 3, or
at least 2 of: A1AT, CATD, CEA, GARS, GELS, and SEPR. In some
embodiments, a diagnostic method provided herein comprises
measuring in the biological sample a biomarker panel comprising at
least 18, of at least 17, at least 16, at least 15, at least 14, at
least 13, at least 12, at least 11, at least 10, at least 9, at
least 8, at least 7, at least 6, at least 5, at least 4, at least
3, or at least 2 of: A1AG1, A1AT, APOA1, CATD, CEA, CLUS, CO3, CO9,
FGB, FIBG, GARS, GELS, HPT, MIF, PRDX1, PSGL, SBP1, and SEPR. In
some embodiments, a diagnostic method provided herein comprises
measuring in the biological sample a biomarker panel comprising at
least 8, at least 7, at least 6, at least 5, at least 4, at least
3, or at least 2 of: A1AG1, A1AT, CATD, CEA, CO9, FIBG, GELS, and
SEPR. In some embodiments, a diagnostic method provided herein
comprises measuring in the biological sample a biomarker panel
comprising at least 3, or at least 2 of: CATD, CEA, and SEPR. In
some embodiments, a diagnostic method provided herein comprises
measuring in the biological sample a biomarker panel consisting at
least 8, at least 7, at least 6, at least 5, at least 4, at least
3, or at least 2 of: CATD, CEA, CO3, CO9, MIF, PSGL, SEPR, and
TFRC. In some embodiments, a diagnostic method provided herein
comprises measuring in the biological sample a biomarker panel
consisting at least 7, at least 6, at least 5, at least 4, at least
3, or at least 2 of: A1AG1, CATD, CEA, CO3, CO9, GELS, and SEPR.
Furthermore, the group of biomarkers in this example can in some
cases additionally comprise polypeptides with the characteristics
found in Table 1.
[0122] In some embodiments, a biomarker panel comprises at least 3
or at least 2 of CATD, CLAUS, GDF15, and SAA1. In some embodiments
a panel comprising CATD, CLAUS, GDF15, and SAA1 is designated for
advanced adenoma detection. In some embodiments, a diagnostic
method provided herein comprises measuring in the biological sample
a biomarker panel comprising A1AG1, A1AT, APOA1, CATD, CEA, CLUS,
CO3, CO9, FGB, FIBG, GARS, GELS, MIF, PRDX1, PSGL, SBP1, and
SEPR.
Biomarker Panel Assessment
[0123] Some methods described herein comprise comparing the amount
of each of the at least two biomarkers in the biological sample to
a reference amount of each of the at least two biomarkers. Some
methods herein comprise comparing the profile of the biomarker
panel in a subject to a reference profile of the biomarker panel.
The reference amount is in some cases an amount of the biomarker in
a control subject. The reference profile of the biomarker panel is
in some cases a biomarker profile of a control subject. The control
subject is in some cases a subject having a known diagnosis. For
example, the control subject can be a negative control subject. The
negative control subject can be a subject that does not have
advanced colorectal adenoma. The negative control subject can be a
subject that does not have CRC. The negative control subject can be
a subject that does not have a colon polyp. For other example, the
control subject can be a positive control subject. The positive
control subject can be a subject having a confirmed diagnosis of
advanced colorectal adenoma. The positive control subject can be a
subject having a confirmed diagnosis of CRC. The positive control
subject can be a subject having a confirmed diagnosis of any stage
of CRC (for example, Stage 0, Stage I, Stage II, Stage IIA, Stage
IIB, Stage IIC, Stage III, Stage IIIA, Stage IIIB, Stage IIIC,
Stage IV, Stage IVA, or Stage IVB). The reference amount can be a
predetermined level of the biomarker, wherein the predetermined
level is set based upon a measured amount of the biomarker in a
control subject.
[0124] Some reference biomarker panel levels comprises average
values for a number of individuals having a common condition
status, such as 10 individuals free of CRC or AA, or 10 individuals
of a known stage of CRC or a known AA status. Alternately, in some
cases references comprise a set of protein accumulation levels, and
age in some embodiments, that correspond to a set of individuals of
known CRC or AA status. In these cases, levels are not averaged;
rather, a patient's levels are compared to each set of accumulation
levels of each standard or reference individual in the set, and a
determination is made if the patient's accumulation levels do not
differ significantly from those of at least one reference set. In
some cases the reference set comprises individuals of known
cancer-free status, while in some cases the reference set comprises
individuals of known CRC or AA stage status, such as Stage 0, Stage
I, Stage II, Stage 11A, Stage IIB, Stage TIC, Stage III, Stage
111A, Stage IIIB, Stage IIIC, Stage IV, Stage IVA, or Stage IVB. In
some cases a patient is categorized as having a condition if the
patient's panel accumulation levels match or do not differ
significantly from those of a reference. In some cases a patient is
categorized as not having a condition if a patient's panel
accumulation levels differ significantly from those of a
reference.
[0125] In some cases, comparing comprises determining a difference
between an amount of the biomarker in the biological sample
obtained from the subject and the reference amount of the
biomarker. The method comprises, in some cases, detecting a
presence or absence of at least one of advanced colorectal adenoma
and CRC based upon a deviation (for example, measured difference)
of the amount of at least one of the measured biomarkers in the
biological sample obtained from the subject as compared to a
reference amount of the at least one measured biomarkers. In some
cases, the method comprises detecting a presence of at least one of
advanced colorectal adenoma and CRC if the deviation of the amount
of the at least one measured biomarker from the biological sample
obtained from the subject as compared to a positive reference value
(for example, an amount of the measured biomarker from a positive
control subject) is low. In other cases, the method comprises
detecting a presence of at least one of advanced colorectal adenoma
and CRC if the deviation of the amount of the at least one measured
biomarker from the biological sample obtained from the subject as
compared to a negative reference value (for example, measured from
a negative control subject) is high. In some cases, the method
comprises detecting an absence of at least one of advanced
colorectal adenoma and CRC if the deviation of the amount of the at
least one measured biomarker from the biological sample obtained
from the subject as compared to a positive reference value (for
example, measured from a positive control subject) is high. In some
examples, the method comprises detecting an absence of at least one
of advanced colorectal adenoma and CRC if the deviation of the
amount of the at least one measured biomarker from the biological
sample obtained from the subject as compared to a negative
reference value (for example, measured from a negative control
subject) is low. In some cases, detection of a presence or absence
of at least one of advanced colorectal adenoma and CRC can be based
upon a clinical outcome score produced by an algorithm described
herein. In some cases, the method comprises detection of a presence
or absence of colorectal cancer based upon a classifier that
divides a feature space into feature values that are predictive of
the presence of colorectal cancer and feature values that are
predictive of the absence of colorectal cancer. In some cases, the
method comprises classifying a subject's colorectal cancer status
as "undetermined" (e.g., "no call") in order to reduce false
positives and/or false negatives. In some cases, patients with an
undetermined colorectal cancer status are retested at a later
point. The algorithm can be used for assessing the deviation
between an amount of a measured biomarker in the biological sample
obtained from the subject and a reference amount of the
biomarker.
[0126] In some cases, a classifier is used to determine the
colorectal cancer status of a subject. For example, given N
measurements as inputs into the classifier (e.g., the biomarkers
comprising proteins and the age of the subject), the subject can be
represented as a point in an N-dimensional space wherein each axis
is a measurement. In some cases, the classifier defines an
N-1)-dimensional shape that divides the N-dimensional space into
two or more categories. In some cases, the two categories are a
subject with cancer and a subject without cancer. In some cases
there are three categories. In some cases the categories are a
subject with cancer, a subject without cancer, and a no-cal 1
region where the cancer status of the subject cannot be reliably
determined. In some cases, the classifier allows `shifting` cutoffs
for particular proteins. For example, consider a classifier defined
by the boundary y=1/x, where x and y are both greater than zero,
and each of the two axes is the accumulation level of a protein
indicative of cancer status. In such a case, all the subjects whose
protein accumulation levels fall beneath the boundary (e.g., [0,
0], [2, 0.3], etc. . . . ) are classified as not having the
condition, whereas any subject whose protein accumulation levels
lie above the boundary are classified as having the condition. If
the x-axis protein has a value of 1, then in this example the
y-axis protein must be more than one to result in a cancer
diagnosis. However, if the x-axis protein has a value of 10, then
the y-axis protein need only have a value more than 0.1 to result
in a cancer diagnosis. This example can be extrapolated to an
N-dimensional shape using an (N-1)-dimensional shape as the
classifier.
[0127] The intrinsic performance of a particular classification
model depends on the distributions and separation of model scores
for the two classes. With the rare exception of perfect class
separation, most classification models make mistakes because of
class overlap across the range of classifier scores. For example,
such an overlap may occur near the middle of the score range where
the probability of being in one class or the other is close to
50%.
[0128] Within such an overlap region, it is sometimes advantageous
to add a third class to the final set of classification calls. The
third class optionally indicates the uncertainty of a call in this
score region. This is implemented, for example, by defining an
indeterminate region of classification scores. Samples with scores
in this region are given an "indeterminate" or "no call" test
result. Samples with scores above or below this region would be
given standard positive or negative test results depending on their
positions relative to the test cutoff. In some cases, the "no call"
rate, or the frequency with which samples fall into the "no call"
region, is about 1%, about 2%, about 3%, about 4%, about 5%, about
10%, about 15%, or about 20%. In particular, the "no call" rate can
be about 10%. The benefit of adding an indeterminate region to a
classification model is that classification performance can improve
for samples outside of the indeterminate region, i.e. mistakes are
less likely for the remaining positive and negative tests. However,
if the indeterminate range is too large, there may be too many
indeterminate results, and the value of the test may be put into
question.
Classifier Construction
[0129] Reference classifiers are readily constructed by one of
skill in the art using any number of available technologies.
Reference classifiers are, for example, generated by assaying panel
levels for a plurality of samples, such as blood sample, obtained
from individuals of known colorectal health status. As many as 1000
samples or more, comprising samples obtained from individuals known
or later confirmed to have colorectal cancer or known or later
confirmed not to have colorectal cancer, as assayed as to their
biomarker panel levels. Age, a non-protein biomarker constituent of
some panels, is also recorded for each individual at the time of
sample collection.
[0130] In some cases, the biomarker panel levels for each sample
are used individually as a reference panel level for comparison so
as to classify an individual's biomarker panel level as indicative
of a healthy colorectal health status or a colorectal health issue
warranting further investigation. A panel level to be classified is
compared to the positive and the negative biomarker panel levels,
and the outcome as judged by, for example, the number samples of
each category from which the testing individual's panel level does
not differ significantly.
[0131] Alternately, a classifier is assembled from the collection
of biomarker panel levels. Classifier assembly is well known to
those of skill in the art. Machine learning models, in particular,
are useful in assembling a classifier from a set of panel levels
obtained from samples of known colorectal health status. Machine
learning models are readily constructed, for example, using any
number of statistical programming programming languages such as R,
scripting languages such as Python and associated machine learning
packages, data mining software such as Weka or Java, Mathematica,
Matlab or SAS.
Implementation of Classifiers in Colorectal Health Assessment
[0132] In practicing any of the methods described herein, comparing
optionally comprises determining a difference between a biomarker
profile of a subject to a reference biomarker profile. The method
can, for example, comprise detecting a presence or absence of at
least one of advanced colorectal adenoma and CRC based upon a
deviation (for example, measured difference) of the biomarker
profile of the subject as compared to a reference biomarker
profile. For example, some methods comprise detecting a presence of
at least one of advanced colorectal adenoma and CRC if the
deviation of the biomarker profile of the subject as compared to a
positive reference biomarker profile (for example, a biomarker
profile based upon measurements of panel biomarkers from a positive
control subject) is low. As an additional example, some methods
comprise detecting a presence of at least one of advanced
colorectal adenoma and CRC if the deviation of the biomarker
profile of the subject as compared to a negative reference
biomarker profile (for example, a biomarker profile based upon
measurements of panel biomarkers from a negative control subject)
is high. In some cases, the method comprises detecting an absence
of at least one of advanced colorectal adenoma and CRC if the
deviation of the biomarker profile of the subject as compared to a
positive reference biomarker profile is high. In some examples, the
method comprises detecting an absence of at least one of advanced
colorectal adenoma and CRC if the deviation of the biomarker
profile of the subject as compared to a negative reference
biomarker profile is low. In some cases, detection of a presence or
absence of at least one of advanced colorectal adenoma and CRC can
be based upon a clinical outcome score produced by an algorithm
described herein. The algorithm can be used for assessing the
deviation between the biomarker profile of the subject to a
reference biomarker profile.
[0133] Some methods comprise detecting a presence or absence of an
advanced colorectal adenoma in the subject in some cases. The
advanced colorectal adenoma can be a colorectal advanced colorectal
adenoma. The methods described herein are be used to detect a
presence or absence of an advanced colorectal adenoma of any size,
such as an advanced adenoma having a dimension that is greater than
1 cm. The methods described herein are used to detect a presence or
absence of an advanced colorectal adenoma of villous, serrated,
sessile or non-pedunculated character.
[0134] In some cases, a diagnostic method provided herein comprises
measuring a biomarker panel comprising at least five biomarkers in
the biological sample, wherein the at least three biomarkers
comprise AACT, CATD, CEA, CO3, CO9, MIF, PSGL, and SEPR. In some
cases, the method comprises providing a positive diagnosis of
advanced colorectal adenoma if a deviation in the panel level of a
panel comprising AACT, CATD, CEA, CO3, CO9, MIF, PSGL, and SEPR in
the biological sample obtained from the subject as compared to a
positive reference value is low. In some cases, the method
comprises providing a positive diagnosis of advanced colorectal
adenoma if a deviation in the panel level of a panel comprising
AACT, CATD, CEA, CO3, CO9, MIF, PSGL, and SEPR in the biological
sample obtained from the subject as compared to a negative
reference value is high. In some cases, the method comprises
providing a positive diagnosis of advanced colorectal adenoma if a
deviation in the panel level of a panel comprising AACT, CATD, CEA,
CO3, CO9, MIF, PSGL, and SEPR in the biological sample obtained
from the subject as compared to a positive reference value is high.
In some cases, the method comprises providing a positive diagnosis
of advanced colorectal adenoma if a deviation in the panel level of
a panel comprising AACT, CATD, CEA, CO3, CO9, MIF, PSGL, and SEPR
in the biological sample obtained from the subject as compared to a
negative reference value is low.
[0135] Methods, compositions, kits and systems disclosed herein
detect advanced colorectal adenoma with a sensitivity greater than
70%, greater than 75%, greater than 80%, greater than 85%, greater
than 90%, greater than 95%, greater than 96%, greater than 97%,
greater than 98%, greater than 99%, or about 100%. Such diagnostic
method detects advanced colorectal adenoma with a sensitivity that
is between about 50%-100%, between about 60%-100%, between about
70%-100%, between about 80%-100%, or between about 90-100%. Such
diagnostic methods detect advanced colorectal adenoma with a
sensitivity of at least 70%, of at least 75%, of at least 80%, of
at least 85%, of at least 90%, of at least 95%, of at least 96%, of
at least 97%, of at least 98%, of at least 99%, or about 100%. Such
diagnostic methods detect advanced colorectal adenoma with a
specificity that is between about 50%-100%, between about 60%-100%,
between about 70%-100%, between about 80%-100%, or between about
90-100%. In particular cases, such diagnostic method detects
advanced colorectal adenoma with a sensitivity and a specificity
that is 50% or greater, 60% or greater, 70% or greater, 75% or
greater, 80% or greater, 85% or greater, 90% or greater. In
particular cases, such diagnostic detects advanced colorectal
adenoma with a sensitivity and a specificity that is between about
50%-100%, between about 60%-100%, between about 70%-100%, between
about 80%-100%, or between about 90-100%.
[0136] In some cases, a panel comprises a ratio of a level of a
first biomarker to a level of a second biomarker. Accordingly, in
some cases, a diagnostic method provided herein comprises
determining a ratio of a level of the first biomarker to a level of
the second biomarker in the biological sample obtained from the
subject. In some cases, the method comprises providing a positive
diagnosis of CRC if a deviation in the ratio of the first biomarker
to the second biomarker in the biological sample obtained from the
subject as compared to a positive reference value is low. In some
cases, the method comprises providing a positive diagnosis of CRC
if a deviation in the ratio of the first biomarker to the second
biomarker in the biological sample obtained from the subject as
compared to a negative reference value is high. In some cases, the
method comprises providing a positive diagnosis of if a deviation
in the ratio of the first biomarker to the second biomarker in the
biological sample obtained from the subject as compared to a
positive reference value is high. In some cases, the method
comprises providing a positive diagnosis of CRC if a deviation in
the ratio of the first biomarker to the second biomarker in the
biological sample obtained from the subject as compared to a
negative reference value is low.
[0137] Diagnostic methods described herein for detection of CRC in
a subject detects CRC with a sensitivity greater than 75%, greater
than 80%, greater than 85%, greater than 90%, greater than 95%,
greater than 96%, greater than 97%, greater than 98%, greater than
99%, or about 100%. Such diagnostic methods detect CRC with a
sensitivity that is between about 70%-100%, between about 80%-100%,
or between about 90-100%. Such diagnostic methods detect CRC with a
specificity greater than 70%, greater than 75%, greater than 80%,
greater than 85%, greater than 90%, greater than 95%, greater than
96%, greater than 97%, greater than 98%, greater than 99%, or about
100%. Such diagnostic methods detect CRC with a specificity that is
between about 50%-100%, between about 60%-100%, between about
70%-100%, between about 80%-100%, or between about 90-100%. In
particular embodiments, such diagnostic methods detect CRC with a
sensitivity and a specificity that is 50% or greater, 60% or
greater, 70% or greater, 75% or greater, 80% or greater, 85% or
greater, 90% or greater. In particular embodiments, such diagnostic
methods detect CRC with a sensitivity and a specificity that is
between about 50%-100%, between about 60%-100%, between about
70%-100%, between about 80%-100%, or between about 90-100%.
[0138] The overall performance of a classifier is assessed in some
cases via the AUC of the ROC as reported herein. An ROC considers
the performance of the classifier at all possible model score
cutoff points. However, when a classification decision needs to be
made (e.g., is this patient sick or healthy?), a cutoff point is
used to define the two groups. Classification scores at or above
the cutoff point are assessed as positive (or sick) while points
below are assessed as negative (or healthy) in various
embodiments.
[0139] For some classification models disclosed herein, a
classification score cutoff point is established by selecting the
point of maximum accuracy on the validation ROC. The point of
maximum accuracy on an ROC is the cutoff point or points for which
the total number of correct classification calls is maximized.
Here, the positive and negative classification calls are weighted
equally. In cases where multiple maximum accuracy points are
present on a given ROC, the point with the associated maximum
sensitivity is selected in some cases.
[0140] Algorithm-Based Methods
[0141] Methods, compositions, kits, and systems described herein
utilize an algorithm-based diagnostic assay for predicting a
presence or absence of at least one of: advanced colorectal adenoma
and CRC in a subject. Expression level of one or more protein
biomarker, and optionally one or more subject characteristics, such
as, for example, age, weight, gender, medical history, risk
factors, or family history are used alone or arranged into
functional subsets to calculate a quantitative score that is used
to predict the likelihood of a presence or absence of at least one
of advanced colorectal adenoma and CRC. Although lead embodiments
herein focus upon biomarker panels that are predominantly protein
or polypeptide panels, the measurements of any of the biomarker
panels may comprise protein and non-protein components such as RNA,
DNA, organic metabolites, or inorganic molecules or metabolites
(e.g. iron, magnesium, selenium, calcium, or others).
[0142] The algorithm-based assay and associated information
provided by the practice of any of the methods described herein can
facilitate optimal treatment decision-making in subjects. For
example, such a clinical tool can enable a physician or caretaker
to identify patients who have a low likelihood of having an
advanced colorectal adenoma or carcinoma and therefore would not
need treatment, or increased monitoring for advanced colorectal
adenoma or CRC, or who have a high likelihood of having an advanced
colorectal adenoma or CRC and therefore would need treatment or
increased monitoring of said advanced colorectal adenoma or
CRC.
[0143] A quantitative score is determined by the application of a
specific algorithm in some cases. The algorithm used to calculate
the quantitative score in the methods disclosed herein may group
the expression level values of a biomarker or groups of biomarkers.
The formation of a particular group of biomarkers, in addition, can
facilitate the mathematical weighting of the contribution of
various expression levels of biomarker or biomarker subsets (for
example classifier) to the quantitative score. Described herein are
exemplary algorithms for calculating the quantitative scores.
[0144] Exemplary biomarkers and, when applicable their human amino
acid sequences, are listed in Tables 1 and 3. Biomarkers may
comprise full length molecules of the polypeptide sequences of
Table 3, as well as uniquely identifiable fragments of the
polypeptide sequences of Table 1. Markers can be but do not need to
be full length to be informative. In many cases, so long as a
fragment is uniquely identifiable as being derived from or
representing a polypeptide of Table 3, it is informative for
purposes herein.
[0145] Exemplary Subjects
[0146] Biological samples are collected from a number of eligible
subjects, such as subjects who want to determine their likelihood
of having at least one of advanced colorectal adenoma and CRC. The
subject is in some cases healthy and asymptomatic. The subject's
age is not constrained. For example, the subject is between the
ages of 0 to about 30 years, about 20 to about 50 years, or about
40 or older. In various cases, the subject is healthy, asymptomatic
and between the ages of 0-30 years, 20-50 years, or 40 or older.
The subject is at least 30 years of age, at least 40 years of age,
or at least 50 years of age. The subject is less than 50 years of
age, less than 40 years of age, or less than 30 years of age. In
various examples, the subject is healthy and asymptomatic. In
various examples, the subject has no family history of at least one
of: CRC, adenoma, and polyps. In various examples, the subject has
not had a colonoscopy, sigmoidoscopy, or colon tissue biopsy. In
various examples, the subject is healthy and asymptomatic and has
not received a colonoscopy, sigmoidoscopy, or colon tissue biopsy.
In some cases, the subject has not received a colonoscopy,
sigmoidoscopy, or colon tissue biopsy and has one or more of: a
symptom of CRC, a family history of CRC, and a risk factor for CRC.
In some cases, a biological sample can be obtained from a subject
during routine examination, or to establish baseline levels of the
biomarkers. In some cases, a subject has no symptoms for colorectal
carcinoma, has no family history for colorectal carcinoma, has no
recognized risk factors for colorectal carcinoma.
[0147] In some cases, a subject presents at least one of: a symptom
for colorectal carcinoma, a family history for colorectal
carcinoma, and a recognized risk factor for colorectal carcinoma.
In some cases, a subject is identified through screening assays
(for example, fecal occult blood testing or sigmoidoscopy) or
rectal digital exam or rigid or flexible colonoscopy or CT scan or
other x-ray techniques as being at high risk for or having CRC. For
example, one or more methods described herein are applied to a
subject undergoing treatment for CRC, to determine the
effectiveness of the therapy or treatment they are receiving.
[0148] Exemplary Biological Samples
[0149] Biological samples in some exemplary embodiments are
circulating blood samples or are samples obtained from the vein or
artery of an individual. Samples are optionally processed, so as to
isolate plasma, circulating free proteins, or a whole protein
fraction from the blood sample. Samples are often treated to
facilitate storage or to allow shipment at room temperature,
although in preferred embodiments samples are shipped frozen, for
example with or on dry ice, to preserve the samples for analysis at
a processing center separate from a phlebotomist's office.
[0150] As a representative sample collection protocol, blood
samples for serum, EDTA plasma, citrate plasma and buffy-coats are
collected with light tournique from an antecubital vein using
endotoxin-, deoxyribonuclease (DNAse-) and ribonuclease (RNAse-)
free collection and handling equipment, collection tubes and
storage vials from Becton-Dickinson, Franklin Lakes, N.J., USA and
Almeco A/S, Esbjerg, Denmark. The blood samples are centrifuged at
3,000.times.G for 10 mins at 21.degree. C. and serum and plasma are
immediately separated from the red cell and buffy-coat layers.
Contamination by white cells and platelets is reduced by leaving
0.5 cm of untouched serum or plasma above the buffy-coat, which is
separately transferred for freezing. All separated samples are
marked with unique barcodes for storage identification, which is
performed using the FreezerWorks.RTM., Seattle, Wash., USA tracking
system. Separated samples are frozen at -80.degree. C. under
continuous electronic surveillance. The entire procedure is
completed within 2 hours of initial sample draw.
[0151] Additional biological samples include one or more of, but
are not limited to: urine, stool, tears, whole blood, serum,
plasma, blood constituent, bone marrow, tissue, cells, organs,
saliva, cheek swab, lymph fluid, cerebrospinal fluid, lesion
exudates and other fluids produced by the body. The biological
sample is in some cases a solid biological sample, for example, a
tissue biopsy. The biopsy can be fixed, paraffin embedded, or
fresh. In many embodiments herein, a preferred sample is a blood
sample drawn from a vein or artery of an individual, or a processed
product thereof.
[0152] Biological samples are optionally processed using any
approach known in the art or otherwise described herein to
facilitate measurement of one or more biomarkers as described
herein. Sample preparation operations comprise, for example,
extraction and/or isolation of intracellular material from a cell
or tissue such as the extraction of nucleic acids, protein, or
other macromolecules. Sample preparation which can be used with the
methods of disclosure include but are not limited to,
centrifugation, affinity chromatography, magnetic separation,
immunoassay, nucleic acid assay, receptor-based assay, cytometric
assay, colorimetric assay, enzymatic assay, electrophoretic assay,
electrochemical assay, spectroscopic assay, chromatographic assay,
microscopic assay, topographic assay, calorimetric assay,
radioisotope assay, protein synthesis assay, histological assay,
culture assay, and combinations thereof.
[0153] Sample preparation optionally includes dilution by an
appropriate solvent and amount to ensure the appropriate range of
concentration level is detected by a given assay.
[0154] Accessing the nucleic acids and macromolecules from the
intercellular space of the sample is performed by either physical,
chemical methods, or a combination of both. In some applications of
the methods, following the isolation of the crude extract, it will
often be desirable to separate the nucleic acids, proteins, cell
membrane particles, and the like. In some applications of the
methods it will be desirable to keep the nucleic acids with its
proteins, and cell membrane particles.
[0155] In some applications of the methods provided herein, nucleic
acids and proteins are extracted from a biological sample prior to
analysis using methods of the disclosure. Extraction is
accomplished, for example through use of detergent lysates,
sonication, or vortexing using glass beads.
[0156] In some applications, molecules can be isolated using any
technique suitable in the art including, but not limited to,
techniques using gradient centrifugation (for example, cesium
chloride gradients, sucrose gradients, glucose gradients, or other
gradients), centrifugation protocols, boiling, purification kits,
and the use of liquid extraction with agent extraction methods such
as methods using Trizol or DNAzol.
[0157] In some cases, the sample is partially prepared at a
separate location prior to being sent for analysis. For example, a
phlebotomist draws a blood sample at a clinic or hospital. The
sample can be partially processed, for example, by placing in
anticoagulant-treated tubes and centrifuging to produce plasma. The
partially processed sample, such as the plasma, is then shipped
(e.g., mailed on ice or in preservative at room temperature) to a
separate facility where any of the methods disclosed herein can be
performed to determine a biomarker panel level and/or CRC or
advanced adenoma health status.
[0158] Samples are prepared according to standard biological sample
preparation depending on the desired detection method. For example,
for mass spectrometry detection, biological samples obtained from a
patient may be centrifuged, filtered, processed by immunoaffinity
column, separated into fractions, partially digested, and
combinations thereof. Various fractions may be resuspended in
appropriate carrier such as buffer or other type of loading
solution for detection and analysis, including LCMS loading
buffer.
Biomarker Assessment
[0159] The present disclosure provides for methods for measuring
one or more biomarker panels in biological samples. Any suitable
method can be used to detect one or more of the biomarkers of any
of the panels described herein.
[0160] In some cases, only values falling within specific ranges
are reported. For example, in some cases, assayed protein
concentrations below a given cutoff indicate a failed assay.
Exemplary acceptable ranges for particular biomarkers are disclosed
in Table 4.
TABLE-US-00004 TABLE 4 Exemplary acceptable ranges for biomarkers
of interest. Protein Low High Units AACT 62.5 4000 .mu.g/ml CATD
62.5 1000 ng/ml CEA 3 120 ng/ml CLUS 30 480 .mu.g/ml CO3 117.25
7500 .mu.g/ml CO9 4.68 300 .mu.g/ml GDF15 187.2 12000 pg/ml MIF
3.13 100 ng/ml PSGL 93.75 1500 U/ml SAA1 18 144 .mu.g/ml SEPR 10
160 ng/ml
[0161] Useful analyte capture agents used in practice of methods
described herein include but are not limited to antibodies, such as
crude serum containing antibodies, purified antibodies, monoclonal
antibodies, polyclonal antibodies, synthetic antibodies, antibody
fragments (for example, Fab fragments); antibody interacting
agents, such as protein A, carbohydrate binding proteins, and other
interactants; protein interactants (for example avidin and its
derivatives); peptides; and small chemical entities, such as enzyme
substrates, cofactors, metal ions/chelates, aptamers, and haptens.
Antibodies may be modified or chemically treated to optimize
binding to targets or solid surfaces (for example biochips and
columns).
[0162] Biomarkers are measured in some cases in a biological sample
using an immunoassay. Some immunoassays use antibodies that
specifically or informatively bind to or recognize an antigen (for
example site on a protein or peptide, biomarker target). Some
immunoassays include the steps of contacting the biological sample
using the antibody and allowing the antibody to form a complex of
with the antigen in the sample, washing the sample and detecting
the antibody-antigen complex with a detection reagent. Antibodies
that recognize the biomarkers may be commercially available. An
antibody that recognizes the biomarkers can be generated by known
methods of antibody production.
[0163] Immunoassays include indirect assays, wherein, for example,
a second, labeled antibody can be used to detect bound
marker-specific antibody. Exemplary detectable labels include
magnetic beads (for example, DYNABEADS.TM.), fluorescent dyes,
radiolabels, enzymes (for example, horseradish peroxide, alkaline
phosphatase and others commonly used), and calorimetric labels such
as colloidal gold or colored glass or plastic beads. The biomarker
in the sample can be measured using a competition or inhibition
assay wherein, for example, a monoclonal antibody which binds to a
distinct epitope of the marker is incubated simultaneously with the
mixture.
[0164] The conditions to detect an antigen using an immunoassay are
dependent on the particular antibody used. Also, the incubation
time can depend upon the assay format, marker, volume of solution,
concentrations and the like. Immunoassays can be carried out at
room temperature, although they can be conducted over a range of
temperatures, such as from about 0 degrees to about 40 degrees
Celsius depending on the antibody used.
[0165] There are various types of immunoassay known in the art that
as a starting basis can be used to tailor the assay for the
detection of the biomarkers of the present disclosure. Useful
assays can include, for example, an enzyme immune assay (EIA) such
as enzyme-linked immunosorbent assay (ELISA). For example, if an
antigen can be bound to a solid support or surface, it can be
detected by reacting it with a specific antibody and the antibody
can be quantitated by reacting it with either a secondary antibody
or by incorporating a label directly into the primary antibody.
Alternatively, an antibody can be bound to a solid surface and the
antigen added. A second antibody that recognizes a distinct epitope
on the antigen can then be added and detected. Such assay can be
referred to as a `sandwich assay` and can be used to avoid problems
of high background or non-specific reactions. These types of assays
can be sensitive and reproducible enough to measure low
concentrations of antigens in a biological sample.
[0166] Immunoassays are used to determine presence or absence of a
marker in a sample as well as the quantity of a marker in a sample.
Methods for measuring the amount of, or presence of,
antibody-marker complex include but are not limited to,
fluorescence, luminescence, chemiluminescence, absorbance,
reflectance, transmittance, birefringence or refractive index (for
example, surface plasmon resonance, ellipsometry, a resonant mirror
method, a grating coupler waveguide method or interferometry). Such
reagents can be used with optical detection methods, such as
various forms of microscopy, imaging methods and non-imaging
methods. Electrochemical methods can include voltammetry and
amperometry methods. Radio frequency methods can include multipolar
resonance spectroscopy.
[0167] Measurement of biomarkers optionally involves use of an
antibody. Antibodies that specifically bind to any of the
biomarkers described herein can be prepared using standard methods
known in the art. For example polyclonal antibodies can be produced
by injecting an antigen into a mammal, such as a mouse, rat,
rabbit, goat, sheep, or horse for large quantities of antibody.
Blood isolated from these animals can contain polyclonal
antibodies--multiple antibodies that bind to the same antigen.
Alternatively, polyclonal antibodies can be produced by injecting
the antigen into chickens for generation of polyclonal antibodies
in egg yolk. In addition, antibodies can be made to specifically
recognize modified forms for the biomarkers such as a
phosphorylated form of the biomarker, for example, they can
recognize a tyrosine or a serine after phosphorylation, but not in
the absence of phosphate. In this way antibodies can be used to
determine the phosphorylation state of a particular biomarker.
[0168] Antibodies are obtained commercially or produced using
well-established methods. To obtain antibodies specific for a
single epitope of an antigen, antibody-secreting lymphocytes are
isolated from the animal and immortalized by fusing them with a
cancer cell line. The fused cells are referred to as hybridomas,
and can continually grow and secrete antibody in culture. Single
hybridoma cells are isolated by dilution cloning to generate cell
clones that all produce the same antibody; these antibodies can be
referred to as monoclonal antibodies.
[0169] Polyclonal and monoclonal antibodies can be purified in
several ways. For example, one can isolate an antibody using
antigen-affinity chromatography which can be couple to bacterial
proteins such as Protein A, Protein G, Protein L or the recombinant
fusion protein, Protein A/G followed by detection of via UV light
at 280 nm absorbance of the eluate fractions to determine which
fractions contain the antibody. Protein A/G can bind to all
subclasses of human IgG, making it useful for purifying polyclonal
or monoclonal IgG antibodies whose subclasses have not been
determined. In addition, Protein A/G can bind to IgA, IgE, IgM and
(in some cases to a lesser extent) IgD. Protein A/G can bind to all
subclasses of mouse IgG but in some cases does not bind mouse IgA,
IgM or serum albumin. This feature can allow Protein A/G to be used
for purification and detection of mouse monoclonal IgG antibodies,
without interference from IgA, IgM and serum albumin.
[0170] Antibodies are derived from different classes or isotypes of
molecules such as, for example, IgA, IgA IgD, IgE, IgM and IgG. The
IgA can be designed for secretion in the bodily fluids while
others, like the IgM are designed to be expressed on the cell
surface. The antibody can be an IgG antibody. In some cases, IgG
comprises two subunits including two "heavy" chains and two "light"
chains. These can be assembled in a symmetrical structure and each
IgG can have two identical antigen recognition domains. The antigen
recognition domain can be a combination of amino acids from both
the heavy and light chains. The molecule can be roughly shaped like
a "Y" and the arms/tips of the molecule comprise the
antigen-recognizing regions or Fab (fragment, antigen binding)
region, while the stem of Fc (Fragment, crystallizable) region is
not necessarily involved in recognition and can be fairly constant.
The constant region can be identical in all antibodies of the same
isotype, but can differ in antibodies of different isotypes.
[0171] It is also possible to use an antibody to detect a protein
after fractionation by western blotting. Western blotting is used
in some cases for the detection and/or measurement of protein or
polypeptide biomarkers.
[0172] Some detection methods can employ flow cytometry. Flow
cytometry can be a laser based, biophysical technology that can be
used for biomarker detection, quantification (cell counting) and
cell isolation. This technology can be used in the diagnosis of
health disorders, especially blood cancers. In general, flow
cytometry can comprise suspending single cells in a stream of
fluid. A beam of light (usually laser light) of a single wavelength
can be directed onto the stream of liquid, and the scatter light
caused by a passing cell can be detected by an electronic detection
apparatus. A flow cytometry methodology useful in one or more
methods described herein can include Fluorescence-activated cell
sorting (FACS). FACS can use florescent-labeled antibodies to
detect antigens on cell of interest. This additional feature of
antibody labeling use in FACS can enable simultaneous
multiparametric analysis and quantification based upon the specific
light scattering and fluorescent characteristics of each cell
florescent-labeled cell and it provides physical separation of the
population of cells of interest as well as traditional flow
cytometry does.
[0173] A wide range of fluorophores can be used as labels in flow
cytometry. Fluorophores can be typically attached to an antibody
that recognizes a target feature on or in the cell. Examples of
suitable fluorescent labels include, but are not limited to:
fluorescein (FITC), 5, 6-carboxymethyl fluorescein, Texas red,
nitrobenz-2-oxa-1,3-diazol-4-yl (NBD), and the cyanine dyes Cy3,
Cy3.5, Cy5, Cy5.5 and Cy7. Other Fluorescent labels such as Alexa
Fluor.RTM. dyes, DNA content dye such as DAPI, and Hoechst dyes are
well known in the art and can be easily obtained from a variety of
commercial sources. Each fluorophore can have a characteristic peak
excitation and emission wavelength, and the emission spectra often
overlap. The absorption and emission maxima, respectively, for
these fluors can be: FITC (490 nm; 520 nm), Cy3 (554 nm; 568 nm),
Cy3.5 (581 nm; 588 nm), Cy5 (652 nm: 672 nm), Cy5.5 (682 nm; 703
nm) and Cy7 (755 nm; 778 nm). The fluorescent labels can be
obtained from a variety of commercial sources. Quantum dots can be
used in place of traditional fluorophores. Other methods that can
be used for detecting include isotope labeled antibodies, such as
lanthanide isotopes.
[0174] Immunoassays optionally comprise immunohistochemistry.
Immunohistochemistry is used to detect expression of the claimed
biomarkers in a tissue sample. The antibodies can be detected by
direct labeling of the antibodies themselves, for example, with
radioactive labels, fluorescent labels, hapten labels such as,
biotin, or an enzyme such as horse radish peroxidase or alkaline
phosphatase. Alternatively, unlabeled primary antibody can be used
in conjunction with a labeled secondary antibody, comprising
antisera, polyclonal antisera or a monoclonal antibody specific for
the primary antibody. Immunohistochemistry protocols are well known
in the art and protocols and antibodies are commercially available.
Alternatively, one raises an antibody to the biomarkers or modified
versions of the biomarker or binding partners as disclosure herein
that would be useful for determining the expression levels of the
proteins in a tissue sample.
[0175] Some measurement of biomarkers comprises use of a biochip.
Biochips can be used to screen a large number of macromolecules.
Biochips can be designed with immobilized nucleic acid molecules,
full-length proteins, antibodies, affibodies (small molecules
engineered to mimic monoclonal antibodies), aptamers (nucleic
acid-based ligands) or chemical compounds. A chip could be designed
to detect multiple macromolecule types on one chip. For example, a
chip could be designed to detect nucleic acid molecules, proteins
and metabolites on one chip. The biochip can be used to and
designed to simultaneously analyze a panel biomarker in a single
sample, producing a subjects profile for these biomarkers. The use
of the biochip allows for the multiple analyses to be performed
reducing the overall processing time and the amount of sample
required.
[0176] Protein microarray can be a particular type of biochip which
can be used with the present disclosure. In some cases, the chip
comprises a support surface such as a glass slide, nitrocellulose
membrane, bead, or microtitre plate, to which an array of capture
proteins can be bound in an arrayed format onto a solid surface.
Protein array detection methods can give a high signal and a low
background. Detection probe molecules, typically labeled with a
fluorescent dye, can be added to the array. Any reaction between
the probe and the immobilized protein can result in emission of a
detectable signal. Such protein microarrays can be rapid,
automated, and offer high sensitivity of protein biomarker
read-outs for diagnostic tests. However, it would be immediately
appreciated to those skilled in the art that there are a variety of
detection methods that can be used with this technology. Exemplary
microarrays include analytical microarrays (also known as capture
arrays), functional protein microarrays (also known as target
protein arrays) and reverse phase protein microarray (RPA).
[0177] Analytical protein microarrays can be constructed using a
library of antibodies, aptamers or affibodies. The array can be
probed with a complex protein solution such as a blood, serum or a
cell lysate that function by capturing protein molecules they
specifically bind to. Analysis of the resulting binding reactions
using various detection systems can provide information about
expression levels of particular proteins in the sample as well as
measurements of binding affinities and specificities. This type of
protein microarray can be especially useful in comparing protein
expression in different samples. Functional protein microarrays can
be constructed by immobilizing large numbers of purified
full-length functional proteins or protein domains and can be used
to identify protein-protein, protein-DNA, protein-RNA,
protein-phospholipid, and protein-small molecule interactions, to
assay enzymatic activity and to detect antibodies and demonstrate
their specificity. These protein microarray biochips can be used to
study the biochemical activities of the entire proteome in a
sample.
[0178] One or more biomarkers can be measured using reverse phase
protein microarray (RPA). Reverse phase protein microarray can be
constructed from tissue and cell lysates that can be arrayed onto
the microarray and probed with antibodies against the target
protein of interest. These antibodies can be detected with
chemiluminescent, fluorescent or colorimetric assays. In addition
to the protein in the lysate, reference control peptides can be
printed on the slides to allow for protein quantification. RPAs
allow for the determination of the presence of altered proteins or
other agents that may be the result of disease and present in a
diseased cell.
[0179] One or more biomarkers can be measured using mass
spectroscopy (alternatively referred to as mass spectrometry). Mass
spectrometry (MS) can refer to an analytical technique that
measures the mass-to-charge ratio of charged particles. It can be
primarily used for determining the elemental composition of a
sample or molecule, and for elucidating the chemical structures of
molecules, such as peptides and other chemical compounds. MS works
by ionizing chemical compounds to generate charged molecules or
molecule fragments and measuring their mass-to-charge ratios MS
instruments typically consist of three modules (1) an ion source,
which can convert gas phase sample molecules into ions (or, in the
case of electrospray ionization, move ions that exist in solution
into the gas phase) (2) a mass analyzer, which sorts the ions by
their masses by applying electromagnetic fields and (3) detector,
which measures the value of an indicator quantity and thus provides
data for calculating the abundances of each ion present.
[0180] Suitable mass spectrometry methods to be used with the
present disclosure include but are not limited to, one or more of
electrospray ionization mass spectrometry (ESI-MS), ESI-MS/MS,
ESI-MS/(MS), matrix-assisted laser desorption ionization
time-of-flight mass spectrometry (MALDI-TOF-MS), surface-enhanced
laser desorption/ionization time-of-flight mass spectrometry
(SELDI-TOF-MS), tandem liquid chromatography-mass spectrometry
(LC-MS/MS) mass spectrometry, desorption/ionization on silicon
(DIOS), secondary ion mass spectrometry (SIMS), quadrupole
time-of-flight (Q-TOF), atmospheric pressure chemical ionization
mass spectrometry (APCI-MS), APCI-MS/MS, APCI-(MS), atmospheric
pressure photoionization mass spectrometry (APPI-MS), APPI-MS/MS,
and APPI-(MS), quadrupole mass spectrometry, Fourier transform mass
spectrometry (FTMS), and ion trap mass spectrometry, where n can be
an integer greater than zero.
[0181] LC-MS can be commonly used to resolve the components of a
complex mixture. LC-MS method generally involves protease digestion
and denaturation (usually involving a protease, such as trypsin and
a denaturant such as, urea to denature tertiary structure and
iodoacetamide to cap cysteine residues) followed by LC-MS with
peptide mass fingerprinting or LC-MS/MS (tandem MS) to derive
sequence of individual peptides. LC-MS/MS can be used for proteomic
analysis of complex samples where peptide masses may overlap even
with a high-resolution mass spectrometer. Samples of complex
biological fluids like human serum may be first separated on an
SDS-PAGE gel or HPLC-SCX and then run in LC-MS/MS allowing for the
identification of over 1000 proteins.
[0182] While multiple mass spectrometric approaches are compatible
with the methods of the disclosure as provided herein, in some
applications it is desired to quantify proteins in biological
samples from a selected subset of proteins of interest. One such MS
technique that is compatible with the present disclosure is
Multiple Reaction Monitoring Mass Spectrometry (MRM-MS), or
alternatively referred to as Selected Reaction Monitoring Mass
Spectrometry (SRM-MS).
[0183] The MRM-MS technique involves a triple quadrupole (QQQ) mass
spectrometer to select a positively charged ion from the peptide of
interest, fragment the positively charged ion and then measure the
abundance of a selected positively charged fragment ion. This
measurement is commonly referred to as a transition and/or
transition ion. By way of illustrative example only, a peptide
fragment comprising the amino acid sequence IAELLSPGSVDPLTR (SEQ ID
NO: 27) can comprise one or more of the following exemplary
transition ion biomarkers provided in Table 5, below.
TABLE-US-00005 TABLE 5 Exemplary transition ions for the peptide
sequence IAELLSPGSVDPLTR (SEQ ID NO: 27) Transition Ion Amino Acid
Sequence b1 I b2 IA b3 IAE b4 IAEL (SEQ ID NO: 28) b5 IAELL (SEQ ID
NO: 29) b6 IAELLS (SEQ ID NO: 30) b7 IAELLSP (SEQ ID NO: 31) b8
IAELLSPG (SEQ ID NO: 32) b9 IAELLSPGS (SEQ ID NO: 33) b10
IAELLSPGSV (SEQ ID NO: 34) b11 IAELLSPGSVD (SEQ ID NO: 35) b12
IAELLSPGSVDP (SEQ ID NO: 36) b13 IAELLSPGSVDPL (SEQ ID NO: 37) b14
IAELLSPGSVDPLT (SEQ ID NO: 38) y14 AELLSPGSVDPLTR (SEQ ID NO: 39)
y13 ELLSPGSVDPLTR (SEQ ID NO: 40) y12 LLSPGSVDPLTR (SEQ ID NO: 41)
y11 LSPGSVDPLTR (SEQ ID NO: 42) y10 SPGSVDPLTR (SEQ ID NO: 43) Y9
PGSVDPLTR (SEQ ID NO: 44) Y8 GSVDPLTR (SEQ ID NO: 45) y7 SVDPLTR
(SEQ ID NO: 46) y6 VDPLTR (SEQ ID NO: 47) Y5 DPLTR(SEQ ID NO: 48)
y4 PLTR(SEQ ID NO: 49) Y3 LTR y2 TR y1 R
[0184] In some applications the MRM-MS is coupled with
High-Pressure Liquid Chromatography (HPLC) and more recently Ultra
High-Pressure Liquid Chromatography (UHPLC). In other applications
MRM-MS can be coupled with UHPLC with a QQQ mass spectrometer to
make the desired LC-MS transition measurements for all of the
peptides and proteins of interest.
[0185] In some applications the utilization of a quadrupole
time-of-flight (qTOF) mass spectrometer, time-of-flight
time-of-flight (TOF-TOF) mass spectrometer, Orbitrap mass
spectrometer, quadrupole Orbitrap mass spectrometer or any
Quadrupolar Ion Trap mass spectrometer can be used to select for a
positively charged ion from one or more peptides of interest. The
fragmented, positively charged ions can then be measured to
determine the abundance of a positively charged ion for the
quantitation of the peptide or protein of interest.
[0186] In some applications the utilization of a time-of-flight
(TOF), quadrupole time-of-flight (qTOF) mass spectrometer,
time-of-flight time-of-flight (TOF-TOF) mass spectrometer, Orbitrap
mass spectrometer or quadrupole Orbitrap mass spectrometer is used
to measure the mass and abundance of a positively charged peptide
ion from the protein of interest without fragmentation for
quantitation. In this application, the accuracy of the analyte mass
measurement can be used as selection criteria of the assay. An
isotopically labeled internal standard of a known composition and
concentration can be used as part of the mass spectrometric
quantitation methodology.
[0187] In some applications, time-of-flight (TOF), quadrupole
time-of-flight (qTOF) mass spectrometer, time-of-flight
time-of-flight (TOF-TOF) mass spectrometer, Orbitrap mass
spectrometer or quadrupole Orbitrap mass spectrometer is used to
measure the mass and abundance of a protein of interest for
quantitation. In this application, the accuracy of the analyte mass
measurement can be used as selection criteria of the assay.
Optionally this application can use proteolytic digestion of the
protein prior to analysis by mass spectrometry. An isotopically
labeled internal standard of a known composition and concentration
can be used as part of the mass spectrometric quantitation
methodology.
[0188] In some applications, various ionization techniques can be
coupled to the mass spectrometers provide herein to generate the
desired information. Non-limiting exemplary ionization techniques
that are used with the present disclosure include but are not
limited to Matrix Assisted Laser Desorption Ionization (MALDI),
Desorption Electrospray Ionization (DESI), Direct Assisted Real
Time (DART), Surface Assisted Laser Desorption Ionization (SALDI),
or Electrospray Ionization (ESI).
[0189] In some applications, HPLC and UHPLC can be coupled to a
mass spectrometer a number of other peptide and protein separation
techniques can be performed prior to mass spectrometric analysis.
Some exemplary separation techniques which can be used for
separation of the desired analyte (for example, peptide or protein)
from the matrix background include but are not limited to Reverse
Phase Liquid Chromatography (RP-LC) of proteins or peptides,
offline Liquid Chromatography (LC) prior to MALDI, 1 dimensional
gel separation, 2-dimensional gel separation, Strong Cation
Exchange (SCX) chromatography, Strong Anion Exchange (SAX)
chromatography, Weak Cation Exchange (WCX), and Weak Anion Exchange
(WAX). One or more of the above techniques can be used prior to
mass spectrometric analysis.
[0190] One or more biomarkers can be measured using a microarray.
Differential gene expression can also be identified, or confirmed
using the microarray technique. Thus, the expression profile
biomarkers can be measured in either fresh or fixed tissue, using
microarray technology. In this method, polynucleotide sequences of
interest (including cDNAs and oligonucleotides) can be plated, or
arrayed, on a microchip substrate. The arrayed sequences can be
then hybridized with specific DNA probes from cells or tissues of
interest. The source of mRNA can be total RNA isolated from a
biological sample, and corresponding normal tissues or cell lines
may be used to determine differential expression.
[0191] One or more biomarkers can be measured by sequencing.
Differential gene expression can also be identified, or confirmed
using the sequencing technique. Thus, the expression profile
biomarkers can be measured in either fresh or fixed sample, using
sequencing technology. In this method, polynucleotide sequences of
interest (including cDNAs and oligonucleotides) can used as
templates to synthesize sequencing libraries. The libraries can be
sequenced, and the reads mapped to an appropriate reference. The
source of mRNA can be total RNA isolated from a biological sample,
and corresponding normal tissues or cell lines may be used to
determine differential expression. Exemplary sequencing techniques
can include, for example emulsion PCR (pyrosequencing from Roche
454, semiconductor sequencing from Ion Torrent, SOLiD sequencing by
ligation from Life Technologies, sequencing by synthesis from
Intelligent Biosystems), bridge amplification on a flow cell (e.g.
Solexa/Illumina), isothermal amplification by Wildfire technology
(Life Technologies) or rolonies/nanoballs generated by rolling
circle amplification (Complete Genomics, Intelligent Biosystems,
Polonator). Sequencing technologies like Heliscope (Helicos), SMRT
technology (Pacific Biosciences) or nanopore sequencing (Oxford
Nanopore) allow direct sequencing of single molecules without prior
clonal amplification may be suitable sequencing platforms.
Sequencing may be performed with or without target enrichment. In
some cases, polynucleotides from a sample are amplified by any
suitable means prior to and/or during sequencing.
[0192] PCR amplified inserts of cDNA clones can be applied to a
substrate in a dense array. Preferably at least 10,000 nucleotide
sequences can be applied to the substrate. The microarrayed genes,
immobilized on the microchip at 10,000 elements each, can be
suitable for hybridization under stringent conditions.
Fluorescently labeled cDNA probes may be generated through
incorporation of fluorescent nucleotides by reverse transcription
of RNA extracted from tissues of interest. Labeled cDNA probes
applied to the chip hybridize with specificity to each spot of DNA
on the array. After stringent washing to remove non-specifically
bound probes, the microarray chip can be scanned by a device such
as, confocal laser microscopy or by another detection method, such
as a CCD camera. Quantitation of hybridization of each arrayed
element allows for assessment of corresponding mRNA abundance. With
dual color fluorescence, separately labeled cDNA probes generated
from two sources of RNA can be hybridized pair-wise to the array.
The relative abundance of the transcripts from the two sources
corresponding to each specified gene can be thus determined
simultaneously. Microarray analysis can be performed by
commercially available equipment, following manufacturer's
protocols.
[0193] One or more biomarkers can be measured using qRT-PCR, which
can be used to compare mRNA levels in different sample populations,
in normal and tumor tissues, with or without drug treatment, to
characterize patterns of gene expression, to discriminate between
closely related mRNAs, and to analyze RNA structure. The first step
in gene expression profiling by RT-PCR can be extracting RNA from a
biological sample followed by the reverse transcription of the RNA
template into cDNA and amplification by a PCR reaction. The reverse
transcription reaction step can be generally primed using specific
primers, random hexamers, or oligo-dT primers, depending on the
goal of expression profiling. Reverse transcriptases can be avilo
myeloblastosis virus reverse transcriptase (AMV-RT) and/or Moloney
murine leukemia virus reverse transcriptase (MLV-RT).
[0194] Although the PCR step can use a variety of thermostable
DNA-dependent DNA polymerases, it typically employs the Taq DNA
polymerase, which can have a 5'-3' nuclease activity but lacks a
3'-5' proofreading endonuclease activity. Thus, TaqMan.TM. PCR
typically utilizes the 5'-nuclease activity of Taq or Tth
polymerase to hydrolyze a hybridization probe bound to its target
amplicon, but any enzyme with equivalent 5' nuclease activity can
be used. Two oligonucleotide primers can be used to generate an
amplicon typical of a PCR reaction. A third oligonucleotide, or
probe, can be designed to detect nucleotide sequence located
between the two PCR primers. The probe can be non-extendible by Taq
DNA polymerase enzyme, and can be labeled with a reporter
fluorescent dye and a quencher fluorescent dye. Any laser-induced
emission from the reporter dye can be quenched by the quenching dye
when the two dyes are located close together as they are on the
probe. During the amplification reaction, the Taq DNA polymerase
enzyme can cleave the probe in a template-dependent manner. The
resultant probe fragments can disassociate in solution, and signal
from the released reporter dye can be freed from the quenching
effect of the second fluorophore. One molecule of reporter dye can
be liberated for each new molecule synthesized, and detection of
the unquenched reporter dye can provide basis for quantitative
interpretation of the data.
[0195] TaqMan.TM. RT-PCR can be performed using commercially
available equipment, such as, for example, ABI PRISM 7700.TM.
Sequence Detection System.TM. (Perkin-Elmer-Applied Biosystems,
Foster City, Calif., USA), or Lightcycler (Roche Molecular
Biochemicals, Mannheim, Germany). In a preferred embodiment, the 5'
nuclease procedure is run on a real-time quantitative PCR device
such as the ABI PRISM 7700.TM. Sequence Detection System.TM.. The
system comprises a thermocycler, laser, charge-coupled device
(CCD), camera and computer. The system includes software for
running the instrument and for analyzing the data. 5'-Nuclease
assay data are initially expressed as Ct, or the threshold cycle.
As discussed above, fluorescence values are recorded during every
cycle and represent the amount of product amplified to that point
in the amplification reaction. The point when the fluorescent
signal is first recorded as statistically significant can be the
threshold cycle (Ct).
[0196] To minimize errors and the effect of sample-to-sample
variation, RT-PCR can be performed using an internal standard. An
internal standard can be expressed at a constant level among
different tissues, and can be unaffected by the experimental
treatment. RNAs most frequently used to normalize patterns of gene
expression are mRNAs for the housekeeping genes
glyceraldehyde-3-phosphate-dehydrogenase (GAPDH) and
Beta-Actin.
[0197] A more recent variation of the RT-PCR technique can include
the real time quantitative PCR, which can measure PCR product
accumulation through a dual-labeled fluorogenic probe (i.e.,
TaqMan.TM. probe). Real time PCR can be compatible both with
quantitative competitive PCR, where internal competitor for each
target sequence can be used for normalization, and with
quantitative comparative PCR using a normalization gene contained
within the sample, or a housekeeping gene for RT-PCR. For further
details see, for example Held et al., Genome Research 6:986-994
(1996).
Normalization of Data
[0198] Measurement data used in the methods, systems, kits and
compositions disclosed herein are optionally normalized.
Normalization refers to a process to correct for example,
differences in the amount of genes or protein levels assayed and
variability in the quality of the template used, to remove unwanted
sources of systematic variation measurements involved in the
processing and detection of genes or protein expression. Other
sources of systematic variation are attributable to laboratory
processing conditions.
[0199] In some instances, normalization methods are used for the
normalization of laboratory processing conditions. Non-limiting
examples of normalization of laboratory processing that may be used
with methods of the disclosure include but are not limited to:
accounting for systematic differences between the instruments,
reagents, and equipment used during the data generation process,
and/or the date and time or lapse of time in the data
collection.
[0200] Assays can provide for normalization by incorporating the
expression of certain normalizing standard genes or proteins, which
do not significantly differ in expression levels under the relevant
conditions, that is to say they are known to have a stabilized and
consistent expression level in that particular sample type.
Suitable normalization genes and proteins that can be used with the
present disclosure include housekeeping genes. (See, for example,
E. Eisenberg, et al., Trends in Genetics 19(7):362-365 (2003). In
some applications, the normalizing biomarkers (genes and proteins),
also referred to as reference genes, known not to exhibit
meaningfully different expression levels in subjects with advanced
colorectal adenoma or CRC as compared to control subjects without
advanced colorectal adenoma or CRC. In some applications, it may be
useful to add a stable isotope labeled standards which can be used
and represent an entity with known properties for use in data
normalization. In other applications, a standard, fixed sample can
be measured with each analytical batch to account for instrument
and day-to-day measurement variability.
Clinical Outcome Score
[0201] Machine learning algorithms for sub-selecting discriminating
biomarkers and optionally subject characteristics, and for building
classification models, are used in some methods and systems herein
to determine clinical outcome scores. These algorithms include, but
are not limited to, elastic networks, random forests, support
vector machines, and logistic regression. These algorithms can aid
in selection of important biomarker features and transform the
underlying measurements into a score or probability relating to,
for example, clinical outcome, disease risk, disease likelihood,
presence or absence of disease, treatment response, and/or
classification of disease status.
[0202] A clinical outcome score is determined by comparing a level
of at least two biomarkers in the biological sample obtained from
the subject to a reference level of the at least two biomarkers.
Alternately or in combination, a clinical outcome score is
determined by comparing a subject-specific profile of a biomarker
panel to a reference profile of the biomarker panel. In some cases,
a reference level or reference profile represents a known
diagnosis. For example, a reference level or reference profile
represents a positive diagnosis of advanced colorectal adenoma. A
reference level or reference profile can represent a positive
diagnosis of CRC. As another example, a reference level or
reference profile represents a negative diagnosis of advanced
colorectal adenoma. Similarly, a reference level or reference
profile can represent a negative diagnosis of CRC
[0203] In some cases, an increase in a score indicates an increased
likelihood of one or more of: a poor clinical outcome, good
clinical outcome, high risk of disease, low risk of disease,
complete response, partial response, stable disease, non-response,
and recommended treatments for disease management. In some cases, a
decrease in the quantitative score indicates an increased
likelihood of one or more of: a poor clinical outcome, good
clinical outcome, high risk of disease, low risk of disease,
complete response, partial response, stable disease, non-response,
and recommended treatments for disease management.
[0204] A similar biomarker profile from a patient to a reference
profile often indicates an increased likelihood of one or more of:
a poor clinical outcome, good clinical outcome, high risk of
disease, low risk of disease, complete response, partial response,
stable disease, non-response, and recommended treatments for
disease management. In some applications, a dissimilar biomarker
profile from a patient to a reference profile indicates one or more
of: an increased likelihood of a poor clinical outcome, good
clinical outcome, high risk of disease, low risk of disease,
complete response, partial response, stable disease, non-response,
and recommended treatments for disease management.
[0205] An increase in one or more biomarker threshold values often
indicates an increased likelihood of one or more of: a poor
clinical outcome, good clinical outcome, high risk of disease, low
risk of disease, complete response, partial response, stable
disease, non-response, and recommended treatments for disease
management. In some applications, a decrease in one or more
biomarker threshold values indicates an increased likelihood of one
or more of: a poor clinical outcome, good clinical outcome, high
risk of disease, low risk of disease, complete response, partial
response, stable disease, non-response, and recommended treatments
for disease management.
[0206] An increase in at least one of a quantitative score, one or
more biomarker thresholds, a similar biomarker profile values
indicates an increased likelihood of one or more of: a poor
clinical outcome, good clinical outcome, high risk of disease, low
risk of disease, complete response, partial response, stable
disease, non-response, and recommended treatments for disease
management. Similarly, a decrease in at least one of a quantitative
score, one or more biomarker thresholds, a similar biomarker
profile values or combinations thereof indicates an increased
likelihood of one or more of: a poor clinical outcome, good
clinical outcome, high risk of disease, low risk of disease,
complete response, partial response, stable disease, non-response,
and recommended treatments for disease management.
[0207] A clinical outcome score is optionally updated based on
additional information derived during treatment. Such updates often
comprise the addition of other biomarkers. Such biomarkers include
additional proteins, metabolite accumulation levels, physical
characteristics of the subject (e.g., age, race, weight,
demographic history), medical history of the subject (e.g., family
history of advanced colorectal adenoma, prior quantitative score of
the protein panels). Such updates can comprise an adjustment of the
test sensitivity. Such updates can comprise an adjustment of the
test sensitivity. Such updates can comprise an adjustment of the
test thresholds. Such updates can comprise an adjustment of the
predicted clinical outcomes.
[0208] For example, in some cases a patient at risk of advanced
colorectal adenoma is tested using a panel as disclosed herein. The
patient may be categorized as having or being likely to have,
advanced colorectal adenoma. In some cases, the thresholds of a
protein panel disclosed herein will be updated based on additional
biomarkers, such as age of the patient. For example, a patient over
the age of 60 is more likely than a patient under 60 to have
advanced colorectal adenoma. Therefore, the positive predictive
value of the protein panel can be higher in the population over 60
than the population under 60. In some cases, the threshold for
proteins in the protein panel can be altered based on an additional
biomarker (e.g., age) to reflect this, such as by lowering the
threshold in a population over 60 compared to a population under
60. A patient's personal threshold may be updated based on previous
test results. For example, a patient may have an indeterminate or
positive clinical outcome score. Such a patient may have additional
tests recommended. Such a patient may have a colonoscopy
recommended. Such additional tests and colonoscopies can come back
negative, and the persistence of an indeterminate or positive
clinical outcome score can lead to the patient's thresholds being
updated to reflect their persistent indeterminate or positive
clinical outcome score.
[0209] In some cases, the specificity and sensitivity of the test
is adjusted based on an additional biomarker. For example, the
protein panels disclosed herein may have different sensitivities or
specificities in populations of individuals with a given genetic or
racial background. In some cases, based on an additional biomarker,
the clinical outcome score may be adjusted to reflect a changing
sensitivity or specificity of the test.
Treatment and Diagnostic Regimens
[0210] Provided herein are treatment and diagnostic regimens for
implementing any of the methods described herein for detecting a
presence or absence of advanced colorectal adenoma and treatment of
the same.
[0211] Provided herein are methods for detecting a presence or
absence of colorectal cancer. Methods disclosed herein can comprise
performing a test for colorectal cancer, performing a colonoscopy,
during which detected colorectal cancers are surgically excised or
otherwise removed, and performing the test for colorectal cancer a
second time at a later date. The second test can be positive and a
second colonoscopy can be performed. In some cases, the second
colonoscopy can include searching for and monitoring sessile
colorectal cancers. In some cases, the second colonoscopy can
include searching for and surgically removing sessile colorectal
cancers. In some cases the second test for colorectal cancer can be
positive and an additional treatment regimen can be recommended. In
some cases, the second test for colorectal cancer can be negative
and no additional testing can be recommended. In some cases, the
second test for advanced colorectal adenoma can be negative and
more frequent testing can be recommended for a given period of
time.
[0212] In some cases, a positive clinical outcome score can lead to
the recommendation of a drug therapeutic regimen. For example, a
positive clinical outcome score can result in the recommendation
that a Wnt pathway inhibitor be administered to the subject. After
the Wnt pathway inhibitor is administered, a second test for
advanced colorectal adenoma can be administered to the subject. A
negative or less severe clinical outcome score can indicate that
the treatment is effective. A second positive or more severe
clinical outcome score can indicate that the treatment is not
effective.
[0213] Computer Systems
[0214] Provided herein are computer systems for implementing any of
the methods described herein for detecting a presence or absence of
at least one of advanced colorectal adenoma and CRC. Also provided
herein are computer systems for detecting a presence or absence of
CRC. Computer systems disclosed herein comprises a memory unit. The
memory unit can be configured to receive data comprising
measurement of a biomarker panel from a biological sample of a
subject. The biomarker panel can be any biomarker panel described
herein. For example, the biomarker panel can comprise at least two
biomarkers selected from the group comprising AACT, CATD, CEA, CO3,
CO9, MIF, PSGL, and SEPR, and in some cases includes age as an
additional biomarker. Optionally, the biomarker panel includes
CATD, CLUS, GDF15, and SAA1, and in some cases includes age as an
additional biomarker.
[0215] Computer systems disclosed herein comprise computer
executable code for performing at least one of: generating a
subject-specific profile of a biomarker panel described herein
based upon the measurement data, comparing the subject-specific
profile of the biomarker panel to a reference profile of the
biomarker panel, and determining a likelihood of advanced
colorectal adenoma in the subject. Computer systems disclosed
herein comprises computer executable code for performing at least
one of: generating a subject-specific profile of a biomarker panel
described herein based upon the measurement data, comparing the
subject-specific profile of the biomarker panel to a reference
profile of the biomarker panel, and determining a likelihood of CRC
in the subject.
[0216] Additionally, provided herein are computer systems for
implementing any of the methods described herein for detecting a
presence or absence of at least one of advanced colorectal adenoma
and CRC. For example, provided herein are computer systems for
detecting a presence or absence of advanced colorectal adenoma.
Also provided herein are computer systems for detecting a presence
or absence of CRC. Computer systems disclosed herein comprises a
memory unit. The memory unit can be configured to receive data
comprising measurement of a biomarker panel from a biological
sample of a subject. The biomarker panel can be any biomarker panel
described herein. For example, the biomarker panel can comprise at
least two biomarkers selected from the group comprising AACT, CATD,
CEA, CO3, CO9, MIF, PSGL, SEPR, CATD, CLUS, GDF15, and SAA1.
[0217] Computer systems disclosed herein optionally comprise
computer executable code for performing at least one of: generating
a subject-specific profile of a biomarker panel described herein
based upon the measurement data, comparing the subject-specific
profile of the biomarker panel to a reference profile of the
biomarker panel, and determining a likelihood of advanced
colorectal adenoma in the subject. Computer systems disclosed
herein optionally comprise computer executable code for performing
at least one of: generating a subject-specific profile of a
biomarker panel described herein based upon the measurement data,
comparing the subject-specific profile of the biomarker panel to a
reference profile of the biomarker panel, and determining a
likelihood of CRC in the subject.
[0218] Computer systems described herein optionally comprise
computer-executable code for performing any of the algorithms
described herein. The computer system can further comprise
computer-executable code for providing a report communicating the
presence or absence of the at least one of advanced colorectal
adenoma and CRC, for recommending a colonoscopy, sigmoidoscopy, or
colorectal tissue biopsy, and/or for recommending a treatment. In
some embodiments, the computer system executes instructions
contained in a computer-readable medium.
[0219] In some embodiments, the processor is associated with one or
more controllers, calculation units, and/or other units of a
computer system, or implanted in firmware. In some embodiments, one
or more steps of the method are implemented in hardware. In some
embodiments, one or more steps of the method are implemented in
software. Software routines may be stored in any computer readable
memory unit such as flash memory, RAM, ROM, magnetic disk, laser
disk, or other storage medium as described herein or known in the
art. Software may be communicated to a computing device by any
known communication method including, for example, over a
communication channel such as a telephone line, the internet, a
wireless connection, or by a transportable medium, such as a
computer readable disk, flash drive, etc. The one or more steps of
the methods described herein may be implemented as various
operations, tools, blocks, modules and techniques which, in turn,
may be implemented in firmware, hardware, software, or any
combination of firmware, hardware, and software. When implemented
in hardware, some or all of the blocks, operations, techniques,
etc. may be implemented in, for example, an application specific
integrated circuit (ASIC), custom integrated circuit (IC), field
programmable logic array (FPGA), or programmable logic array
(PLA).
[0220] FIG. 19 depicts an exemplary computer system 1900 adapted to
implement a method described herein. The system 1900 includes a
central computer server 1901 that is programmed to implement
exemplary methods described herein. The server 1901 includes a
central processing unit (CPU, also "processor") 1905 which can be a
single core processor, a multi core processor, or plurality of
processors for parallel processing. The server 1901 also includes
memory 1910 (for example random access memory, read-only memory,
flash memory); electronic storage unit 1915 (for example hard
disk); communications interface 1920 (for example network adaptor)
for communicating with one or more other systems; and peripheral
devices 1925 which may include cache, other memory, data storage,
and/or electronic display adaptors. The memory 1910, storage unit
1915, interface 1920, and peripheral devices 1925 are in
communication with the processor 1905 through a communications bus
(solid lines), such as a motherboard. The storage unit 1915 can be
a data storage unit for storing data. The server 1901 is
operatively coupled to a computer network ("network") 1930 with the
aid of the communications interface 1920. The network 1930 can be
the Internet, an intranet and/or an extranet, an intranet and/or
extranet that is in communication with the Internet, a
telecommunication or data network. The network 1930 in some cases,
with the aid of the server 1901, can implement a peer-to-peer
network, which may enable devices coupled to the server 1901 to
behave as a client or a server.
[0221] The storage unit 1915 can store files, such as subject
reports, and/or communications with the caregiver, sequencing data,
data about individuals, or any aspect of data associated with the
invention.
[0222] The server can communicate with one or more remote computer
systems through the network 1930. The one or more remote computer
systems may be, for example, personal computers, laptops, tablets,
telephones, Smart phones, or personal digital assistants.
[0223] In some situations the system 1900 includes a single server
1901. In other situations, the system includes multiple servers in
communication with one another through an intranet, extranet and/or
the Internet.
[0224] The server 1901 can be adapted to store measurement data,
patient information from the subject, such as, for example,
polymorphisms, mutations, medical history, family history,
demographic data and/or other information of potential relevance.
Such information can be stored on the storage unit 1915 or the
server 1901 and such data can be transmitted through a network.
[0225] Methods as described herein are in some cases implemented by
way of machine (or computer processor) executable code (or
software) stored on an electronic storage location of the server
1901, such as, for example, on the memory 1910, or electronic
storage unit 1915. During use, the code can be executed by the
processor 1905. In some cases, the code can be retrieved from the
storage unit 1915 and stored on the memory 1910 for ready access by
the processor 1905. In some situations, the electronic storage unit
115 can be precluded, and machine-executable instructions are
stored on memory 1910. Alternatively, the code can be executed on a
second computer system 1940.
[0226] Aspects of the systems and methods provided herein, such as
the server 1901, can be embodied in programming. Various aspects of
the technology may be thought of as "products" or "articles of
manufacture" typically in the form of machine (or processor)
executable code and/or associated data that is carried on or
embodied in a type of machine readable medium. Machine-executable
code can be stored on an electronic storage unit, such memory (for
example, read-only memory, random-access memory, flash memory) or a
hard disk. "Storage" type media can include any or all of the
tangible memory of the computers, processors or the like, or
associated modules thereof, such as various semiconductor memories,
tape drives, disk drives and the like, which may provide
non-transitory storage at any time for the software programming.
All or portions of the software may at times be communicated
through the Internet or various other telecommunication networks.
Such communications, for example, may enable loading of the
software from one computer or processor into another, for example,
from a management server or host computer into the computer
platform of an application server. Thus, another type of media that
may bear the software elements includes optical, electrical, and
electromagnetic waves, such as used across physical interfaces
between local devices, through wired and optical landline networks
and over various air-links. The physical elements that carry such
waves, such as wired or wireless likes, optical links, or the like,
also may be considered as media bearing the software. As used
herein, unless restricted to non-transitory, tangible "storage"
media, terms such as computer or machine "readable medium" can
refer to any medium that participates in providing instructions to
a processor for execution.
[0227] Hence, a machine readable medium, such as
computer-executable code, may take many forms, including but not
limited to, tangible storage medium, a carrier wave medium, or
physical transmission medium. Non-volatile storage media can
include, for example, optical or magnetic disks, such as any of the
storage devices in any computer(s) or the like, such may be used to
implement the system. Tangible transmission media can include:
coaxial cables, copper wires, and fiber optics (including the wires
that comprise a bus within a computer system). Carrier-wave
transmission media may take the form of electric or electromagnetic
signals, or acoustic or light waves such as those generated during
radio frequency (RF) and infrared (IR) data communications. Common
forms of computer-readable media therefore include, for example: a
floppy disk, a flexible disk, hard disk, magnetic tape, any other
magnetic medium, a CD-ROM, DVD, DVD-ROM, any other optical medium,
punch cards, paper tame, any other physical storage medium with
patterns of holes, a RAM, a ROM, a PROM and EPROM, a FLASH-EPROM,
any other memory chip or cartridge, a carrier wave transporting
data or instructions, cables, or links transporting such carrier
wave, or any other medium from which a computer may read
programming code and/or data. Many of these forms of computer
readable media may be involved in carrying one or more sequences of
one or more instructions to a processor for execution.
[0228] The results of detection of a presence or absence of at
least one of an advanced colorectal adenoma and CRC, generating a
subject report, and/or communicating the report to a caregiver can
be presented to a user with the aid of a user interface, such as a
graphical user interface.
[0229] A computer system may be used to implement one or more steps
of a method described herein, including, for example, sample
collection, sample processing, measurement of an amount of one or
more proteins described herein to produce measurement data,
determination of a ratio of a protein to another protein to produce
measurement data, comparing measurement data to a reference amount,
generating a subject-specific profile of a biomarker panel,
comparing the subject-specific profile to a reference profile,
receiving medical history, receiving medical records, receiving and
storing measurement data obtained by one or more methods described
herein, analyzing said measurement data to determine a presence or
absence of at least one of an advanced colorectal adenoma and CRC
(for example, by performing an algorithm described herein),
generating a report, and reporting results to a receiver.
[0230] A client-server and/or relational database architecture can
be used in any of the methods described herein. In general, a
client-server architecture is a network architecture in which each
computer or process on the network is either a client or a server.
Server computers can be powerful computers dedicated to managing
disk drives (file servers), printers (print servers), or network
traffic (network servers). Client computers can include PCs
(personal computers) or workstations on which users run
applications, as well as example output devices as disclosed
herein. Client computers can rely on server computers for
resources, such as files, devices, and even processing power. The
server computer handles all of the database functionality. The
client computer can have software that handles front-end data
management and receive data input from users.
[0231] After performing a calculation, a processor can provide the
output, such as from a calculation, back to, for example, the input
device or storage unit, to another storage unit of the same or
different computer system, or to an output device. Output from the
processor can be displayed by a data display, for example, a
display screen (for example, a monitor or a screen on a digital
device), a print-out, a data signal (for example, a packet), a
graphical user interface (for example, a webpage), an alarm (for
example, a flashing light or a sound), or a combination of any of
the above. In an embodiment, an output is transmitted over a
network (for example, a wireless network) to an output device. The
output device can be used by a user to receive the output from the
data-processing computer system. After an output has been received
by a user, the user can determine a course of action, or can carry
out a course of action, such as a medical treatment when the user
is medical personnel. In some embodiments, an output device is the
same device as the input device. Example output devices include,
but are not limited to, a telephone, a wireless telephone, a mobile
phone, a PDA, a flash memory drive, a light source, a sound
generator, a fax machine, a computer, a computer monitor, a
printer, an iPod, and a webpage. The user station may be in
communication with a printer or a display monitor to output the
information processed by the server. Such displays, output devices,
and user stations can be used to provide an alert to the subject or
to a caregiver thereof.
[0232] Data relating to the present disclosure can be transmitted
over a network or connections for reception and/or review by a
receiver. The receiver can be but is not limited to the subject to
whom the report pertains; or to a caregiver thereof, for example, a
health care provider, manager, other healthcare professional, or
other caretaker; a person or entity that performed and/or ordered
the genotyping analysis; a genetic counselor. The receiver can also
be a local or remote system for storing such reports (for example
servers or other systems of a "cloud computing" architecture). In
one embodiment, a computer-readable medium includes a medium
suitable for transmission of a result of an analysis of a
biological sample.
Kits
[0233] The present disclosure also provides kits. In some cases, a
kit described herein comprises one or more compositions, reagents,
and/or device components for measuring and/or detecting one or more
biomarkers described herein. A kit as described herein can further
comprise instructions for practicing any of the methods provided
herein. The kits can further comprise reagents to enable the
detection of biomarker by various assays types such as ELISA assay,
immunoassay, protein chip or microarray, mass spectrometry,
immunohistochemistry, flow cytometry, or high content cell
screening. Kits can also comprise a computer readable medium
comprising computer executable code for implementing a method
described herein.
[0234] In some embodiments, a kit provided herein comprises
antibodies to the biomarkers described elsewhere in the disclosure.
A kit may comprise at least two antibodies that are each reactive
against a biomarkers selected from the group consisting of CATD,
CLUS, GDF15, SAA1, AACT, CATD, CEA, CO3, CO9, MIF, PSGL, and SEPR.
In some cases, a kit provided herein comprises antibodies to AACT,
CATD, CEA, CO3, CO9, MIF, PSGL, and SEPR. In other cases, a kit
provided herein comprises antibodies to CATD, CLUS, GDF15, and
SAA1.
[0235] In some embodiments, kits described herein include a
packaging material. As used herein, the term "packaging material"
can refer to a physical structure housing the components of the
kit. The packaging material can maintain sterility of the kit
components, and can be made of material commonly used for such
purposes (for example, paper, corrugated fiber, glass, plastic,
foil, ampules, etc.). Kits can also include a buffering agent, a
preservative, or a protein/nucleic acid stabilizing agent. Kits can
include components for obtaining a biological sample from a
patient. Non-limiting examples of such components can be gloves,
hypodermic needles or syringes, tubing, tubes or vessels to hold
the biological sample, sterilization components (e.g. isopropyl
alcohol wipes or sterile gauze), and/or cooling material (e.g.,
freezer pack, dry ice, or ice).
[0236] In some cases, kits disclosed herein are used in accordance
of any of the disclosed methods.
Panel Development
Study Design and Patient Sample Collection
[0237] 300 total samples were selected for analysis, taken from the
Endoscopy II study performed at the Hvidovre Hospital in Denmark.
In this study, 45-mL blood samples were collected from enrolled
participants across seven different centers prior to performing a
colonoscopy. Blood samples were stored at -80.degree. C. with
constant monitoring. Co-morbidities were recorded by ICD codes, and
pathology, disease, and death reports were retained on file.
Participants entered the study based upon observed symptoms, such
as pain, bleeding, and anemia, which suggested further medical
follow-up. Participants had no prior history of malignancy.
Participants had no previous bowel neoplasia. Participants were not
members of FAP or HNPCC families. Participants had not had a major
operation in the preceding three months. Participants had not
undergone a prior bowel endoscopy.
TABLE-US-00006 TABLE 5 Characteristics of patients enrolled in
study Group Count CRC 512 Colon/Rectal 320/192 Other primary 177
malignancies Adenoma 699 High/Low risk 198/501 Colonic/Rectal
498/201 Benign bowel lesions 1,176 Negative findings, with co-
1,014 morbidity Negative findings, without 1,113 co-morbidity Total
4,698
[0238] Enrolled patients received colonoscopies to diagnosis any
problems associated with the colon and rectum, and the results were
used to confirm the presence or absence of colorectal cancers
and/or polyps. For the biomarker discovery study performed here,
the 302 blood plasma samples selected for analysis comprised 150
control samples that had no comorbidities and no adverse findings
from colonoscopy, and 150 disease samples that had confirmed
colorectal cancer or advanced adenoma lesions in advanced stage.
For this study, advanced colorectal adenomas were defined as having
at least one of the following: any adenoma >=1 cm, sessile
serrated polyps >=1 cm, adenomas with high grade dysplasia, or
adenomas with villous histological features. The control and
disease samples were matched in pairs for age, gender, and
enrollment site (see FIGS. 17A-17B). The 300 samples were further
divided into discovery and validation sets, each with 75 control
samples and 75 disease samples. To more rigorously test the
generalization performance of the investigated biomarker panels in
the validation set, the discovery and validation sets consisted of
patent samples from non-overlapping sites. A summary table of the
samples and their characteristic is provided in Table 7.
Data Preparation
[0239] A total of 300 samples were analyzed using ELISA for 30
different proteins, resulting in a concentration measurement (e.g.
accumulation level) for each of the 30 proteins across the 302
samples. 300 total samples were analyzed using ELISA, targeted
proteomics (TP) and SAT platforms quantifying protein levels for
226 total proteins (ELISA: 30, SAT: 9, TP: 187). An additional mode
of data collection was used, comprising unlabeled liquid
chromatography/mass spectrometry (LCMS) measurements. For the LCMS
data collection, the protein identity of the measured signals is
not known a priori so the resulting measurements are treated as
anonymous marker values, simply referred to with arbitrary ID
numbers and their m/z and LC time locations. Data from these four
assay platforms were analyzed both individually and in combination
with one another to find the top performing biomarker panels within
the discovery set. Unlabeled LCMS features present in the marker
panel included C3218600, having an m/z of 1465.78, an LC time of
14.3 minutes and a charge state 1; C387796, having an m/z 1051.55,
an LC of 3.1 minutes, and a charge state 1; C597612, having an m/z
of 845.44 and an LC of 2.8 minutes and a charge state of 1;
C979276, having m/z 752.91, 20.6 minutes and a charge state of
2.
[0240] After data collection, the concentration values were
prepared in a variety of ways. For some analyses, the concentration
measurements were log 2 transformed, while for others, the
concentration values were left untransformed. Analyses were also
performed on measurements that were both standardized (zero mean,
unit variance) and un-standardized (i.e. original measurements).
For some analyses, age interaction terms were added to the standard
marker concentration values. Here, the product of all age and
marker pairs were calculated and added into the total set of
markers for analysis. In other analyses, the ratios of marker pairs
were calculated and used as new marker values for classification
builds.
Classification Analysis
[0241] The goal of the classification analysis was to determine the
top performing marker panels and classification models that
distinguish between samples with and without colorectal cancer.
Classifier models and the associated classification performance
were assessed using a 10 by 10-fold cross validation procedure. The
10 by 10-fold cross validation was performed using the discovery
set only, and incorporated feature selection and classification
model assembly. In the cross validation procedure, feature
selection was first applied to reduce the number of features used,
followed by development of the classifier model and subsequent
classification performance evaluation. For each of the 10-fold
cross validations, the data were segregated into 10 splits each
containing 90% of the samples as a training set and the remaining
10% of the samples as a testing set. In this process, each sample
was evaluated one time in a test set. The feature selection and
model assembly was performed using the training set only, and these
models were then applied to the testing set to evaluate classifier
performance, typically via the area under the curve (AUC) from the
receiver operating characteristic (ROC) plot. Here, the mean or
median AUC value obtained from each of the 10 10-fold cross
validation procedures was used to assess the overall marker panel
and classification model performance.
[0242] To investigate the performance of different sized marker
panels, a variety of feature selection and reduction methods were
used including Elastic Network feature selection, Random Forest
feature importance ranking, t-test p-value ranking, hierarchical
clustering, and exhaustive combination search. With the exception
of exhaustive combination search, the feature selection methods
were embedded within the individual folds of the cross validation
procedure to incorporate the variability of marker selection into
the final performance assessment for a given classifier model
build. For the exhaustive combination search, all n-choose-r
combinations of features were evaluated, where a particular
combination was selected prior to model building and used across
all the cross validation folds. For both computational feasibility
reasons and to limit the possibility for over-fitting, n and r were
chosen to have relatively small values, with n typically <=30
total markers, and r typically between 2 and 10.
[0243] Within the 10 by 10-fold cross validation folds and after
the feature selection step, a classifier model was built using one
of several classification algorithms including, as examples, the
support vector machine (SVM) algorithm, the Random Forest
algorithm, Elastic Network (ENet) regression models with and
without boosting, k-nearest neighbors (kNN), and combinations of
these models applied in an ensemble. The classification models were
built using established classification modeling packages
implemented in the R statistical programming language. In the case
of the ensemble models, individual classification models were built
using two or more of the described algorithms, and the resulting
classification scores were combined in a linear combination to
obtain a final classification score. Another classification model
approach was also used for some analyses, referred to here as
Status of Univariates (SUn). In the SUn approach, all samples are
initially evaluated using a standard multivariate model as
described above. Next, univariate classification performance from
single markers is used to potentially adjust the multivariate
prediction score. If a particular sample's value for a given single
marker is particularly high or low (i.e. in a score region of 100%
positive or negative predictive value as assessed in the training
set), the sample's probability score is changed to 0 or 1
accordingly. Overall, this approach enables augmentation of the
complex multivariate models with simple high confidence
classification calls based on individual markers.
[0244] After construction of the classifier model on the training
set, it was directly applied without modification to the testing
set resulting in classification scores for the held-out test set
samples. After the completion of a complete 10-fold cross
validation iteration, the test set classification scores from all
the samples were merged into a single dataset or set of values, and
the associated receiver operating characteristic (ROC) curve was
generated. From this ROC, the area under the curve (AUC) was
computed, with one AUC value for each of the 10 iterations of
10-fold cross validation. The mean and median AUC's across the 10
iterations was then used to assess the performance of the
particular classifier assembly process, representing an estimate of
the anticipated hold-out set validation performance utilizing only
the discovery data.
[0245] To investigate the performance of different sized marker
panels, a variety of feature selection and reduction methods were
used including Elastic Network feature selection, Random Forest
feature importance ranking, t-test p-value ranking, hierarchical
clustering, and exhaustive combination search. With the exception
of exhaustive combination search, the feature selection methods
were embedded within the individual folds of the cross validation
procedure to incorporate the variability of marker selection into
the final performance assessment for a given classifier model
build. For the exhaustive combination search, all n-choose-r
combinations of features were evaluated, where a particular
combination was selected prior to model building and used across
all the cross validation folds. For both computational feasibility
reasons and to limit the possibility for over-fitting, n and r were
chosen to have relatively small values, with n typically <=30
total markers, and r typically between 2 and 10.
[0246] Within the 10 by 10-fold cross validation folds and after
the feature selection step, a classifier model was built using one
of several classification algorithms including, as examples, the
support vector machine (SVM) algorithm, the Random Forest
algorithm, Elastic Network (ENet) regression models with and
without boosting, and k-nearest neighbors (kNN). The classification
models were built using established classification modeling
packages implemented in the R statistical programming language.
[0247] After construction of the classifier model on the training
set, it was directly applied without modification to the testing
set resulting in classification scores for the held-out test set
samples. After the completion of a complete 10-fold cross
validation iteration, the test set classification scores from all
the samples were merged into a single set of values and the
associated receiver operating characteristic (ROC) curve was
generated. From this ROC, the area under the curve (AUC) was
computed, with one AUC value for each of the 10 iterations of
10-fold cross validation. The mean and median AUC's across the 10
iterations was then used to assess the performance of the
particular classifier assembly process, representing an estimate of
the anticipated hold-out set validation performance utilizing only
the discovery data.
Classification Model Results
[0248] Utilizing the 10 by 10-fold cross validation procedure
described above, a large number of classifier assembly methods were
evaluated. Of these methods, 10 were selected for validation that
provided the highest classification performance across a range of
different feature selection and classification model methods. To
validate a particular classifier model, a final model was built
using all of the discovery data and the same feature selection and
classifier model methods used in the associated 10 by 10-fold cross
validation procedure. Each final model consisted of a set of
markers and a classification model with associated model
parameters. This model was locked prior to validation and directly
applied to the validation set with no addition tuning. A final ROC
was generated from the validation set classification scores, and
the final validation performance was measured via the AUC with 95%
confidence intervals on the ROC/AUC calculated from a bootstrap
sampling procedure.
[0249] Table 7 provides a summary of the 10 classification models
that were validated. Across the models, the discovery set AUC's
range between 0.81 and 0.86, and the validation AUC's range between
0.75 and 0.82. In all models except model 10, the discovery AUC's
were within the 95% confidence intervals of the validation AUC
indicating good validation was achieved with the selected
models.
[0250] The associated discovery and validation ROC curves are shown
in FIGS. 7A-18. Table 8 gives a summary of the 10 classification
models that were validated. Across the models, the discovery set
AUC's range between 0.81 and 0.86, and the validation AUC's range
between 0.75 and 0.82. In all models except model 10, the discovery
AUC's were within the 95% confidence intervals of the validation
AUC indicating good validation was achieved with the selected
models.
TABLE-US-00007 TABLE 8 Summary of 13 high performing models for CRC
assessment. Validation Input Feature No. of Discovery Validation
AUC Model Data Selection Classifier Features Proteins AUC (95% CI)
1 ELISA-28 + Random Random 7 A1AG1, A1AT, 0.84 0.80 Age Forest
Forest CATD, CEA, (0.73-0.86) Interactions CO9, OSTPxAge, SEPR 2
ELISA-28 GLMNet SVM 17 A1AG1, A1AT, 0.83 0.81 APOA1, CATD,
(0.74-0.88) CEA, CLUS, CO3, CO9, FGB, FIBG, GARS, GELS, MIF, PRDX1,
PSGL, SBP1, SEPR 3 ELISA-28 + GLMNet GLMNet 7 A1AG1, A1AT, 0.82
0.82 TP CATD, CEA, (0.75-0.88) CO9, GARS, SEPR 4 ELISA-28 + GLMNet
GLMBoost 25 A1AG1, A1AT, 0.81 0.81 TP AACT, CATD, (0.74-0.88) CEA,
CO9, CRP, AACT, CO9, CRP, CRP, CRP, CRP, CRP, CRP, GELS, S10A8,
S10A8, S10A8, S10A8, S10A9, S10A9, GARS, SAA1, SEPR 5 ELISA-28
Brute Force SVM 8 CATD, CEA, 0.86 0.82 CO3, CO9, GARS, (0.75-0.88)
GELS, SEPR, TFRC 6 ELISA-28 + Brute Force SVM 5 CATD, CEA, 0.86
0.80 TP AACT, CO9, (0.72-0.86) (Trace SEPR Classifi- cation
Filtered) 7 ELISA-28 + GLMNet + SVM 10 A1AT, C3218600, 0.83 0.81
Unlabeled Top by p- C387796, (0.74-0.88) LCMS Value C597612,
C979276, CATD, CEA, GARS, GELS, SEPR 8 ELISA-28 GLMNet SVM + 18
A1AG1, A1AT, 0.84 0.78 SUn APOA1, CATD, (0.71-0.85) CEA, CLUS, CO3,
CO9, FGB, FIBG, GARS, GELS, HPT, MIF, PRDX1, PSGL, SBP1, SEPR 9
ELISA-28 Random 2 SVM 11 A1AG1, A1AT, 0.85 0.80 (Individual Forest
Models CATD, CEA, (0.73-0.87) Features CO9, SEPR, and Pair
CATD/SEPR, Ratios) CATD/GELS, CO9/SEPR, A1AT/FIBG 10 ELISA-28 + H-
GLMNet 41 H-Clustered 0.85 0.75 TP Clustering + Agglomerated
(0.67-0.82) (Trace GLMNet Features Classifi- cation filtered) +
SAT-29 11 ELISA-28+ Brute SVM 8 CATD, CEA, 0.85 0.815 TP Force,
CO3, CO9, (0.75-0.88) (model 5 GARS S10A8, GELS, with Swap by SEPR,
TFRC GARS Correlation feature swap) 12 ELISA-28 Brute SVM 8 AACT,
CATD, 0.85 0.815 Force, CEA, CO3, CO9, (0.75-0.88) Protein MIF,
PSGL, SEPR Subset 1 13 ELISA-28 Brute SVM 7 A1AG, CATD, 0.86 0.80
Force, CEA, CO3, CO9, (0.73-0.87) Protein GELS, SEPR Subset 2
[0251] Model 1, as referenced in Table 8, included seven proteins
which were A1AG1, A1AT, CATD, CEA, CO9, OSTP, and SEPR. ROC curves
resulting from the discovery set and the validation set for Model 1
are depicted in FIGS. 7A and 7B, respectively. The resulting
discovery set AUC was 0.84 and the validation set AUC was 0.80. At
a validation ROC specificity of 90%, the sensitivity is >50%, at
a specificity of 75%, the sensitivity is >60%, and at a
specificity of 50%, the sensitivity is >80%.
[0252] Model 2, as referenced in Table 8, included seven proteins
which were A1AG1, A1AT, APOA1, CATD, CEA, CLUS, CO3, CO9, FGB,
FIBG, GARS, GELS, MIF, PRDX1, PSGL, SBP1, and SEPR. ROC curves
resulting from the discovery set and the validation set for Model 2
are depicted in FIGS. 8A and 8B, respectively. The resulting
discovery set AUC was 0.83 and the validation set AUC was 0.81. At
a validation ROC specificity of 90%, the sensitivity is about 50%,
at a specificity of 75%, the sensitivity is >60%, and at a
specificity of 50%, the sensitivity is >80%.
[0253] Model 3, as referenced in Table 8, included seven proteins
which were A1AG1, A1AT, CATD, CEA, CO9, GARS, and SEPR. ROC curves
resulting from the discovery set and the validation set for Model 3
are depicted in FIGS. 9A and 9B, respectively. The resulting
discovery set AUC was 0.82 and the validation set AUC was 0.82. At
a validation ROC specificity of 90%, the sensitivity is >50%, at
a specificity of 75%, the sensitivity is >70%, and at a
specificity of 50%, the sensitivity is about 80%.
[0254] Model 4, as referenced in Table 8, included seven proteins
which were A1AG1, A1AT, AACT, CATD, CEA, CO9, CRP, GARS, GELS,
S10A8, S10A9, SAA1, and SEPR. ROC curves resulting from the
discovery set and the validation set for Model 4 are depicted in
FIGS. 10A and 10B, respectively. The resulting discovery set AUC
was 0.81 and the validation set AUC was 0.81. At a validation ROC
specificity of 90%, the sensitivity is about 60%, at a specificity
of 75%, the sensitivity is >70%, and at a specificity of 50%,
the sensitivity is >80%.
[0255] Model 5, as referenced in Table 8, included seven proteins
which were CATD, CEA, CO3, CO9, GARS, GELS, SEPR, and TFRC. ROC
curves resulting from the discovery set and the validation set for
Model 5 are depicted in FIGS. 11A and 11B, respectively. The
resulting discovery set AUC was 0.86 and the validation set AUC was
0.82. At a validation ROC specificity of 90%, the sensitivity is
about 50%, at a specificity of 75%, the sensitivity is >70%, and
at a specificity of 50%, the sensitivity is about 90%.
[0256] Model 6, as referenced in Table 8, included seven proteins
which were CATD, CEA, AACT, CO9, and SEPR. ROC curves resulting
from the discovery set and the validation set for Model 6 are
depicted in FIGS. 12A and 12B, respectively. The resulting
discovery set AUC was 0.86 and the validation set AUC was 0.80. At
a validation ROC specificity of 90%, the sensitivity is >40%, at
a specificity of 75%, the sensitivity is >60%, and at a
specificity of 50%, the sensitivity is >80%.
[0257] Model 7, as referenced in Table 8, included seven proteins
which were A1AT, CATD, CEA, GARS, GELS, and SEPR. ROC curves
resulting from the discovery set and the validation set for Model 7
are depicted in FIGS. 13A and 13B, respectively. The resulting
discovery set AUC was 0.83 and the validation set AUC was 0.81. At
a validation ROC specificity of 90%, the sensitivity is >50%, at
a specificity of 75%, the sensitivity is >60%, and at a
specificity of 50%, the sensitivity is >80%.
[0258] Model 8, as referenced in Table 8, included seven proteins
which were A1AG1, A1AT, APOA1, CATD, CEA, CLUS, CO3, CO9, FGB,
FIBG, GARS, GELS, HPT, MIF, PRDX1, PSGL, SBP1, and SEPR. ROC curves
resulting from the discovery set and the validation set for Model 8
are depicted in FIGS. 14A and 14B, respectively. The resulting
discovery set AUC was 0.84 and the validation set AUC was 0.78. At
a validation ROC specificity of 90%, the sensitivity is >30%, at
a specificity of 75%, the sensitivity is >60%, and at a
specificity of 50%, the sensitivity is >80%.
[0259] Model 9, as referenced in Table 8, included seven proteins
which were A1AG1, A1AT, CATD, CEA, CO9, FIBG, GELS, and SEPR. ROC
curves resulting from the discovery set and the validation set for
Model 9 are depicted in FIGS. 15A and 15B, respectively. The
resulting discovery set AUC was 0.85 and the validation set AUC was
0.80. At a validation ROC specificity of 90%, the sensitivity is
>50%, at a specificity of 75%, the sensitivity is >60%, and
at a specificity of 50%, the sensitivity is about 80%.
[0260] Model 11, as referenced in Table 8, included seven proteins
which were CATD, CEA, CO3, CO9, S10A8, GELS, SEPR, TFRC. The
resulting discovery set AUC was 0.85 and the validation set AUC was
0.82.
[0261] Model 12, as referenced in Table 8, included seven proteins
which were AACT, CATD, CEA, CO3, CO9, MIF, PSGL, SEPR. The
resulting discovery set AUC was 0.85 and the validation set AUC was
0.82.
[0262] Model 13, as referenced in Table 8, included seven proteins
which were A1AG, CATD, CEA, CO3, CO9, GELS, SEPR. The resulting
discovery set AUC was 0.86 and the validation set AUC was 0.80,
[0263] Models 4 and 6 incorporated data from the targeted
proteomics platform, and therefore included measurements from
transition ions from specific peptides from the underlying protein
measurements. The transitions used in these models are given in
Table 9.
TABLE-US-00008 TABLE 9 Transition ions from specific peptides SEQ
Model ID Number Protein Peptide NO: Transition 4 AACT ADLSGITGAR 50
b3 4 CO9 TEHYEEQIEAFK 51 y2 4 CRP ESDTSYVSLK 52 y3 4 CRP ESDTSYVSLK
52 y5 4 CRP GYSIFSYATK 53 y7 4 CRP GYSIFSYATK 53 y8 4 CRP KAFVFPK
54 y5 4 CRP KAFVFPK 54 y6 4 GELS AGALNSNDAFVLK 55 b4 4 S10A8
ALNSIIDVYHK 56 y6 4 S10A8 ALNSIIDVYHK 56 y7 4 S10A8 GADVWFK 57 b3 4
S10A8 GADVWFK 57 y5 4 S10A9 DLQNFLK 58 y5 4 S10A9 LGHPDTLNQGEFK 59
y10 6 AACT GKITDLIK 60 y5 6 CO9 TEHYEEQIEAFK 51 y2
[0264] Of the ten models, model 5 is of particular note because of
the high discovery AUC of 0.86 and associated high validation AUC
of 0.82. This model comprises 8 individual proteins all from a
single assay platform (ELISA), facilitating the measurement of this
marker panel for clinical applications.
[0265] Model 3 is also of interest because of the high validation
AUC of 0.82, though the discovery AUC was slightly lower, also at
0.82. Though targeted proteomics markers were included as input to
this model, only ELISA markers were selected in the final model.
This panel is also slightly smaller, comprising 5 proteins.
[0266] While preferred embodiments of the present invention have
been shown and described herein, it will be obvious to those
skilled in the art that such embodiments are provided by way of
example only. Numerous variations, changes, and substitutions will
now occur to those skilled in the art without departing from the
invention. It should be understood that various alternatives to the
embodiments of the invention described herein may be employed in
practicing the invention. It is intended that the following claims
define the scope of the invention and that methods and structures
within the scope of these claims and their equivalents be covered
thereby.
Incorporation of Indeterminate Classification Calls (NoC
Method)
[0267] The intrinsic performance of a particular classification
model depends on the distributions and separation of model scores
for the two classes. With the rare exception of perfect class
separation, most classification models make mistakes because of
class overlap across the range of classifier scores. For example,
such an overlap may occur near the middle of the score range where
the probability of being in one class or the other is close to
50%.
[0268] Within such an overlap region, it may be advantageous to add
a third class to the final set of classification calls; the third
class would indicate the uncertainty of a call in this score
region. This could be implemented, for example, by defining an
indeterminate region of classification scores. Samples with scores
in this region would be given an "indeterminate" or "no call" test
result. Samples with scores above or below this region would be
given standard positive or negative test results depending on their
positions relative to the test cutoff. The benefit of adding an
indeterminate region to a classification model is that
classification performance can improve for samples outside of the
indeterminate region, i.e. mistakes are less likely for the
remaining positive and negative tests. However, if the
indeterminate range is too large, there may be too many
indeterminate results, and the value of the test may be put into
question.
[0269] In another analysis, referred to here as NoC ("No Call"),
the effect of using an indeterminate region with the classification
models was investigated. In this analysis, the percentage of
samples targeted to receive a "no call" result was set to 10%. To
determine the optimal score range for the indeterminate region (NoC
region) with 10% of the samples, the specificity was maximized at a
sensitivity of >=90% as follows: All possible contiguous sets of
10% of samples were determined across the classifier scores range.
For each set, the associated set of 10% of samples were marked as
no calls. These samples were removed from the analysis set and the
ROC curve was generated from the remaining 90% of the samples. The
maximum specificity at >=90% sensitivity was then determined and
used as the evaluation score for the NoC region in question. After
all NoC regions were evaluated in this manner, the region with the
highest specificity score was selected as the optimal NoC region.
The score range defining this NOC region was taken from the upper
and lower classification scores of the associated 10% no call
samples.
[0270] To predict how the NoC procedure would affect classification
performance in the hold-out validation set, the analysis was
performed within the 10 by 10-fold cross validation assessment of
model 5 described above. Like all previous model builds, only the
discovery set was used in this assessment. The resulting median AUC
determined from this 10 by 10-fold validation procedure was 0.87,
slightly higher than the original discovery AUC of 0.86 without the
application of NoC, suggesting the NoC procedure could be
beneficial to employ in practice.
[0271] A final NoC region was determined by using the same NoC
procedure described above on all of the discovery samples. This
yielded a NoC region encompassing scores between 0.298 and 0.396.
This NoC region was applied directly to the validation set with 20
samples (13.3%) falling within the region (10 disease, 10 control).
The ROC determined from the remaining validation samples yielded an
AUC of 0.85 (95% CI's: 0.78-0.91), an improvement of 0.03 over the
validation ROC without application of NoC. The results from the NoC
analysis are given in Table 10 and the discovery and validation ROC
data in FIGS. 17A-17B.
TABLE-US-00009 TABLE 10 Summary of Model 5 with subset of samples
categorized as indeterminate # of # of Samples Samples NoC in NoC
Discovery Discovery in NoC Validation Validation Score Region AUC
AUC w/ Region AUC w/o AUC w/ Model Region Discovery w/o NoC NoC
Validation NoC NoC 5 0.298- 15 0.86 0.87 20 0.82 0.85 0.396
[0272] Comparing the ROC curves with and without NOC applied, NoC
improved performance most in the region around 80%--60%
specificity. With NOC, a clear improvement in sensitivity is
apparent. In particular, the point at 85% sensitivity and 78%
specificity is of interest because of the good overall performance
for both sensitivity and specificity.
Selection of Classifier Cutoff Points
[0273] The overall performance of a classifier can be assessed via
the AUC of the ROC as reported above. An ROC considers the
performance of the classifier at all possible model score cutoff
points. However, when a classification decision needs to be made
(i.e. is this patient sick or healthy?), a cutoff point must be
used to define the two groups. Classification scores at or above
the cutoff point are assessed as positive (or sick) while points
below are assessed as negative (or healthy).
[0274] For the 10 classification models and the single model with
NoC applied, summarized above, classification score cutoff points
were established by selecting the point of maximum accuracy on the
validation ROC's. The point of maximum accuracy on an ROC is the
cutoff point or points for which the total number of correct
classification calls is maximized. Here, the positive and negative
classification calls were weighted equally. In cases where multiple
maximum accuracy points were present on a given ROC, the point with
the associated maximum sensitivity was selected.
[0275] The results for the cutoff point selection process are
summarized in Table 11 and FIG. 13. The cutoff scores selected are
representative of the type of score output by the associated model.
For some models, the resulting classification score represents a
probability and the scores span 0-1. For other models, e.g. Model
10, the classification score is simply a score, with larger scores
more likely to represent CRC patients. In these cases, the cutoff
score can be greater than 1.
TABLE-US-00010 TABLE 11 Cutoff points for classification of a
subject for colorectal cancer biomarker panels Model # Sensitivity
Specificity Accuracy Cutoff 1 0.63 0.87 0.75 0.60 2 0.68 0.83 0.75
0.56 3 0.72 0.84 0.78 0.54 4 0.69 0.85 0.77 0.51 5 0.73 0.81 0.77
0.62 5 w/NoC 0.85 0.78 0.82 0.62 6 0.80 0.65 0.73 0.41 7 0.61 0.88
0.75 0.66 8 0.77 0.69 0.73 0.44 9 0.65 0.83 0.74 1.07 10 0.65 0.76
0.71 8.69
Advanced Adenoma Panel Combination
[0276] Advanced colorectal adenoma and CRC are assayed in parallel
in some cases as described herein. For example a panel for
colorectal cancer and a panel for advanced adenoma, having a single
biomarker overlap at CATD, are measured in combination. In these
embodiments a panel for diagnosing advance adenoma may be derived
using the methods previously disclosed. One panel for assessing a
risk for advanced adenoma, and variants as disclosed herein was
derived using the steps of classification analysis from previous
studies including the classification analysis on samples taken from
the Endoscopy II study.
[0277] For advanced adenoma biomarker discovery with the Endoscopy
II study, 302 samples selected for analysis comprised 151 control
samples that had no comorbidities and no adverse findings from
colonoscopy, and 151 disease samples that had confirmed colon or
rectal adenoma lesions in advanced stage. For this study, advanced
colorectal adenomas were defined as having at least one of the
following: any adenoma >=1 cm, sessile serrated polyps >=1
cm, adenomas with high grade dysplasia, or adenomas with villous
histological features. The control and disease samples were matched
in pairs for age, gender, and enrollment site. The 302 samples were
further divided into discovery and validation sets, with 75 control
and 75 advanced colorectal adenoma samples in the discovery set,
and 76 control and 76 advanced colorectal adenomas samples in the
validation set. To more rigorously test the generalization
performance of the investigated biomarker panels in the validation
set, the discovery and validation sets consisted of patient samples
from non-overlapping sites. A summary table of the samples and
their characteristics is provided in Table 12.
[0278] For data preparation, the 302 total samples were analyzed
using ELISA assays for 30 different proteins, resulting in a
concentration measurement (e.g. accumulation level) for each of the
30 proteins across the 302 samples. After data collection, the
concentration values were prepared in a variety of ways. For some
analyses, the concentration measurements were log 2 transformed,
while for others, the concentration values were left untransformed.
Analyses were also performed on measurements that were both
standardized (zero mean, unit variance) and un-standardized (i.e.
original measurements).
[0279] Classification analysis was also performed. The goal of the
classification analysis was to determine the top performing marker
panels and classification models that distinguish between samples
with and without advanced adenomas. Classifier models and the
associated classification performance were assessed using a 10 by
10-fold cross validation procedure. The 10 by 10-fold cross
validation was performed using the discovery set only, and
incorporated feature selection and classification model assembly.
In the cross validation procedure, feature selection was first
applied to reduce the number of features used, followed by
development of the classifier model and subsequent classification
performance evaluation. For each of the 10-fold cross validations,
the data were segregated into 10 splits each containing 90% of the
samples as a training set and the remaining 10% of the samples as a
testing set. In this process, each sample was evaluated one time in
a test set. The feature selection and model assembly was performed
using the training set only, and these models were then applied to
the testing set to evaluate classifier performance, typically via
the area under the curve (AUC) from the receiver operating
characteristic (ROC) plot. Here, the mean or median AUC value
obtained from each of the 10 10-fold cross validation procedures
was used to assess the overall marker panel and classification
model performance.
[0280] To investigate the performance of different sized marker
panels, a variety of feature selection and reduction methods were
used including Elastic Network feature selection, Random Forest
feature importance ranking, t-test p-value ranking, hierarchical
clustering, and exhaustive combination search. With the exception
of exhaustive combination search, the feature selection methods
were embedded within the individual folds of the cross validation
procedure to incorporate the variability of marker selection into
the final performance assessment for a given classifier model
build. For the exhaustive combination search, all n-choose-r
combinations of features were evaluated, where a particular
combination was selected prior to model building and used across
all the cross validation folds. For both computational feasibility
reasons and to limit the possibility for over-fitting, n and r were
chosen to have relatively small values, with n typically <=30
total markers, and r typically between 2 and 10.
[0281] Within the 10 by 10-fold cross validation folds and after
the feature selection step, a classifier model was built using one
of several classification algorithms including, as examples, the
support vector machine (SVM) algorithm, the Random Forest
algorithm, Elastic Network (ENet) regression models with and
without boosting, and k-nearest neighbors (kNN). The classification
models were built using established classification modeling
packages implemented in the R statistical programming language.
[0282] After construction of the classifier model on the training
set, it was directly applied without modification to the testing
set resulting in classification scores for the held-out test set
samples. After the completion of a complete 10-fold cross
validation iteration, the test set classification scores from all
the samples were merged into a single set of values and the
associated receiver operating characteristic (ROC) curve was
generated. From this ROC, the area under the curve (AUC) was
computed, with one AUC value for each of the 10 iterations of
10-fold cross validation. The mean and median AUC's across the 10
iterations was then used to assess the performance of the
particular classifier assembly process, representing an estimate of
the anticipated hold-out set validation performance utilizing only
the discovery data.
[0283] The classification model results were analyzed. Utilizing
the 10 by 10-fold cross validation procedure described above, a
large number of classifier assembly methods were evaluated. Of
these methods, one was selected for validation that provided the
highest classification performance across a range of different
feature selection and classification model methods. To validate
this classifier model, a final model was built using all of the
discovery data and the same feature selection and classifier model
methods used in the associated 10 by 10-fold cross validation
procedure. The final model consisted of a set of markers and a
classification model with associated model parameters. This model
was locked prior to validation and directly applied to the
validation set with no addition tuning A final ROC was generated
from the validation set classification scores, and the final
validation performance was measured via the AUC with 95% confidence
intervals on the ROC/AUC calculated from a bootstrap sampling
procedure.
[0284] In sum, the AA model demonstrated the following parameters.
The model consisted of 4 protein measurements from CATD, CLUS,
GDF15 and SAA1. The median discovery AUC was 0.77 and AUC
performance in the validation set was 0.65. Despite the AUC drop
from discovery to validation, the 95% confidence intervals on the
ROC were 0.56 to 0.74 indicating that the model provides
classification discrimination significantly above random
performance. The input data was ELISA-30 input and the classifier
used was KNN.
[0285] The overall performance of a classifier is assessed in some
cases via the AUC of the ROC as reported herein. An ROC considers
the performance of the classifier at all possible model score
cutoff points. However, when a classification decision needs to be
made (e.g., is this patient sick or healthy?), a cutoff point is
used to define the two groups. Classification scores at or above
the cutoff point are assessed as positive (or sick) while points
below are assessed as negative (or healthy) in various
embodiments.
[0286] For some classification models disclosed herein, a
classification score cutoff point is established by selecting the
point of maximum accuracy on the validation ROC. The point of
maximum accuracy on an ROC is the cutoff point or points for which
the total number of correct classification calls is maximized.
Here, the positive and negative classification calls are weighted
equally. In cases where multiple maximum accuracy points are
present on a given ROC, the point with the associated maximum
sensitivity is selected in some cases. For some AA panels herein,
the following parameters were observed: sensitivity of 0.83,
specificity of 0.45, accuracy of 0.64 and a cutoff of 0.25. For
some AA panels herein, the following parameters were observed:
sensitivity of 0.80 and specificity of 0.50.
Additional Reference to Figures
[0287] The disclosure herein is delineated throughout the
specification and claims appended herewith, supported by the
figures. Referring to the figures in more detail, one observes the
following.
[0288] FIG. 1 depicts a workflow pipeline for the development of a
lead CRC biomarker panel. In box 1, at top, 28 best proteins are
identified using a targeted-mass spectrometry platform from 187
candidates compiled from literature. In box 2, a CRC test panel of
8 proteins is identified via machine-learning in an unbiased,
case-control study using ELISA. In box 3, age as a biomarker is
added to model as a parameter using a CRC vs. no comorbidities-no
findings, case-control subset. In box 4, indeterminate call
boundaries are added to the model using an intent-to-test patient
subset. In box 5, at bottom, the 8 protein plus age classifier is
validated using an intent-to-test patient subset.
[0289] FIG. 2 depicts a CRC panel AUC. The X axis indicates
Specificity, at intervals of 20%, from 100% to 0%. The Y axis
indicates Sensitivity, at intervals of 20%, from 0% to 100%. The
slope along the diagonal indicates a 50% sensitivity and 50%
Specificity. Shaded areas indicate the 95% confidence interval for
the graph. The dark curve indicates performance for the nine-member
CRC panel comprising the proteins AACT, CO3, CO9, MIF, PSGL, CATD,
CEA and SEPR, and the non-protein biomarker of age. The AUC
position corresponding to 81% sensitivity and 78% specificity is
indicated. The performance is assessed using a 20% targeted
indeterminate rate in discovery and a 15% validated indeterminate
rate.
[0290] Our study indicated that there was no significant difference
in early verses late CRC performance. For CRC Stage I-II, there
were 15 true values verses 5 false values with a sensitivity of
0.75. For CRC Stage there were 15 true values verses 2 false values
with a sensitivity of 0.88. The average for both CRC Stage I-II
results and CRC Stage III-IV results was 15 true values and 7 false
values with a sensitivity of 0.81. The Fisher's Test p-value for
this CRC stage assay was 0.415, and the Chi-Square Test p-value was
0.546. No preferential class of samples was excluded in the
indeterminate call group. Our study results indicated that for the
no call group (NoC), the CRC class had 5 true verses 37 false. The
Non-CRC class had 51 true verses 280 false. The average of the CRC
class and nonCRC class NoC groups was 56 true verses 317 false. For
the NoC group, the Fisher's Test p-value for this assay was 0.652,
and the Chi-Square Test p-value was 0.712.
[0291] FIG. 3 depicts an AA panel AUC. The X axis indicates
1-Specificity, at intervals of 0.2, from 0.0 to 1.0. The Y axis
indicates Sensitivity, at intervals of 0.2, from 0.0 to 1.0. The
slope at x=y indicates a 50% sensitivity and 50% (1-Specificity).
Shaded areas indicate the 95% confidence interval for the graph.
The dark curve indicates performance for the four-member panel,
while the light grey lines indicate performance of
constituents.
[0292] FIG. 4 presents validation data for the CRC panel of FIG. 2.
The CRC panel is developed on a `Discovery 1` sample collection,
labeled `a`. The CRC panel is then re-derived and validated on a
second sample set, divided into `Discovery 2,` labeled `b,` and a
`Validation` population, labeled `c`. As seen in FIG. 4, counts for
columns b and c do not differ significantly for any given category.
This indicates that the CRC panel, as generated in the Discovery 1
set and recovered in the Discovery 2 set, for a given category, was
reliably validated. The close correlation between the discovery 2
and Validation results is an indication of the repeatability of the
test. Columns are labeled, left to right, as follows: Colon cancer,
Rectal Cancer, No comorbidity--No finding, Adenoma--colon,
Adenoma-rectum, Comorbidity--no finding, Other indication, and
Other cancer.
[0293] FIG. 4 demonstrates that the CRC panel tested distinguishes
not only between CRC and healthy samples generally, but between CRC
and non-CRC samples, even those having other types of cancers.
Accordingly, FIG. 4 demonstrates that CRC panels disclosed herein
distinguish CRC from non-CRC as indicated in circulating blood
samples, even in samples from individuals suffering from other
cancers.
[0294] FIG. 5 depicts Protein levels for CRC and healthy control
samples for protein markers relevant to the panels herein. For each
protein, the left or upper boxplot range indicates the control
sample population protein level, and the right or lower boxplot
indicates the CRC positive sample population protein level. Log 2
(concentration) ranges from 2-20 across the top of the image.
Proteins discussed herein are listed across the left side of the
image. The proteins in order are A1AG1, A1AT, AACT, ANAX1, APOA1,
CAH1, CATD, CEA, CLUS, CO3, CO9, CRP, DPP4, FGB, FIBG, GARS, GDF15,
GELS, HPT, MIF, OSTP, PKM, PRDX1, PSGL, SAA1, SBP1, SEPR, TFF3,
TFRC, and TIMP1. FIG. 5 demonstrates that individual markers often
do not vary substantially between CRC and healthy control samples,
emphasizing the synergistic improvement of the biomarker panels as
presented herein over their individual biomarker constituents.
[0295] FIG. 6 depicts Protein levels for AA and healthy control
samples for protein markers relevant to the panels herein. For each
protein, the left or upper boxplot range indicates the control
sample population protein level, and the right or lower boxplot
indicates the CRC positive sample population protein level. Log 2
(concentration) ranges from 2-20 across the top of the image.
Proteins discussed herein are listed across the left side of the
image. The proteins in order are A1AG1, A1AT, AACT, ANAX1, APOA1,
CAH1, CATD, CEA, CLUS, CO3, CO9, CRP, DPP4, FGB, FIBG, GARS, GDF15,
GELS, HPT, MIF, OSTP, PKM, PRDX1, PSGL, SAA1, SBP1, SEPR, TFF3,
TFRC, and TIMP1. FIG. 5 demonstrates that individual markers often
do not vary substantially between AA and healthy control samples,
emphasizing the synergistic improvement of the biomarker panels as
presented herein over their individual biomarker constituents.
[0296] FIGS. 7A-16B present Discovery and Validation AUC plots for
Panel Models 1-10 as presented herein. For each figure, the X axis
indicates Specificity, at intervals of 20%, from 0% to 100%, or
alternately 1-Specificity, at intervals of 0.2, from 0.0 to 1.0.
The Y axis indicates Sensitivity, at intervals of 20%, from 0% to
100%. The slope along the diagonal indicates a 50% sensitivity and
50% Specificity. The box-plot indicated the 95% confidence interval
for the graph.
[0297] Model 1 included A1AG1, A1AT, CATD, CEA, CO9, OSTP, and
SEPR. ROC curves resulting from the discovery set and the
validation set for Model 1 are depicted in FIGS. 7A and 7B,
respectively. The resulting discovery set AUC was 0.84 and the
validation set AUC was 0.80. At a validation ROC specificity of
90%, the sensitivity is >50%, at a specificity of 75%, the
sensitivity is >60%, and at a specificity of 50%, the
sensitivity is >80%. Model 2 included A1AG1, A1AT, APOA1, CATD,
CEA, CLUS, CO3, CO9, FGB, FIBG, GARS, GELS, MIF, PRDX1, PSGL, SBP1,
and SEPR. ROC curves resulting from the discovery set and the
validation set for Model 2 are depicted in FIGS. 8A and 8B,
respectively. The resulting discovery set AUC was 0.83 and the
validation set AUC was 0.81. At a validation ROC specificity of
90%, the sensitivity is about 50%, at a specificity of 75%, the
sensitivity is >60%, and at a specificity of 50%, the
sensitivity is >80%. Model 3 included A1AG1, A1AT, CATD, CEA,
CO9, GARS, and SEPR. ROC curves resulting from the discovery set
and the validation set for Model 3 are depicted in FIGS. 9A and 9B,
respectively. The resulting discovery set AUC was 0.82 and the
validation set AUC was 0.82. At a validation ROC specificity of
90%, the sensitivity is >50%, at a specificity of 75%, the
sensitivity is >70%, and at a specificity of 50%, the
sensitivity is about 80%. Model 4 included A1AG1, A1AT, AACT, CATD,
CEA, CO9, CRP, GARS, GELS, S10A8, S10A9, SAM, and SEPR. ROC curves
resulting from the discovery set and the validation set for Model 4
are depicted in FIGS. 10A and 10B, respectively. The resulting
discovery set AUC was 0.81 and the validation set AUC was 0.81. At
a validation ROC specificity of 90%, the sensitivity is about 60%,
at a specificity of 75%, the sensitivity is >70%, and at a
specificity of 50%, the sensitivity is >80%. Model 5 included
CATD, CEA, CO3, CO9, GARS, GELS, SEPR, and TFRC. ROC curves
resulting from the discovery set and the validation set for Model 5
are depicted in FIGS. 11A and 11B, respectively. The resulting
discovery set AUC was 0.86 and the validation set AUC was 0.82. At
a validation ROC specificity of 90%, the sensitivity is about 50%,
at a specificity of 75%, the sensitivity is >70%, and at a
specificity of 50%, the sensitivity is about 90%. Model 6 included
seven proteins which were CATD, CEA, AACT, CO9, and SEPR. ROC
curves resulting from the discovery set and the validation set for
Model 6 are depicted in FIGS. 12A and 12B, respectively. The
resulting discovery set AUC was 0.86 and the validation set AUC was
0.80. At a validation ROC specificity of 90%, the sensitivity is
>40%, at a specificity of 75%, the sensitivity is >60%, and
at a specificity of 50%, the sensitivity is >80%. Model 7, as
referenced in Table 5 included seven proteins which were A1AT,
CATD, CEA, GARS, GELS, and SEPR. ROC curves resulting from the
discovery set and the validation set for Model 7 are depicted in
FIGS. 13A and 13B, respectively. The resulting discovery set AUC
was 0.83 and the validation set AUC was 0.81. At a validation ROC
specificity of 90%, the sensitivity is >50%, at a specificity of
75%, the sensitivity is >60%, and at a specificity of 50%, the
sensitivity is >80%. Model 8, as referenced in Table 5, included
A1AG1, A1AT, APOA1, CATD, CEA, CLUS, CO3, CO9, FGB, FIBG, GARS,
GELS, HPT, MIF, PRDX1, PSGL, SBP1, and SEPR.
[0298] ROC curves resulting from the discovery set and the
validation set for Model 8 are depicted in FIGS. 14A and 14B,
respectively. The resulting discovery set AUC was 0.84 and the
validation set AUC was 0.78. At a validation ROC specificity of
90%, the sensitivity is >30%, at a specificity of 75%, the
sensitivity is >60%, and at a specificity of 50%, the
sensitivity is >80%. Model 9 included A1AG1, A1AT, CATD, CEA,
CO9, FIBG, GELS, and SEPR. ROC curves resulting from the discovery
set and the validation set for Model 9 are depicted in FIGS. 15A
and 15B, respectively. The resulting discovery set AUC was 0.85 and
the validation set AUC was 0.80. At a validation ROC specificity of
90%, the sensitivity is >50%, at a specificity of 75%, the
sensitivity is >60%, and at a specificity of 50%, the
sensitivity is about 80%. Model 10 curves resulting from the
discovery set and the validation set for Model 10 are depicted in
FIGS. 16A and 16B, respectively. The resulting discovery set AUC
was 0.85 and the validation set AUC was 0.75.
[0299] FIGS. 17A-17B depict an alternate analysis of Model 5 using
`NOC` analysis. The X axis indicates Specificity, at intervals of
20%, from 100% to 0%. The Y axis indicates Sensitivity, at
intervals of 20%, from 0% to 100%. The slope along the diagonal
indicates a 50% sensitivity and 50% Specificity. The box-plot
indicated the 95% confidence interval for the graph.
[0300] In this analysis, referred to here as NoC ("No Call"), the
effect of using an indeterminate region with the classification
models was investigated. In this analysis, the percentage of
samples targeted to receive a "no call" result was set to 10%. To
determine the optimal score range for the indeterminate region (NoC
region) with 10% of the samples, the specificity was maximized at a
sensitivity of >=90% as follows: All possible contiguous sets of
10% of samples were determined across the classifier scores range.
For each set, the associated set of 10% of samples were marked as
no calls. These samples were removed from the analysis set and the
ROCcurve was generated from the remaining 90% of the samples. The
maximum specificity at >=90% sensitivity was then determined and
used as the evaluation score for the NoC region in question. After
all NoC regions were evaluated in this manner, the region with the
highest specificity score was selected as the optimal NoC region.
The score range defining this NOC region was taken from the upper
and lower classification scores of the associated 10% no call
samples. To predict how the NoC procedure would affect
classification performance in the hold-out validation set, the
analysis was performed within the 10 by 10-fold cross validation
assessment of model 5 described above. Like all previous model
builds, only the discovery set was used in this assessment. The
resulting median AUC determined from this 10 by 10-fold validation
procedure was 0.87, slightly higher than the original discovery AUC
of 0.86 without the application of NoC, suggesting the NoC
procedure could be beneficial to employ in practice.
[0301] A final NoC region was determined by using the same NoC
procedure described above on all of the discovery samples. This
yielded a NoC region encompassing scores between 0.298 and 0.396.
This NoC region was applied directly to the validation set with 20
samples (13.3%) falling within the region (10 disease, 10 control).
The ROC determined from the remaining validation samples yielded an
AUC of 0.85 (95% CI's: 0.78-0.91), an improvement of 0.03 over the
validation ROC without application of NoC.
[0302] Comparing the ROC curves with and without NOC applied, NoC
improved performance most in the region around 80%--60%
specificity. With NOC, a clear improvement in sensitivity is
apparent. In particular, the point at 85% sensitivity and 78%
specificity is of interest because of the good overall performance
for both sensitivity and specificity.
[0303] FIG. 17B depicts further NOC analysis results. The X axis
indicates 1-Specificity, at intervals of 0.2, from 0.0 to 1.0. The
Y axis indicates Sensitivity, at intervals of 0.2, from 0.0 to 1.0.
The slope at x=y indicates a 50% sensitivity and 50%
(1-Specificity). Shaded areas indicate the 95% confidence interval
for the graph. The dark curve indicates performance for the
four-member panel, while the light grey lines indicate performance
of constituents.
[0304] FIG. 18 depicts Sensitivity and Specificity for Models 1-10
at the point of their AUCs corresponding to Maximum Accuracy.
Sensitivity, on the Y axis, ranges from 0-1 in intervals of 0.25.
The X axis depicts 1-Specificity, ranging from 0 to 1 in intervals
of 0.25. Models 1-10 are labeled a-k, respectively.
[0305] FIG. 19 depicts a Computer System consistent with the
methods, systems, kits and compositions disclosed herein.
[0306] FIG. 20 depicts AUC values for randomly generated panels
from a biomarker set enriched to be predictive of CRC. The mean and
median AUC values are well below those of the CRC panels disclosed
herein.
NUMBERED EMBODIMENTS
The disclosure is further understood through review of the numbered
embodiments recited herein. 1. An ex vivo method of assessing a
colorectal cancer risk status in a blood sample of an individual,
comprising the steps of obtaining a circulating blood sample from
the individual; obtaining a biomarker panel level for a biomarker
panel comprising a list of proteins in the sample comprising AACT,
CO3, CO9, MIF, and PSGL to comprise panel information from said
individual; comparing said panel information from said individual
to a reference panel information set corresponding to a known
colorectal cancer status; and categorizing said individual as
having said colorectal cancer risk status if said individual's
reference panel information does not differ significantly from said
reference panel information set. 2. The method of embodiment 1,
wherein obtaining a circulating blood sample comprises drawing
blood from a vein or artery of the individual. 3. The method of any
one of embodiments 1-2, wherein the panel information comprises age
information for the individual. 4. The method of any one of
embodiments 1-3, wherein the list of proteins comprises AACT, CO3,
CO9, MIF, PSGL, CATD, CEA and SEPR. 5. The method of any one of
embodiments 1-4, wherein the list of proteins comprises no more
than 15 proteins. 6. The method of any one of embodiments 1-5,
wherein the list of proteins comprises no more than 8 proteins. 7.
The method of any one of embodiments 1-6, wherein the list of
proteins comprises AACT, CO3, CO9, MIF, PSGL, CATD, CEA and SEPR.
8. The method of any one of embodiments 1-7, wherein the
categorizing has a sensitivity of at least 81% and a specificity of
at least 78%. 9. The method of any one of embodiments 1-8,
comprising transmitting a report of results of said categorizing a
health practitioner. 10. The method of any one of embodiments 1-9,
wherein the report indicates a sensitivity of at least 81%. 11. The
method of any one of embodiments 1-9, wherein the report indicates
a specificity of at least 78%. 12. The method of any one of
embodiments 1-9, wherein the report recommends that a colonoscopy
be performed. 13. The method of any one of embodiments 1-12,
comprising performing a colonoscopy on the individual. 14. The
method of any one of embodiments 1-9, wherein the report recommends
an independent surgical intervention. 15. The method of any one of
embodiments 1-14, comprising performing an independent surgical
intervention on the individual. 16. The method of any one of
embodiments 1-9, wherein the report recommends undergoing an
independent cancer assay. 17. The method of any one of embodiments
1-16, comprising performing an independent cancer assay on the
individual. 18. The method of any one of embodiments 1-9, wherein
the report recommends undergoing a stool cancer assay. 19. The
method of any one of embodiments 1-18, comprising performing a
stool cancer assay. 20. The method of any one of embodiments 1-9,
wherein the report recommends administering an anticancer
composition. 21. The method of any one of embodiments 1-18,
comprising administering an anticancer composition. 22. The method
of any one of embodiments 1-9, wherein the report recommends
continued monitoring. 23. The method of any one of embodiments
1-22, wherein at least one biomarker level of said individual's
panel information differs significantly from a corresponding value
from said reference panel, and wherein said individual's panel
level as a whole does not differ significantly from said reference
panel level. 24. The method of any one of embodiments 1-23, wherein
no parameter of said individual's reference panel information in
isolation is indicative of said colorectal cancer status in said
individual at a sensitivity of greater than 65% or a specificity of
greater than 65%. 25. The method of any one of embodiments 1-24,
wherein the obtaining protein levels comprises contacting a
fraction of the circulating blood sample to a set of antibodies,
wherein the set of antibodies comprises antibodies specific to
AACT, CO3, CO9, MIF, and PSGL. 26. The method of any one of
embodiments 1-25, wherein the obtaining protein levels comprises
subjecting a fraction of the circulating blood sample to a mass
spectrometric analysis. 27. The method of any one of embodiments
1-26, wherein at least one of said comparing and said categorizing
is performed on a computer configured to analyze reference panel
information. 28. The method of any one of embodiments 1-27, wherein
said reference panel information set corresponding to a known
colorectal cancer status comprises a product of a machine learning
model. 29. The method of any one of embodiments 1-28, wherein the
machine learning model is trained using at least 100 biomarker
panels corresponding to known colorectal health status. 30. An ex
vivo method of monitoring efficacy of a colorectal cancer treatment
in an individual, comprising the steps of obtaining a first sample
comprising circulating blood from the individual at a first time
point; obtaining a second sample comprising circulating blood from
the same individual receiving a colorectal cancer treatment at a
second time point; obtaining a first panel level comprising protein
levels for a list of proteins in the first sample and a second
panel level comprising protein levels for a list of proteins in the
second sample, said list comprising AACT, CO3, CO9, MIF, and PSGL
to comprise panel information for said first sample and said second
sample; wherein a change in protein levels indicates efficacy of
the colorectal cancer treatment. 31. The method of embodiment 30,
wherein obtaining the first sample comprises drawing blood from a
vein or artery of the individual. 32. The method of any one of
embodiments 30-31, wherein the colorectal cancer treatment
comprises administration of a pharmaceutical composition. 33. The
method of any one of embodiments 30-32, wherein the colorectal
cancer treatment comprises administration of a chemotherapeutic
agent. 34. The method of any one of embodiments 30-33, wherein the
colorectal cancer treatment comprises a colonoscopy. 35. The method
of any one of embodiments 30-34, wherein the colorectal cancer
treatment comprises a polypectomy. 36. The method of any one of
embodiments 30-35, wherein the colorectal cancer treatment
comprises radiotherapy. 37. The method of any one of embodiments
30-36, comprising comparing said first sample panel level and said
second panel level to at least one panel level of a healthy
reference, wherein the second sample panel level being more similar
to the panel level of the healthy reference indicates efficacy of
the colorectal cancer treatment. 38. The method of any one of
embodiments 30-37, comprising said first sample panel level and
said second panel level to at least one panel level of a healthy
reference, wherein the first sample panel level being more similar
to the panel level of the colorectal cancer reference indicates
efficacy of the colorectal cancer treatment. 39. The method of any
one of embodiments 30-38, wherein the list of proteins comprises
AACT, CO3, CO9, MIF, PSGL, CATD, CEA and SEPR. 40. The method of
any one of embodiments 30-39, wherein the list of proteins
comprises no more than 15 proteins. 41. The method of any one of
embodiments 30-40, wherein the list of proteins comprises no more
than 8 proteins. 42. The method of any one of embodiments 30-41,
wherein the list of proteins comprises AACT, CO3, CO9, MIF, PSGL,
CATD, CEA and SEPR. 43. The method of any one of embodiments 30 to
42, comprising changing the colorectal cancer treatment if no
efficacy is indicated. 44. The method of any one of embodiments 30
to 42, comprising repeating the colorectal cancer treatment if no
efficacy is indicated. 45. The method of any one of embodiments 30
to 42, comprising continuing the colorectal cancer treatment if no
efficacy is indicated. 46. The method of any one of embodiments 30
to 42, comprising discontinuing the colorectal cancer treatment if
efficacy is indicated. 47. A panel of proteins indicative of an
individual's colorectal cancer status, comprising at least 5
proteins selected from the list consisting of AACT, CO3, CO9, MIF,
PSGL, CATD, CEA and SEPR, wherein measurement of the panel at a
level that does not differ significantly from a reference panel
from circulating blood of an individual is indicative of the
individual's colorectal cancer status corresponding to a reference
panel colorectal cancer status at a sensitivity of at least 81% and
a specificity of at least 78%; and wherein no constituent protein
level of said panel is indicative of the individual's colorectal
cancer status at a sensitivity of greater than 65% and a
specificity of greater than 65%. 48. The panel of embodiment 47,
comprising at least 6 proteins selected from the list consisting of
AACT, CO3, CO9, MIF, PSGL, CATD, CEA and SEPR. 49. The panel of any
one of embodiments 47-48, comprising no more than 12 proteins, of
which at least 4 proteins selected from the list consisting of
AACT, CO3, CO9, MIF, PSGL, CATD, CEA and SEPR. 50. The panel of any
one of embodiments 47-49, comprising no more than 12 proteins,
wherein the panel of proteins comprises AACT, CO3, CO9, MIF, PSGL,
CATD, CEA and SEPR. 51. The panel of any one of embodiments 47-50,
consisting of AACT, CO3, CO9, MIF, PSGL, CATD, CEA and SEPR. 52.
The panel of proteins according to any one of embodiments 47-51,
for use in a method of assessing a colorectal cancer status
according to any one of embodiments 1-29, or for use in a method of
monitoring efficacy of a colorectal cancer treatment according to
any one of embodiments 30-46. 53. A kit comprising an antibody
panel, said antibody panel comprising antibodies that identify at
least 5 proteins selected from the list consisting of AACT, CO3,
CO9, MIF, PSGL, CATD, CEA and SEPR. 54. The kit of embodiment 53,
comprising an antibody that binds to a control protein. 55. The kit
of any one of embodiments 53-54, wherein said antibody panel
comprises no more than 15 antibodies. 56. The kit of any one of
embodiments 53-55, wherein said antibody panel comprises no more
than 12 antibodies. 57. The kit of any one of embodiments 53-56,
wherein said antibody panel comprises antibodies that identify all
of AACT, CO3, CO9, MIF, PSGL, CATD, CEA and SEPR. 58. The kit of
any one of embodiments 53-57, comprising instructions functionally
related to use of the kit to assess a patient colorectal cancer
status. 59. The kit comprising an antibody panel according to any
one of embodiments 47-52, for use in a method of assessing a
colorectal cancer status according to any one of embodiments 1-29,
or for use in a method of monitoring efficacy of a colorectal
cancer treatment according to any one of embodiments 30-46. 60. A
computer system configured to assess a colorectal cancer risk in an
individual, said computer system comprising A memory unit for
receiving data comprising measurement of a panel of proteins
comprising at least 5 proteins selected from the list consisting of
AACT, CO3, CO9, MIF, PSGL, CATD, CEA and SEPR from a biological
sample comprising circulating blood Computer-executable
instructions for assessing a colorectal cancer risk associated with
said measurement of said panel of proteins An output unit for
delivering a report assessing said colorectal cancer risk
associated with said measurement of said panel of proteins. 61. The
computer system of embodiment 60, wherein said panel comprises at
least 6 proteins selected from the list consisting of AACT, CO3,
CO9, MIF, PSGL, CATD, CEA and SEPR. 62. The computer system of any
one of embodiments 60-61, wherein said panel comprises no more than
12 proteins, of which at least 5 proteins selected from the list
consisting of AACT, CO3, CO9, MIF, PSGL, CATD, CEA and SEPR. 63.
The computer system of any one of embodiments 60-62, wherein said
panel comprises no more than 12 proteins, wherein the panel of
proteins comprises AACT, CO3, CO9, MIF, PSGL, CATD, CEA and SEPR.
64. The computer system of any one of embodiments 60-63, wherein
said panel consists of AACT, CO3, CO9, MIF, PSGL, CATD, CEA and
SEPR. 65. The computer system of any one of embodiments 60-64,
wherein the memory unit is configured for receiving data comprising
measurement of a second panel of proteins. 66. The computer system
of any one of embodiments 60-65, wherein said data comprising
measurement of a panel of proteins comprises ELISA data. 67. The
computer system of any one of embodiments 60-66, wherein said data
comprising measurement of a panel of proteins comprises mass
spectrometry data. 68. The computer system of any one of
embodiments 60-67, wherein assessing a colorectal cancer risk
comprises comparing said data to a reference panel associated with
a known colorectal cancer status. 69. The computer system of any
one of embodiments 60-68, wherein said individual is assigned said
known colorectal cancer status when said data does not differ
significantly from said reference panel. 70. The computer system of
any one of embodiments 60-68, wherein said reference panel
indicates presence of colorectal cancer. 71. The computer system of
any one of embodiments 60-68, wherein said reference panel
indicates absence of colorectal cancer. 72. The computer system of
any one of embodiments 60-71, wherein assessing a colorectal cancer
risk is performed on a computer configured to analyze reference
panel information. 73. The computer system of any one of
embodiments 60-72, wherein said memory unit comprises at least one
reference panel information set corresponding to a known colorectal
cancer status. 74. The computer system of any one of embodiments
60-73, wherein the at least one reference panel information set
comprises a machine learning model. 75. The computer system of any
one of embodiments 60-74, wherein the machine learning model is
trained using at least 100 biomarker panels corresponding to known
colorectal health status. 76. The computer system of any one of
embodiments 60-75, wherein said report indicates a sensitivity of
at least 81% and a specificity of at least 78%. 77. The computer
system of any one of embodiments 60-76, wherein said report
indicates a sensitivity of at least 81%. 78. The computer system of
any one of embodiments 60-77, wherein said report indicates a
specificity of at least 78%. 79. The computer system of any one of
embodiments 60-78, wherein said report recommends that a
colonoscopy be performed. 80. The computer system of any one of
embodiments 60-79, wherein said report recommends an independent
surgical intervention. 81. The computer system of any one of
embodiments 60-80, wherein said report recommends undergoing an
independent cancer assay. 82. The computer system of any one of
embodiments 60-81, wherein said report recommends undergoing a
stool cancer assay. 83. The computer system of any one of
embodiments 60-82, wherein said report recommends administering an
anticancer composition. 84. The computer system of any one of
embodiments 60-83, wherein said report recommends continued
monitoring. 85. The computer system of any one of embodiments
60-84, wherein at least one parameter of said individual's
reference panel information differs significantly from a
corresponding value from said reference panel information set, and
wherein said individual's reference panel information does not
differ significantly from said reference panel information set. 86.
The computer system of any one of embodiments 60-85, wherein no
single protein of said panel indicates the individual's colorectal
cancer status at a specificity of greater than 65% or a sensitivity
of greater than 65%. 87. The computer system of any one of
embodiments 60-86, wherein the memory unit is configured to receive
age information from said individual. 88. The computer system of
any one of embodiments 60-87, wherein the computer-executable
instructions factor in age of the individual when assessing said
colorectal cancer risk associated with said measurement of said
panel of proteins. 89. An ex vivo method of assessing an advanced
adenoma risk status in a blood sample of an individual, comprising
the steps of obtaining a circulating blood sample from the
individual; obtaining protein levels for a list of proteins
relevant to advanced adenoma in the sample comprising at least
three of CATD, CLUS, GDF15 and SAA1 to comprise biomarker panel
information from said individual; comparing said panel information
from said individual to a reference panel information set
corresponding to a known advanced adenoma status; and categorizing
said individual as having said advanced adenoma risk status if said
individual's reference panel information does not differ
significantly from said reference panel information set. 90. The
method of any one of embodiments 89, wherein obtaining a
circulating blood sample comprises drawing blood from a vein or
artery of the individual 91. The method of any one of embodiments
89-90, wherein the panel information comprises age information for
the individual. 92. The method of any one of embodiments 89-91,
wherein the list of proteins comprises no more than 15 proteins.
93. The method of any one of embodiments 89-92, wherein the list of
proteins comprises no more than 5 proteins. 94. The method of any
one of embodiments 89-93, wherein the list of proteins comprises
CATD, CLUS, GDF15 and SAA1. 95. The method of any one of
embodiments 89-94, wherein the categorizing has a sensitivity of at
least 50% and a specificity of at least 80%. 96. The method of any
one of embodiments 89-95, comprising transmitting a report of
results of said categorizing to a healthcare professional. 97.
The
method of any one of embodiments 89-96, wherein the report
indicates a sensitivity of at least 50%. 98. The method of any one
of embodiments 89-96, wherein the report indicates a specificity of
at least 80%. 99. The method of any one of embodiments 89-96,
wherein the report recommends that a colonoscopy be performed. 100.
The method of any one of embodiments 89-99, wherein the individual
undergoes a colonoscopy. 101. The method of any one of embodiments
89-96, wherein the report recommends an independent surgical
intervention. 102. The method of any one of embodiments 89-101,
wherein the individual undergoes an independent surgical
intervention. 103. The method of any one of embodiments 89-96,
wherein the report recommends undergoing an independent cancer
assay. 104. The method of any one of embodiments 89-103, wherein
the individual undergoes an independent cancer assay. 105. The
method of any one of embodiments 89-96, wherein the report
recommends undergoing a stool cancer assay. 106. The method of any
one of embodiments 89-105, wherein the individual undergoes a stool
cancer assay. 107. The method of any one of embodiments 89-96,
wherein the report recommends administering an anticancer
composition. 108. The method of any one of embodiments 89-107,
wherein an anticancer composition is administered to the
individual. 109. The method of any one of embodiments 89-96,
wherein the report recommends continued monitoring. 110. The method
of any one of embodiments 89-109, wherein at least one parameter of
said individual's reference panel differs significantly from a
corresponding value from said reference panel set, and wherein said
individual's reference panel information as a whole does not differ
significantly from said reference panel information set. 111. The
method of any one of embodiments 89-110, wherein no parameter of
said individual's reference panel information in isolation is
indicative of said advanced adenoma status in said individual at a
sensitivity of greater than 65% or a specificity of greater than
65%. 112. The method of any one of embodiments 89-111, wherein the
obtaining protein levels comprises contacting a fraction of the
circulating blood sample to a set of antibodies, wherein the set of
antibodies comprises antibodies specific to CATD, CLUS, GDF15 and
SAA1. 113. The method of any one of embodiments 89-112, wherein the
obtaining protein levels comprises subjecting a fraction of the
circulating blood sample to a mass spectrometric analysis. 114. The
method of any one of embodiments 89-113, wherein the obtaining
protein levels comprises contacting the sample to protein binding
DNA aptamers. 115. The method of any one of embodiments 89-114,
wherein the obtaining protein levels comprises contacting the
sample to an antibody array. 116. The method of any one of
embodiments 89-115, wherein at least one of said comparing and said
categorizing is performed on a computer configured to analyze
reference panel information. 117. The method of any one of
embodiments 89-116, wherein said reference panel information set
corresponding to a known advanced adenoma status comprises is a
product of a machine learning model. 118. The method of any one of
embodiments 89-117, wherein the machine learning model is trained
using at least 100 biomarker panels corresponding to known
colorectal health status. 119. An ex vivo method of monitoring
efficacy of an advanced adenoma treatment in an individual,
comprising the steps of obtaining a first sample comprising
circulating blood from the individual at a first time point;
obtaining a second sample comprising circulating blood from the
same individual receiving an advanced adenoma treatment at a second
time point; obtaining a first panel level protein levels for a list
of proteins relevant to advanced adenoma assessment in the first
sample and a second panel level protein levels for a list of
proteins relevant to advanced adenoma assessment in the second
sample, said list comprising CATD, CLUS, GDF15 and SAA1 to comprise
panel information for said first sample and said second sample;
wherein a change in protein levels indicates efficacy of the
advanced adenoma treatment. 120. The method of embodiment 119,
wherein obtaining the first sample comprises drawing blood from a
vein or artery of the individual. 121. The method of any one of
embodiments 119-120, wherein the advanced adenoma treatment
comprises administration of a pharmaceutical composition. 122. The
method of any one of embodiments 119-121, wherein the advanced
adenoma treatment comprises administration of a chemotherapeutic
agent. 123. The method of any one of embodiments 119-122, wherein
the advanced adenoma treatment comprises a colonoscopy. 124. The
method of any one of embodiments 119-123, wherein the advanced
adenoma treatment comprises a polypectomy. 125. The method of any
one of embodiments 119-124, wherein the advanced adenoma treatment
comprises radiotherapy. 126. The method of any one of embodiments
119-125, comprising comparing said first sample protein levels and
said second panel protein levels to protein levels of a healthy
reference, wherein the second sample levels being more similar to
the protein levels of the healthy reference indicates efficacy of
the advanced adenoma treatment. 127. The method of any one of
embodiments 119-126, comprising comparing said first sample protein
levels and said second panel protein levels to protein levels of an
advanced adenoma reference, wherein the first sample levels being
more similar to the protein levels of the advanced adenoma
reference indicates efficacy of the advanced adenoma treatment.
128. The method of any one of embodiments 119-127, wherein the list
of proteins relevant to advanced adenoma assessment comprises CATD,
CLUS, GDF15 and SAA1. 129. The method of any one of embodiments
119-128, wherein the list of proteins relevant to advanced adenoma
assessment comprises no more than 12 proteins. 130. The method of
any one of embodiments 119-129, wherein the list of proteins
relevant to advanced adenoma assessment comprises no more than 8
proteins. 131. The method of any one of embodiments 119-130,
wherein the list of proteins relevant to advanced adenoma
assessment consists of CATD, CLUS, GDF15 and SAA1. 132. The method
of any one of embodiments 119 to 131, comprising changing the
advanced adenoma treatment if no efficacy is indicated. 133. The
method of any one of embodiments 119 to 131, comprising repeating
the advanced adenoma treatment if no efficacy is indicated. 134.
The method of any one of embodiments 119 to 131, comprising
continuing the advanced adenoma treatment if no efficacy is
indicated. 135. The method of any one of embodiments 119 to 131,
comprising discontinuing the advanced adenoma treatment if efficacy
is indicated. 136. A panel of proteins indicative of an
individual's advanced adenoma status, comprising at least 3
proteins relevant to advanced adenoma assessment selected from the
list consisting of CATD, CLUS, GDF15 and SAA1, wherein measurement
of the panel at a level that does not differ significantly from a
reference panel from circulating blood of an individual is
indicative of the individual's advanced adenoma status
corresponding to a reference panel advanced adenoma status at a
sensitivity of at least 50% and a specificity of at least 80%; and
wherein no constituent protein level of said panel is indicative of
the individual's advanced adenoma status at a sensitivity of
greater than 65% and a specificity of greater than 65%. 137. The
panel of embodiment 136, comprising proteins relevant to advanced
adenoma assessment CATD, CLUS, GDF15 and SAA1. 138. The panel of
proteins according to any one of embodiments 136-137, for use in a
method of assessing an advanced adenoma status according to any one
of embodiments 89-119, or for use in a method of monitoring
efficacy of an advanced adenoma treatment according to any one of
embodiments 120-136. 139. A kit comprising an antibody panel, said
antibody panel comprising antibodies that identify at least 3
proteins relevant to advanced adenoma assessment selected from the
list consisting of CATD, CLUS, GDF15 and SAA1. 140. The kit of any
one of embodiments 139, comprising an antibody that binds to a
control protein. 141. The kit of any one of embodiments 139-140,
wherein said antibody panel comprises no more than 15 antibodies.
142. The kit of any one of embodiments 139-141, wherein said
antibody panel comprises no more than 12 antibodies. 143. The kit
of any one of embodiments 139-142, wherein said antibody panel
comprises antibodies that identify all of CATD, CLUS, GDF15 and
SAA1. 144. The kit of any one of embodiments 139-143, comprising
instructions functionally related to use of the kit to assess a
patient advanced adenoma status. 145. The kit comprising an
antibody panel according to any one of embodiments 136-138, for use
in a method of assessing an advanced adenoma status according to
any one of embodiments 89-119, or for use in a method of monitoring
efficacy of an advanced adenoma treatment according to any one of
embodiments 120-136. 146. A computer system configured to assess an
advanced adenoma risk in an individual, said computer system
comprising A memory unit for receiving data comprising measurement
of a panel of proteins comprising at least 3 proteins indicative of
an individual's advanced adenoma status selected from the list
consisting of CATD, CLUS, GDF15 and SAA1 from a biological sample
comprising circulating blood Computer-executable instructions for
assessing an advanced adenoma risk associated with said measurement
of said panel of proteins An output unit for delivering a report
assessing said advanced adenoma risk associated with said
measurement of said panel of proteins. 147. The computer system of
embodiment 146, wherein said panel comprises CATD, CLUS, GDF15 and
SAA1. 148. The computer system of any one of embodiments 146-147,
wherein said panel comprises no more than 12 proteins. 149. The
computer system of any one of embodiments 146-148, wherein the
memory unit is configured for receiving data comprising measurement
of a second panel of proteins. 150. The computer system of any one
of embodiments 146-149, wherein said data comprising measurement of
a panel of proteins comprises ELISA data. 151. The computer system
of any one of embodiments 146-150, wherein said data comprising
measurement of a panel of proteins comprises mass spectrometry
data. 152. The computer system of any one of embodiments 146-151,
wherein assessing an advanced adenoma risk comprises comparing said
data to a reference panel associated with a known advanced adenoma
status. 153. The computer system of any one of embodiments 146-152,
wherein said individual is assigned said known advanced adenoma
status when said data does not differ significantly from said
reference panel. 154. The computer system of any one of embodiments
146-152, wherein said reference panel indicates presence of
colorectal cancer. 155. The computer system of any one of
embodiments 146-152, wherein said reference panel indicates absence
of colorectal cancer. 156. The computer system of any one of
embodiments 146-155, wherein assessing an advanced adenoma risk is
performed on a computer configured to analyze reference panel
information. 157. The method of any one of embodiments 146-156,
wherein said memory unit comprises at least one reference panel
information set corresponding to a known advanced adenoma status.
158. The method of any one of embodiments 146-157, wherein the at
least one reference panel information set comprises a machine
learning model. 159. The method of any one of embodiments 146-158,
wherein the machine learning model is trained using at least 100
biomarker panels corresponding to known colorectal health status.
160. The computer system of any one of embodiments 146-159, wherein
said report indicates a sensitivity of at least 50% and a
specificity of at least 80%. 161. The computer system of any one of
embodiments 146-160, wherein said report indicates a sensitivity of
at least 50%. 162. The computer system of any one of embodiments
146-161, wherein said report indicates a specificity of at least
80%. 163. The computer system of any one of embodiments 146-162,
wherein said report recommends that a colonoscopy be performed.
164. The computer system of any one of embodiments 146-163, wherein
said report recommends an independent surgical intervention. 165.
The computer system of any one of embodiments 146-164, wherein said
report recommends undergoing an independent cancer assay. 166. The
computer system of any one of embodiments 146-165, wherein said
report recommends undergoing a stool cancer assay. 167. The
computer system of any one of embodiments 146-166, wherein said
report recommends administering an anticancer composition. 168. The
computer system of any one of embodiments 146-167, wherein said
report recommends continued monitoring. 169. The computer system of
any one of embodiments 146-168, wherein at least one parameter of
said individual's reference panel information differs significantly
from a corresponding value from said reference panel information
set, and wherein said individual's reference panel information does
not differ significantly from said reference panel information set.
170. The computer system of any one of embodiments 146-169, wherein
no single protein of said panel indicates the individual's advanced
adenoma status at a specificity of greater than 65% or a
sensitivity of greater than 65%. 171. The computer system of any
one of embodiments 146-170, wherein the memory unit is configured
to receive age information from said individual. 172. The computer
system of any one of embodiments 146-171, wherein the
computer-executable instructions factor in age of the individual
when assessing said advanced adenoma risk associated with said
measurement of said panel of proteins. 173. An ex vivo method of
assessing a colorectal health risk status in a blood sample of an
individual, comprising the steps of obtaining a circulating blood
sample from the individual; obtaining a biomarker panel level for a
biomarker panel comprising a list of proteins in the sample
comprising AACT, CO3, CO9, MIF, PSGL, SEPR, CEA, CATD, CLUS, GDF15
and SAA1, and obtaining an age for the individual, wherein AACT,
CO3, CO9, MIF, PSGL, SEPR, CEA, CATD, and age comprise colorectal
cancer panel information from said individual; and wherein CATD,
CLUS, GDF15 and SAA1 comprise advanced adenoma panel information
from said individual; comparing said colorectal cancer panel
information from said individual to a reference colorectal cancer
panel information set corresponding to a known colorectal cancer
status; comparing said advanced adenoma panel information from said
individual to a reference advanced adenoma panel information set
corresponding to a known advanced adenoma status; and categorizing
said individual as having a colorectal health risk if either of
said colorectal cancer panel or said advanced adenoma panel does
not differ significantly from a reference panel positive for a
colorectal health risk. 174. The method of any one of embodiments
173, wherein obtaining a circulating blood sample comprises drawing
blood from a vein or artery of the individual. 175. The method of
any one of embodiments 173-174, wherein the list of proteins
comprises no more than 20 proteins. 176. The method of any one of
embodiments 173-175, wherein the list of proteins comprises no more
than 11 proteins. 177. The method of any one of embodiments
173-176, wherein the categorizing has a sensitivity of at least 8%
and a specificity of at least 50%. 178. The method of any one of
embodiments 173-177, comprising transmitting a report of results of
said categorizing to a health practitioner. 179. The method of any
one of embodiments 173-178, wherein the report recommends that a
colonoscopy be performed. 180. The method of any one of embodiments
173-179, wherein the individual undergoes a colonoscopy. 181. The
method of any one of embodiments 173-178, wherein the report
recommends an independent surgical intervention. 182. The method of
any one of embodiments 173-181, wherein the individual undergoes an
independent surgical intervention. 183. The method of any one of
embodiments 178-82, wherein the report recommends undergoing an
independent cancer assay. 184. The method of any one of embodiments
173-183, wherein the individual undergoes an independent cancer
assay. 185. The method of any one of embodiments 173-178, wherein
the report recommends undergoing a stool cancer assay. 186. The
method of any one of embodiments 173-185, wherein the individual
undergoes a stool cancer assay. 187. The method of any one of
embodiments 173-178, wherein the report recommends administering an
anticancer composition. 188. The method of any one of embodiments
173-187, wherein the individual is administered an anticancer
composition. 189. The method of any one of embodiments 173-178,
wherein the report recommends continued monitoring. 190. The method
of any one of embodiments 173-178, wherein at least one biomarker
level of said individual's panel information differs significantly
from a corresponding value from at least one of said reference
panels, and wherein said individual's panel level as a whole does
not differ significantly from said reference panel level. 191. The
method of any one of embodiments 178-190, wherein no parameter of
said individual's reference panel information in isolation is
indicative of said colorectal cancer status in said individual at
a
sensitivity of greater than 65% or a specificity of greater than
65%. 192. The method of any one of embodiments 173-178, wherein the
obtaining protein levels comprises contacting a fraction of the
circulating blood sample to a set of antibodies, wherein the set of
antibodies comprises antibodies specific to AACT, CO3, CO9, MIF,
PSGL, SEPR, CEA, CATD, CLUS, GDF15 and SAA1. 193. The method of any
one of embodiments 173-178, wherein the obtaining protein levels
comprises subjecting a fraction of the circulating blood sample to
a mass spectrometric analysis. 194. The method of any one of
embodiments 173-178, wherein the obtaining protein levels comprises
contacting the sample to protein binding DNA aptamers. 195. The
method of any one of embodiments 173-178, wherein the obtaining
protein levels comprises contacting the sample to an antibody
array. 196. The method of any one of embodiments 173-178, wherein
the obtaining protein levels comprises subjecting a fraction of the
circulating blood sample to a mass spectrometric analysis. 197. The
method of any one of embodiments 173-178, wherein at least one of
said comparing and said categorizing is performed on a computer
configured to analyze reference panel information. 198. The method
of any one of embodiments 173-178, wherein said reference panel
information set corresponding to a known colorectal cancer status
comprises a product of a machine learning model. 199. The method of
any one of embodiments 173-198, wherein the machine learning model
is trained using at least 100 biomarker panels corresponding to
known colorectal health status. 200. The embodiment of any one of
1-199, wherein the panel comprises more biomarkers than those
listed, but wherein a significant colorectal health assessment
arises from the listed biomarkers, alone or in combination with
age. 201. An embodiment of any one of 1-200, wherein the panel
distinguishes CRC samples from samples derived from a CRC-negative
individual that is positive for at least one non-CRC cancer.
[0307] Reference Art and Definitions
[0308] Throughout this application, various embodiments of this
invention may be presented in a range format. It should be
understood that the description in range format is merely for
convenience and brevity and should not be construed as an
inflexible limitation on the scope of the invention. Accordingly,
the description of a range should be considered to have
specifically disclosed all the possible subranges as well as
individual numerical values within that range. For example,
description of a range such as from 1 to 6 should be considered to
have specifically disclosed subranges such as from 1 to 3, from 1
to 4, from 1 to 5, from 2 to 4, from 2 to 6, from 3 to 6 etc., as
well as individual numbers within that range, for example, 1, 2, 3,
4, 5, and 6. This applies regardless of the breadth of the
range.
[0309] The practice of the present invention can employ, unless
otherwise indicated, conventional techniques of immunology,
biochemistry, chemistry, molecular biology, microbiology, cell
biology, genomics and recombinant DNA, which are within the skill
of the art. See, for example, Sambrook, Fritsch and Maniatis,
MOLECULAR CLONING: A LABORATORY MANUAL, 4th edition (2012); CURRENT
PROTOCOLS IN MOLECULAR BIOLOGY (F. M. Ausubel, et al. eds.,
(1987)); the series METHODS IN ENZYMOLOGY (Academic Press, Inc.):
PCR 2: A PRACTICAL APPROACH (M. J. MacPherson, B. D. Hames and G.
R. Taylor eds. (1995)), CULTURE OF ANIMAL CELLS: A MANUAL OF BASIC
TECHNIQUE AND SPECIALIZED APPLICATIONS, 6th Edition (R. I.
Freshney, ed. (2010), and Lange, et. al., Molecular Systems Biology
Vol. 4:Article 222 (2008), which are hereby incorporated by
reference.
Definitions
[0310] As used in the specification and claims, the singular forms
"a", "an" and "the" include plural references unless the context
clearly dictates otherwise. For example, the term "a sample"
includes a plurality of samples, including mixtures thereof.
[0311] The terms "determining", "measuring", "evaluating",
"assessing," "assaying," and "analyzing" are often used
interchangeably herein to refer to forms of measurement, and
include determining if an element is present or not (for example,
detection). These terms can include quantitative, qualitative or
quantitative and qualitative determinations. Assessing is
alternatively relative or absolute. "Detecting the presence of"
includes determining the amount of something present, as well as
determining whether it is present or absent.
[0312] The terms "panel", "biomarker panel", "protein panel",
"classifier model", and "model" are used interchangeably herein to
refer to a set of biomarkers, wherein the set of biomarkers
comprises at least two biomarkers. Exemplary biomarkers are
proteins or polypeptide fragments of proteins that are uniquely or
confidently mapped to particular proteins. However, additional
biomarkers are also contemplated, for example age or gender of the
individual providing a sample. The biomarker panel is often
predictive and/or informative of a subject's health status,
disease, or condition.
[0313] The "level" of a biomarker panel refers to the absolute and
relative levels of the panel's constituent markers and the relative
pattern of the panel's constituent biomarkers.
[0314] The terms "colorectal cancer" and "CRC" are used
interchangeably herein. The term "colorectal cancer status", "CRC
status" can refer to the status of the disease in subject. Examples
of types of CRC statuses include, but are not limited to, the
subject's risk of cancer, including colorectal carcinoma, the
presence or absence of disease (for example, polyp or
adenocarcinoma), the stage of disease in a patient (for example,
carcinoma), and the effectiveness of treatment of disease.
[0315] The term "mass spectrometer" can refer to a gas phase ion
spectrometer that measures a parameter that can be translated into
mass-to-charge (m/z) ratios of gas phase ions. Mass spectrometers
generally include an ion source and a mass analyzer. Examples of
mass spectrometers are time-of-flight, magnetic sector, quadrupole
filter, ion trap, ion cyclotron resonance, electrostatic sector
analyzer and hybrids of these. "Mass spectrometry" can refer to the
use of a mass spectrometer to detect gas phase ions.
[0316] The term "tandem mass spectrometer" can refer to any mass
spectrometer that is capable of performing two successive stages of
m/z-based discrimination or measurement of ions, including ions in
an ion mixture. The phrase includes mass spectrometers having two
mass analyzers that are capable of performing two successive stages
of m/z-based discrimination or measurement of ions tandem-in-space.
The phrase further includes mass spectrometers having a single mass
analyzer that can be capable of performing two successive stages of
m/z-based discrimination or measurement of ions tandem-in-time. The
phrase thus explicitly includes Qq-TOF mass spectrometers, ion trap
mass spectrometers, ion trap-TOF mass spectrometers, TOF-TOF mass
spectrometers, Fourier transform ion cyclotron resonance mass
spectrometers, electrostatic sector-magnetic sector mass
spectrometers, and combinations thereof.
[0317] The term "biochip" can refer to a solid substrate having a
generally planar surface to which an adsorbent is attached. In some
cases, a surface of the biochip comprises a plurality of
addressable locations, each of which location may have the
adsorbent bound there. Biochips can be adapted to engage a probe
interface, and therefore, function as probes. Protein biochips are
adapted for the capture of polypeptides and can be comprise
surfaces having chromatographic or biospecific adsorbents attached
thereto at addressable locations. Microarray chips are generally
used for DNA and RNA gene expression detection.
[0318] The term "biomarker" and "marker" are used interchangeably
herein, and can refer to a polypeptide, gene, nucleic acid (for
example, DNA and/or RNA) which is differentially present in a
sample taken from a subject having a disease for which a diagnosis
is desired (for example, CRC) as compared to a comparable sample
taken from control subject that does not have the disease (for
example, a person with a negative diagnosis or undetectable CRC,
normal or healthy subject, or, for example, from the same
individual at a different time point). Common biomarkers herein
include proteins, or protein fragments that are uniquely or
confidently mapped to a particular protein, transition ion of an
amino acid sequence, or one or more modifications of a protein such
as phosphorylation, glycosylation or other post-translational or
co-translational modification. In addition, a protein biomarker can
be a binding partner of a protein, protein fragment, or transition
ion of an amino acid sequence.
[0319] The terms "polypeptide," "peptide" and "protein" are often
used interchangeably herein in reference to a polymer of amino acid
residues. A protein, generally, refers to a full-length polypeptide
as translated from a coding open reading frame, or as processed to
its mature form, while a polypeptide or peptide informally refers
to a degradation fragment or a processing fragment of a protein
that nonetheless uniquely or identifiably maps to a particular
protein. A polypeptide can be a single linear polymer chain of
amino acids bonded together by peptide bonds between the carboxyl
and amino groups of adjacent amino acid residues. Polypeptides can
be modified, for example, by the addition of carbohydrate,
phosphorylation, etc. Proteins can comprise one or more
polypeptides.
[0320] An "immunoassay" is an assay that uses an antibody to
specifically bind an antigen (for example, a marker). The
immunoassay can be characterized by the use of specific binding
properties of a particular antibody to isolate, target, and/or
quantify the antigen.
[0321] The term "antibody" can refer to a polypeptide ligand
substantially encoded by an immunoglobulin gene or immunoglobulin
genes, or fragments thereof, which specifically binds and
recognizes an epitope. Antibodies exist, for example, as intact
immunoglobulins or as a number of well-characterized fragments
produced by digestion with various peptidases. This includes, for
example, Fab'' and F(ab)''2 fragments. As used herein, the term
"antibody" also includes antibody fragments either produced by the
modification of whole antibodies or those synthesized de novo using
recombinant DNA methodologies. It also includes polyclonal
antibodies, monoclonal antibodies, chimeric antibodies, humanized
antibodies, or single chain antibodies. "Fc" portion of an antibody
can refer to that portion of an immunoglobulin heavy chain that
comprises one or more heavy chain constant region domains, but does
not include the heavy chain variable region.
[0322] The term "tumor" can refer to a solid or fluid-filled lesion
or structure that may be formed by cancerous or non-cancerous
cells, such as cells exhibiting aberrant cell growth or division.
The terms "mass" and "nodule" are often used synonymously with
"tumor". Tumors include malignant tumors or benign tumors. An
example of a malignant tumor can be a carcinoma which is known to
comprise transformed cells.
[0323] The term "binding partners" can refer to pairs of molecules,
typically pairs of biomolecules that exhibit specific binding.
Protein--protein interactions can occur between two or more
proteins, when bound together they often to carry out their
biological function. Interactions between proteins are important
for the majority of biological functions. For example, signals from
the exterior of a cell are mediated via ligand receptor proteins to
the inside of that cell by protein--protein interactions of the
signaling molecules. For example, molecular binding partners
include, without limitation, receptor and ligand, antibody and
antigen, biotin and avidin, and others.
[0324] The term "control reference" can refer to a known or
determined amount of a biomarker associated with a known condition
that can be used to compare to an amount of the biomarker
associated with an unknown condition. A control reference can also
refer to a steady-state molecule which can be used to calibrate or
normalize values of a non-steady state molecule. A control
reference value can be a calculated value from a combination of
factors or a combination of a range of factors, such as a
combination of biomarker concentrations or a combination of ranges
of concentrations.
[0325] The terms "subject," "individual," or "patient" are often
used interchangeably herein. A "subject" can be a biological entity
containing expressed genetic materials. The biological entity can
be a plant, animal, or microorganism, including, for example,
bacteria, viruses, fungi, and protozoa. The subject can be tissues,
cells and their progeny of a biological entity obtained in vivo or
cultured in vitro. The subject can be a mammal. The mammal can be a
human. The subject may be diagnosed or suspected of being at high
risk for a disease. The disease can be cancer. The cancer can be
CRC (CRC). In some cases, the subject is not necessarily diagnosed
or suspected of being at high risk for the disease.
[0326] The term "in vivo" is used to describe an event that takes
place in a subject's body.
[0327] The term "ex vivo" is used to describe an event that takes
place outside of a subject's body. An "ex vivo" assay is not
performed on a subject. Rather, it is performed upon a sample
separate from a subject. An example of an `ex vivo` assay performed
on a sample is an `in vitro` assay.
[0328] The term "in vitro" is used to describe an event that takes
places contained in a container for holding laboratory reagent such
that it is separated from the living biological source organism
from which the material is obtained. In vitro assays can encompass
cell-based assays in which cells alive or dead are employed. In
vitro assays can also encompass a cell-free assay in which no
intact cells are employed.
[0329] The term specificity, or true negative rate, can refer to a
test's ability to exclude a condition correctly. For example, in a
diagnostic test, the specificity of a test is the proportion of
patients known not to have the disease, who will test negative for
it. In some cases, this is calculated by determining the proportion
of true negatives (i.e. patients who test negative who do not have
the disease) to the total number of healthy individuals in the
population (i.e., the sum of patients who test negative and do not
have the disease and patients who test positive and do not have the
disease).
[0330] The term sensitivity, or true positive rate, can refer to a
test's ability to identify a condition correctly. For example, in a
diagnostic test, the sensitivity of a test is the proportion of
patients known to have the disease, who will test positive for it.
In some cases, this is calculated by determining the proportion of
true positives (i.e. patients who test positive who have the
disease) to the total number of individuals in the population with
the condition (i.e., the sum of patients who test positive and have
the condition and patients who test negative and have the
condition).
[0331] The quantitative relationship between sensitivity and
specificity can change as different diagnostic cut-offs are chosen.
This variation can be represented using ROC curves. The x-axis of a
ROC curve shows the false-positive rate of an assay, which can be
calculated as (1-specificity). The y-axis of a ROC curve reports
the sensitivity for an assay. This allows one to easily determine a
sensitivity of an assay for a given specificity, and vice
versa.
[0332] As used herein, the term `about` a number refers to that
number plus or minus 10% of that number. The term `about` a range
refers to that range minus 10% of its lowest value and plus 10% of
its greatest value.
[0333] As used herein, the terms "treatment" or "treating" are used
in reference to a pharmaceutical or other intervention regimen for
obtaining beneficial or desired results in the recipient.
Beneficial or desired results include but are not limited to a
therapeutic benefit and/or a prophylactic benefit. A therapeutic
benefit may refer to eradication or amelioration of symptoms or of
an underlying disorder being treated. Also, a therapeutic benefit
can be achieved with the eradication or amelioration of one or more
of the physiological symptoms associated with the underlying
disorder such that an improvement is observed in the subject,
notwithstanding that the subject may still be afflicted with the
underlying disorder. A prophylactic effect includes delaying,
preventing, or eliminating the appearance of a disease or
condition, delaying or eliminating the onset of symptoms of a
disease or condition, slowing, halting, or reversing the
progression of a disease or condition, or any combination thereof.
For prophylactic benefit, a subject at risk of developing a
particular disease, or to a subject reporting one or more of the
physiological symptoms of a disease may undergo treatment, even
though a diagnosis of this disease may not have been made.
EXAMPLES
Example 1
[0334] A patient at risk of colorectal cancer is tested using a
panel as disclosed herein. A blood sample is taken from the patient
and protein accumulation levels are measured for a panel comprising
AACT, CATD, CEA, CO3, CO9, MIF, PSGL, and SEPR. The patient's age
is also factored in to the assessment, with age (in units of time)
treated as a biomarker of the panel much like the other markers.
The patient's panel results are compared to panel results of known
status, and the patient is categorized with an 81% sensitivity, a
78% specificity, and a 31% positive predictive value as having
colon cancer.
[0335] A colonoscopy is recommended and evidence of colorectal
cancer is detected in the individual.
Example 2
[0336] The patient of Example 1 is prescribed a treatment regimen
comprising a surgical intervention. A blood sample is taken from
the patient prior to surgical intervention and protein accumulation
levels are measured for a panel comprising AACT, CATD, CEA, CO3,
CO9, MIF, PSGL, and SEPR. The patient's age is also factored in to
the assessment, with age treated as an `accumulation level` of time
rather than protein. The patient's panel results are compared to
panel results of known status, and the patient is categorized with
an 81% sensitivity, a 78% specificity, and a 31% positive
predictive value as having colon cancer.
[0337] A blood sample is taken from the patient subsequent to
surgical intervention and protein accumulation levels are measured
for a panel comprising AACT, CATD, CEA, CO3, CO9, MIF, PSGL, and
SEPR. The patient's age is also factored in to the assessment, with
age treated as an `accumulation level` of time rather than protein.
The patient's panel results are compared to panel results of known
status, and the patient is categorized with an 81% sensitivity, a
78% specificity, and a 31% positive predictive value as no longer
having colon cancer.
Example 3
[0338] The patient of Example 1 is prescribed a treatment regimen
comprising a chemotherapeutic intervention comprising 5-FU
administration. A blood sample is taken from the patient prior to
chemotherapeutic intervention and protein accumulation levels are
measured for a panel comprising AACT, CATD, CEA, CO3, CO9, MIF,
PSGL, and SEPR. The patient's age is also factored in to the
assessment, with age treated as an `accumulation level` of time
rather than protein. The patient's panel results are compared to
panel results of known status, and the patient is categorized an
81% sensitivity, a 78% specificity, and a 31% positive predictive
value as having colon cancer.
[0339] A blood sample is taken from the patient at weekly intervals
during chemotherapy treatment and protein accumulation levels are
measured for a panel comprising AACT, CATD, CEA, CO3, CO9, MIF,
PSGL, and SEPR. The patient's age is also factored in to the
assessment, with age treated as an `accumulation level` of time
rather than protein. The patient's panel results are compared to
panel results of known status. The patient's panel results over
time indicate that the cancer has responded to the chemotherapy
treatment and that the colorectal cancer is no longer detectable by
completion of the treatment regimen.
Example 4
[0340] The patient of Example 1 is prescribed a treatment regimen
comprising a chemotherapeutic intervention comprising oral
capecitabine administration. A blood sample is taken from the
patient prior to chemotherapeutic intervention and protein
accumulation levels are measured for a panel comprising AACT, CATD,
CEA, CO3, CO9, MIF, PSGL, and SEPR. The patient's age is also
factored in to the assessment, with age treated as an `accumulation
level` of time rather than protein. The patient's panel results are
compared to panel results of known status, and the patient is
categorized with an 81% sensitivity, a 78% specificity, and a 31%
positive predictive value as having colon cancer.
[0341] A blood sample is taken from the patient at weekly intervals
during chemotherapy treatment and protein accumulation levels are
measured for a panel comprising AACT, CATD, CEA, CO3, CO9, MIF,
PSGL, and SEPR. The patient's panel results are compared to panel
results of known status. The patient's panel results over time
indicate that the cancer has responded to the chemotherapy
treatment and that the colorectal cancer is no longer detectable by
completion of the treatment regimen.
Example 5
[0342] The patient of Example 1 is prescribed a treatment regimen
comprising a chemotherapeutic intervention comprising oral
oxaliplatin administration. A blood sample is taken from the
patient prior to chemotherapeutic intervention and protein
accumulation levels are measured for a panel comprising AACT, CATD,
CEA, CO3, CO9, MIF, PSGL, and SEPR. The patient's age is also
factored in to the assessment, with age treated as an `accumulation
level` of time rather than protein. The patient's panel results are
compared to panel results of known status, and the patient is
categorized with an 81% sensitivity, a 78% specificity, and a 31%
positive predictive value as having colon cancer.
[0343] A blood sample is taken from the patient at weekly intervals
during chemotherapy treatment and protein accumulation levels are
measured for a panel comprising AACT, CATD, CEA, CO3, CO9, MIF,
PSGL, and SEPR. The patient's age is also factored in to the
assessment, with age treated as an `accumulation level` of time
rather than protein. The patient's panel results are compared to
panel results of known status. The patient's panel results over
time indicate that the cancer has responded to the chemotherapy
treatment and that the colorectal cancer is no longer detectable by
completion of the treatment regimen.
Example 6
[0344] The patient of Example 1 is prescribed a treatment regimen
comprising a chemotherapeutic intervention comprising oral
oxaliplatin administration in combination with bevacizumab. A blood
sample is taken from the patient prior to chemotherapeutic
intervention and protein accumulation levels are measured for a
panel comprising AACT, CATD, CEA, CO3, CO9, MIF, PSGL, and SEPR.
The patient's age is also factored in to the assessment, with age
treated as an `accumulation level` of time rather than protein. The
patient's panel results are compared to panel results of known
status, and the patient is categorized with an 81% sensitivity, a
78% specificity, and a 31% positive predictive value as having
colon cancer.
[0345] A blood sample is taken from the patient at weekly intervals
during chemotherapy treatment and protein accumulation levels are
measured for a panel comprising AACT, CATD, CEA, CO3, CO9, MIF,
PSGL, and SEPR. The patient's age is also factored in to the
assessment, with age treated as an `accumulation level` of time
rather than protein. The patient's panel results are compared to
panel results of known status. The patient's panel results over
time indicate that the cancer has responded to the chemotherapy
treatment and that the colorectal cancer is no longer detectable by
completion of the treatment regimen.
Example 7
[0346] A patient at risk of colorectal cancer is tested using a
panel as disclosed herein. A blood sample is taken from the patient
and protein accumulation levels are measured using reagents in an
ELISA kit to detect members of a panel comprising AACT, CATD, CEA,
CO3, CO9, MIF, PSGL, and SEPR. The patient's age is also factored
in to the assessment, with age treated as an `accumulation level`
of time rather than protein. The patient's panel results are
compared to panel results of known status, and the patient is
categorized with an 81% sensitivity, a 78% specificity, and a 31%
positive predictive value as having colon cancer. A colonoscopy is
recommended and evidence of colorectal cancer is detected in the
individual.
Example 8
[0347] A patient at risk of colorectal cancer is tested using a
panel as disclosed herein. A blood sample is taken from the patient
and protein accumulation levels are measured using mass
spectrometry to detect members of a panel comprising AACT, CATD,
CEA, CO3, CO9, MIF, PSGL, and SEPR. The patient's age is also
factored in to the assessment, with age treated as an `accumulation
level` of time rather than protein. The patient's panel results are
compared to panel results of known status, and the patient is
categorized with an 81% sensitivity, a 78% specificity, and a 31%
positive predictive value as having colon cancer. A colonoscopy is
recommended and evidence of colorectal cancer is detected in the
individual.
Example 9
[0348] 1000 patients at risk of colorectal cancer are tested using
a panel as disclosed herein. A blood sample is taken from the
patient and protein accumulation levels are measured to detect
members of a panel comprising AACT, CATD, CEA, CO3, CO9, MIF, PSGL,
and SEPR. The patient's age is also factored in to the assessment,
with age treated as an `accumulation level` of time rather than
protein. The patients' panel results are compared to panel results
of known status, and the patients are categorized with an 81%
sensitivity, a 78% specificity, and a 31% positive predictive value
into a colon cancer category. A colonoscopy is recommended for
patients categorized as positive. Of the patients categorized as
having colon cancer, 80% are independently confirmed to have colon
cancer. Of the patients categorized as not having colon cancer, 20%
are later found to have colon cancer through an independent follow
up test, confirmed via a colonoscopy.
Example 10
[0349] A patient at risk of colorectal cancer is tested using a
panel as disclosed herein. A blood sample is taken from the patient
and protein accumulation levels are measured for a panel comprising
CATD, CLUS, GDF15, and SAA1. The patient's panel results are
compared to panel results of known status, and the patient is
categorized with a 50% sensitivity and an 80% specificity as having
advanced colorectal adenoma. A colonoscopy is recommended and
evidence of advanced colorectal adenoma is detected in the
individual.
Example 11
[0350] A patient at risk of colorectal cancer is tested using a
panel as disclosed herein. A blood sample is taken from the patient
and protein accumulation levels are measured for a panel comprising
CATD, CLUS, GDF15, and SAA1. The patient's panel results are
compared to panel results of known status, and the patient is
categorized with a 45% sensitivity and an 80% specificity as having
advanced colorectal adenoma. Further monitoring is recommended and
the health professional obtains subsequent blood or stool tests for
colorectal cancer and/or advanced adenoma.
Example 12
[0351] A patient at risk of colorectal cancer is tested using a
panel as disclosed herein. A blood sample is taken from the patient
and protein accumulation levels are measured using reagents in an
ELISA kit to detect members of a panel comprising CATD, CLUS,
GDF15, and SAA1. The patient's panel results are compared to panel
results of known status, and the patient is categorized with a 45%
sensitivity and an 80% specificity as having advanced colorectal
adenoma. A colonoscopy is recommended and evidence of advanced
colorectal adenoma is detected in the individual.
Example 13
[0352] A patient at risk of colorectal cancer is tested using a
panel as disclosed herein. A blood sample is taken from the patient
and protein accumulation levels are measured using mass
spectrometry to detect members of a panel comprising CATD, CLUS,
GDF15, and SAA1. The patient's panel results are compared to panel
results of known status, and the patient is categorized with a 45%
sensitivity and an 80% specificity as having advanced colorectal
adenoma. A colonoscopy is recommended and evidence of colorectal
cancer is detected in the individual.
Example 14
[0353] A patient at risk of colorectal cancer is tested using a
panel as disclosed herein. A blood sample is taken from the
patient. The blood sample is mailed to a facility, where protein
accumulation levels are measured using mass spectrometry to detect
members of a panel comprising AACT, CATD, CEA, CO3, CO9, MIF, PSGL,
and SEPR. The patient's age is also factored in to the assessment,
with age treated as an `accumulation level` of time rather than
protein. The patient's panel results are compared to panel results
of known status, and the patient is categorized with an 81%
sensitivity, a 78% specificity, and a 31% positive predictive value
as having colon cancer. A colonoscopy is recommended and evidence
of colorectal cancer is detected in the individual.
Example 15
[0354] A patient at risk of colorectal cancer is tested using a
panel as disclosed herein. A blood sample is taken from the
patient. The blood sample is mailed to a facility, where protein
accumulation levels are measured using ELISA to detect members of a
panel comprising AACT, CATD, CEA, CO3, CO9, MIF, PSGL, and SEPR.
The patient's age is also factored in to the assessment, with age
treated as an `accumulation level` of time rather than protein. The
patient's panel results are compared to panel results of known
status, and the patient is categorized with an 81% sensitivity, a
78% specificity, and a 31% positive predictive value as having
colon cancer. A colonoscopy is recommended and evidence of
colorectal cancer is detected in the individual.
Example 16
[0355] A patient at risk of colorectal cancer is tested using a
panel as disclosed herein. A blood sample is taken from the
patient. The blood sample is mailed to a facility, where plasma is
prepared and protein accumulation levels are measured using ELISA
to detect members of a panel comprising AACT, CATD, CEA, CO3, CO9,
MIF, PSGL, and SEPR. The patient's age is also factored in to the
assessment, with age treated as an `accumulation level` of time
rather than protein. The patient's panel results are compared to
panel results of known status, and the patient is categorized with
an 81% sensitivity, a 78% specificity, and a 31% positive
predictive value as having colon cancer. A colonoscopy is
recommended and evidence of colorectal cancer is detected in the
individual.
Example 17
[0356] A patient at risk of colorectal cancer is tested using a
panel as disclosed herein. A blood sample is taken from the
patient. The blood sample is mailed to a facility, where plasma is
prepared and protein accumulation levels are measured using mass
spectrometry to detect members of a panel comprising AACT, CATD,
CEA, CO3, CO9, MIF, PSGL, and SEPR. The patient's age is also
factored in to the assessment, with age treated as an `accumulation
level` of time rather than protein. The patient's panel results are
compared to panel results of known status, and the patient is
categorized with an 81% sensitivity, a 78% specificity, and a 31%
positive predictive value as having colon cancer. A colonoscopy is
recommended and evidence of colorectal cancer is detected in the
individual.
Example 18
[0357] Potential protein biomarkers were tested in an
intent-to-test study design that included factors that would be
present in an above-average-risk population (e.g., co-morbidities,
other GI pathologies, age). 1,045 samples were evaluated by ELISA.
Age was added as a model parameter in a case-control discovery
partition of 309 patients (see FIG. 1). Indeterminate call
boundaries were added in an intent-to-test discovery partition of
373 patients. The final protein biomarker panel comprising AACT,
CATD, CEA, CO3, CO9, MIF, PSGL, and SEPR, and the age of the
subject, was validated in 373 patients to have an 81% sensitivity
and a 78% specificity with a 15% indeterminate call rate. No
statistical difference was detected between early and late CRC
performance.
Example 19
[0358] For a CRC protein marker panel discovery and validation
study, 137 CRC patient plasma samples and 137 age- and
gender-matched controls from three different commercial sample
biobanks were acquired to conduct a study with case-control design.
Samples were selected across the relevant age range for CRC
screening guidelines, 50-75, across the stages of CRC, I-IV, and
across the site of cancer, colon versus rectum. The patients were
divided into a discovery partition of 138 paired samples and a
validation partition of 136 paired samples. A 187 protein targeted
MS assay was used to collect data from all 274 patients selected
for this validation study, and the 138 paired patient samples in
the discovery partition were used, to determine the abundance
levels for the proteins to be evaluated in a variety of feature
selection and classifier assembly workflows.
[0359] Based on the analysis, 12 models were built and selected for
validation 30 of the original 187 proteins. These 12 models had
AUCs that ranged from about 0.77 to 0.83. Classifier models were
then selected and their protein components and algorithms locked to
evaluate them using the data collected from the held-out validation
partition. The samples were blinded to the laboratory and analysis
staff. All 12 models validated successfully and their AUC's were
not significantly different than predicted from the discovery
partition. One classifier with 13 component proteins had a
validation AUC of 0.91 and a test performance of 87% sensitivity
and 81% specificity at the point of maximum accuracy. This
classifier's performance on early CRC was 90% sensitivity (46 out
of 51 stage I/II cancers correctly classified).
[0360] To confirm clinical validity, selected proteins were
evaluated in a new cohort of samples and with another detection
technology, ELISA. This approach helps ensure the results achieved
in the first study were not the result of technological or study
design bias. For a second validation sample set, patient plasma
samples were obtained from a Danish study, Endoscopy II, performed
by Dr. Hans Nielsen of Hvidovre Hospital/University of Copenhagen.
This study collected samples from 4, 698 patients who were referred
for diagnostic colonoscopy based on at least one symptom of bowel
neoplasia. Plasma was collected prior to colonoscopy and processed
to plasma and stored using validated standard operating procedures.
Using this cohort of patient samples, 150 CRC plasma samples and
150 age- and gender-matched controls were selected for a second
discovery and validation study. The samples collected ranged from
patient ages 50 to 75, across all four CRC stages, and across the
colon and rectum. The controls were designed from the subset of
patients who had no comorbidities and no findings on colonoscopy in
order to most closely mimic anticipated intent-to-test population:
patients with above-average risk but no prior clear indications for
colonoscopy. Commercially available ELISA reagents were used for 28
of the 30 proteins that comprised the 12 classifiers from the first
study.
[0361] Using the 300-patient plasma samples selected from the
Endoscopy II study and the 28 ELISAs for proteins previously
validated, protein abundance data was collected target. Based on
new ELISA data for the 28 proteins in the 150 sample discovery
partition, a machine learning approach was used in ten rounds of
10-fold cross validation to build 5 models for evaluation. The
models ranged in size from 7 to 18 proteins and produced a range of
discovery performance from 0.83 to 0.86, based on Receiver
Operating Characteristic, or ROC, area under the curve, or AUC. An
ideal test, with 100% sensitivity and 100% specificity would begin
in the lower left corner, go straight to the upper left corner,
then to the upper right corner, and the AUC would be 1.00. On the
other hand, a test without predictive value would be a straight
diagonal line from the lower left corner to the upper right corner,
with an AUC of 0.50. Once models were selected and their components
and algorithm were locked, the data from the validation partition
were used to evaluate the models.
[0362] CRC marker proteins were further validated for their ability
to comprise panels that have significant detection performance for
advanced adenoma, the precursor lesion to CRC. In the natural
history of CRC development it is generally accepted that all CRC's
come from advanced adenomas but not all advanced adenomas become
CRCs. Nevertheless, several studies have demonstrated that the
removal of advanced adenomas during screening colonoscopy
significantly reduces the incidence of subsequent colorectal
cancer.
[0363] Using the Danish Endoscopy II study, a new 302 patient, age-
and gender-matched, site-stratified, subset of samples was selected
using the definition for advanced adenoma commonly used in other
recent, external studies. Using the same ELISAs for the 28 proteins
as in the prior CRC validation study, data were collected from each
of the 302 samples, divided into a 150-sample discovery partition
and a 152-sample validation partition. Using the same methods for
classifier assembly in cross-validation and final validation as
described above, an advanced adenoma classifier was identified that
comprises 4 of the 28 proteins and has 45% sensitivity and 80%
specificity (ROC AUC 0.65) Example 20
[0364] A total of 6 biomarkers were selected at random from a panel
comprising: AACT, CATD, CEA, CO3, CO9, MIF, PSGL, and SEPR. A total
of 6 biomarkers were also selected at random from the mass spec
analyzed validation study comprising 187 proteins. The panel
comprising 6 proteins selected from a biomarker panel comprising
AACT, CATD, CEA, CO3, CO9, MIF, PSGL, and SEPR was validated in 373
patients and performed 95% better than the 6 biomarkers selected at
random from the mass spec analyzed validation study comprising 187
proteins.
Example 21--Panel Comparison
[0365] Panels disclosed herein were compared to randomly determined
panels derived from enriched biomarker lists to assess their
performance relative to background chance.
[0366] As discussed above and as demonstrated in FIG. 1, panels
disclosed herein were derived by generating a 187 member list of
markers identified in the literature as being of potential
relevance to cancer detection. Biomarkers in this list were then
assayed in a sample set derived from individuals of known
colorectal health status, and 28 biomarkers that correlated
strongly with sample colorectal health status were identified.
These 28 markers were assayed through an ELISA based approach on a
second set of samples derived from a second set of individuals of
known colorectal health status, and the panels disclosed herein
were produced.
[0367] Thus, the MS-identified 28 marker set was already
substantially enriched over the initial 187 member set identifiable
to one of skill in the art. Nonetheless, an investigation was made
into the performance of the panels disclosed herein relative to the
MS-enriched biomarker dataset.
[0368] Panels of various sizes were generated from the 28-member MS
enriched set, and these panels were assessed as to their predictive
value on a marker-quantified sample set derived from individuals of
known colorectal health status. Random panels were generated using
Random Forest models and using SVM models. AUC values were
determined for each random panel. AUC distribution curves for
panels of a given size were generated.
[0369] The AUC distribution curves are presented in FIG. 20. The
three top graphs represent panels generated through SVM, while the
three bottom graphs depict panels generated through Random Forest
modeling. For each plot, the panel size is listed at top with grey
back shading. The Y axis indicates number of panels, while the X
axis indicates AUC value for the panel columns indicated. The
dashed line indicates the AUC value which 95% of the randomly
generated panels from the MS-enriched dataset fall below.
[0370] The results are summarized in Tables 13 and 14.
TABLE-US-00011 TABLE 13 SVM MS-Enriched Panel Characteristics Panel
Number Min Max Mean Stdev Median 95% Size of Combos AUC AUC AUC AUC
AUC AUC 2 378 0.380 0.741 0.544 0.074 0.545 0.667 3 3276 0.389
0.806 0.594 0.079 0.600 0.714 4 10000 0.387 0.822 0.637 0.076 0.644
0.748 5 10000 0.401 0.834 0.669 0.068 0.676 0.769 6 10000 0.406
0.837 0.694 0.061 0.701 0.782 7 10000 0.416 0.843 0.711 0.055 0.716
0.792 8 10000 0.416 0.851 0.725 0.049 0.730 0.797 9 10000 0.409
0.848 0.734 0.045 0.737 0.800 10 10000 0.427 0.848 0.743 0.041
0.746 0.803
TABLE-US-00012 TABLE 14 Random forest-Enriched Panel
Characteristics Panel Number Min Max Mean Stdev Median 95% Size of
Combos AUC AUC AUC AUC AUC AUC 2 378 0.410 0.799 0.610 0.083 0.616
0.746 3 3276 0.391 0.832 0.644 0.077 0.654 0.755 4 10000 0.388
0.840 0.668 0.070 0.678 0.765 5 10000 0.395 0.835 0.685 0.062 0.693
0.774 6 10000 0.397 0.834 0.697 0.059 0.703 0.781 7 10000 0.439
0.836 0.708 0.054 0.713 0.789 8 10000 0.443 0,.839 0.718 0.049
0.722 0.791 9 10000 0.448 0.835 0.723 0.046 0.725 0.794 10 10000
0.483 0.833 0.730 0.043 0.732 0.796
[0371] As indicated in the graphs and models, panels of 8-10
members demonstrate mean and median AUC values of about 0.71-0.73.
95% of the curves display an AUC of 0.80 or less.
[0372] Referring to FIG. 2, one sees that a lead 9 member panel
disclosed herein for the assessment of colorectal health has a
validated AUC value of 0.83. This value is greater than the 95%
threshold AUC of comparable 9 and even 10 member panels, and is
comparable to the maximum AUC values observed for the entire
datasets.
[0373] Referring also to Table 8, one sees that comparable AUC
values, far superior to those of the randomly generated panels, are
obtained for Models 1-13. Model 12, it is observed, differs from
the panel of FIG. 2 in that age is excluded as a biomarker.
[0374] This analysis makes clear that panels herein outperform
randomly generated panels, even randomly derived panels selected
from biomarkers that are already experimentally enriched to the 28
best targeted-MS identified markers from a 187 member set
identified in the art. That is, even upon 6.times. enrichment of
markers above a set taught in the art, panels herein outperform
essentially 100% of the randomly generated panels derived
therefrom.
Example 22--CRC and AA Test Implementation
[0375] Throughout this example, patients 1, 2, and 3 are
representative of patient data generated through the methods, kits,
systems and compositions herein but in the interest of patient
confidentiality, none of patients 1, 2 and 3 represent any
patient's actual data.
[0376] An exemplary first patient, second patient and third patient
each provide a blood sample for analysis. The samples are shipped
to a processing center and ELISA reagents are used to determine CRC
and AA panel levels using reagents to determine levels of AACT,
CEA, CO3, CO9, MIF, PSGL, SEPR, CATD, CLUS, GDF15, SAA1. Patient
age is also provided.
[0377] Biomarkers are measured and the results presented in Table
15.
TABLE-US-00013 TABLE 15 CRC/AA Test Input Measurements Panel CRC
CRC/AA AA Patient AACT CEA CO9 SEPR CO3 MIF PSGL Age CATD CLUS
GDF15 SAA1 1 246600 19 161800 105500 820 8 500 46 37100 5440 119
4537 2 171300 7 20800 108100 270 90 290 68 6190 8450 179 2290 3
215000 7 54100 16600 490 85 500 79 45100 5310 24 4178
[0378] The biomarker panel levels for each of the three patients
are assigned Model Scores according to a Machine Learning Model
assembled from panel levels of samples from reference individuals
of known colorectal health status as depicted in FIG. 1. From the
Machine Learning Model, a cutoff score of 2.9 is calculated as the
lower limit for a positive CRC score. Scores below this cutoff are
called negative for colorectal cancer. An `indeterminate range` is
identified among the negative scores, such that patient scores
falling within the intermediate range are marked for further
analysis. The indeterminate range spans scores of 1.24-2.46. Scores
above the intermediate range but below the positive cutoff are in
some cases additionally scrutinized. Through a similar approach, a
cutoff score of 0.25 is calculated as the lower limit for a
positive AA score.
[0379] Patient panel levels are assessed and a score assigned to
each panel for CRC and AA. Depending on the score, a follow up
assay is recommended and a diagnosis is generated according to this
follow-up assay. The results are presented in Table 16.
TABLE-US-00014 TABLE 16 CRC/AA Test Output Scores and Measurements
CRC CRC CRC AA AA Patient Score Call Diagnosis Score AA Call
Diagnosis 1 1.7 Indeterminate Adenoma 1.0 Positive Adv. Adenoma 2
0.7 Negative No 0.3 Negative No findings findings 3 5.9 Positive
Colon 0.9 Positive No Cancer findings
[0380] Patient 1 is assigned a CRC model score of 1.7. The score is
below the 2.9 cutoff score for a positive call, but is scored as
indeterminate. Patient 1 is assigned an AA score of 1.0, and is
called positive for advanced adenoma. A report is generated and
provided to the patient.
[0381] The patient undergoes a colonoscopy. No colorectal cancer is
detected, but a noncancerous adenoma is detected. The adenoma is
removed and the patient is later confirmed to be colon cancer and
adenoma free by a follow-up test. The patient is observed for 5
years and no symptoms or change in colorectal cancer status is
observed, indicating that the test correctly identified the
patient's status as negative for colon cancer.
[0382] Patient 2 is assigned a CRC model score of 0.72 and is
called negative for colorectal cancer. Patient 2 is assigned an AA
model score of 0.29 and is called negative for advanced adenoma. A
report is generated and provided to the patient.
[0383] The patient follows up with a stool sample test and the
results are similarly negative. The patient is observed for 5 years
and no symptoms or change in colorectal health status is observed,
indicating that the test correctly predicted no colorectal cancer
and no advanced adenoma in the individual.
[0384] Patient 3 is assigned a CRC model score of 5.9 and is called
positive for colorectal cancer. Patient 3 is assigned an AA score
of 0.9 and is called positive for AA. A report is generated and
provided to the patient.
[0385] The patient undergoes a colonoscopy. Early stage colorectal
cancer is detected, but no adenoma is detected.
[0386] The patient undergoes colon cancer treatment and symptoms
are alleviated. A second blood sample is taken from the patient
following treatment and a CRC score below 2.9 is assigned. A
colonoscopy confirms that the colorectal cancer is no longer
present in the individual.
[0387] This example demonstrates various features of the panels
herein. The CRC and AA panels are used in combination and share
common markers. The panels are derived from blood and are shipped
to be tested elsewhere. A report is generated and provided to the
patient. The results are independently corroborated using an
invasive approach such as a colonoscopy or noninvasive approach
such as a stool test. The test results are largely corroborated by
independent assays. Example 23--CRC and AA score analysis
[0388] The data in Table 15 allows further analysis of the CRC and
AA panel performances.
[0389] For instance, an examination of Table 15 is illustrative of
relevant aspects of panel performance relative to the predictive
value of its individual markers.
[0390] One sees that for some markers, the individual marker level
corresponds with the overall panel result. For example, SEPR levels
for patient 1 and patient 2 are similar at about 10,000, while
patient 3 scores substantially lower at 1,600. This grouping is
consistent with the overall scoring of patient 1 and patient 2 as
negative or indeterminate for CRC, while patient 3 scored
positive.
[0391] However, in the majority of the cases, individual marker
levels do not predict the outcome that one finds upon analyzing the
panel level as a whole. For biomarkers AACT, CO9, and CO3, patient
3 levels are intermediate between those of patient 1 and patient 2.
For biomarkers CEAMIF and PSGL, patient 3 levels roughly match
those of either patient 1 or patient 2.
[0392] Thus, looking at these biomarkers individually, one does not
find an indication that patient 3 rather than patient 1 or patient
2 is likely positive for CRC.
[0393] These measurements indicate that the CRC panel as a whole
possesses a predictive value that surpasses that of its constituent
biomarker members. Furthermore, the CRC biomarker panel as a whole
provides a predictive value that in some cases, contradicts the
prediction of its individual members. Accordingly, the CRC
biomarker panel as a whole provides a predictive value that is
better than its components and that is more than a simple
collection of its individual marker results. Example 24--Clinical
Utility of Noninvasive, Accurate Colorectal Health Assay
[0394] A recalcitrant patient demonstrated symptoms of CRC but
refused a colonoscopy. The patient's primary care physician ordered
a SimpliPro colorectal health assessment test. The results
indicated that the patient was at a high risk for CRC and for AA.
The patient consulted with family and was convinced to schedule a
colonoscopy. The colonoscopy revealed polyps and an early stage
cancerous mass, all of which were removed during the procedure. A
follow-up colorectal health assessment indicated that the patient
is cancer free. The patient's early stage cancerous mass would
likely have progressed to advanced disease with a high probability
of death without the colonoscopy and concurrent polypectomy.
[0395] This Example demonstrates the benefit to the public of
offering a noninvasive colorectal health assay that is both
sensitive and specific, and is easily complied with. In combination
with Example 25, below, this example demonstrates that the
reluctance to undergo a colonoscopy is common, and that it can have
severe health consequences if it results in an early stage cancer
not being detected when it is relatively easily treated.
Example 25--Clinical Utility of Noninvasive, Accurate Colorectal
Health Assay
[0396] A recalcitrant patient demonstrated symptoms of CRC but
delayed a colonoscopy for over 6 months. The patient's primary care
physician ordered a SimpliPro colorectal health assessment test.
The results indicated that the patient was at a high risk for CRC
and for AA. The patient scheduled a colonoscopy. During the
procedure, a 6 cm malignant mass was identified and removed. A
follow-up colorectal health assessment indicated that the patient
is cancer free. The patient's early stage cancerous mass would
likely have progressed to advanced disease with a high probability
of death without the colonoscopy and concurrent polypectomy.
[0397] This Example demonstrates the benefit to the public of
offering a noninvasive colorectal health assay that is both
sensitive and specific, and is easily complied with. In combination
with Example 24, above, this example demonstrates that the
reluctance to undergo a colonoscopy is common, and that it can have
severe health consequences if it results in an early stage cancer
not being detected when it is relatively easily treated.
[0398] While preferred embodiments of the disclosure have been
shown and described herein, it will be obvious to those skilled in
the art that such embodiments are provided by way of example only.
Numerous variations, changes, and substitutions will now occur to
those skilled in the art without departing from the disclosure. It
should be understood that various alternatives to the embodiments
of the disclosure described herein may be employed in practicing
the disclosure. It is intended that the following claims define the
scope of the disclosure and that methods and structures within the
scope of these claims and their equivalents be covered thereby.
Sequence CWU 1
1
591201PRTHomo sapiens 1Met Ala Leu Ser Trp Val Leu Thr Val Leu Ser
Leu Leu Pro Leu Leu1 5 10 15Glu Ala Gln Ile Pro Leu Cys Ala Asn Leu
Val Pro Val Pro Ile Thr 20 25 30Asn Ala Thr Leu Asp Gln Ile Thr Gly
Lys Trp Phe Tyr Ile Ala Ser 35 40 45Ala Phe Arg Asn Glu Glu Tyr Asn
Lys Ser Val Gln Glu Ile Gln Ala 50 55 60Thr Phe Phe Tyr Phe Thr Pro
Asn Lys Thr Glu Asp Thr Ile Phe Leu65 70 75 80Arg Glu Tyr Gln Thr
Arg Gln Asp Gln Cys Ile Tyr Asn Thr Thr Tyr 85 90 95Leu Asn Val Gln
Arg Glu Asn Gly Thr Ile Ser Arg Tyr Val Gly Gly 100 105 110Gln Glu
His Phe Ala His Leu Leu Ile Leu Arg Asp Thr Lys Thr Tyr 115 120
125Met Leu Ala Phe Asp Val Asn Asp Glu Lys Asn Trp Gly Leu Ser Val
130 135 140Tyr Ala Asp Lys Pro Glu Thr Thr Lys Glu Gln Leu Gly Glu
Phe Tyr145 150 155 160Glu Ala Leu Asp Cys Leu Arg Ile Pro Lys Ser
Asp Val Val Tyr Thr 165 170 175Asp Trp Lys Lys Asp Lys Cys Glu Pro
Leu Glu Lys Gln His Glu Lys 180 185 190Glu Arg Lys Gln Glu Glu Gly
Glu Ser 195 2002418PRTHomo sapiens 2Met Pro Ser Ser Val Ser Trp Gly
Ile Leu Leu Leu Ala Gly Leu Cys1 5 10 15Cys Leu Val Pro Val Ser Leu
Ala Glu Asp Pro Gln Gly Asp Ala Ala 20 25 30Gln Lys Thr Asp Thr Ser
His His Asp Gln Asp His Pro Thr Phe Asn 35 40 45Lys Ile Thr Pro Asn
Leu Ala Glu Phe Ala Phe Ser Leu Tyr Arg Gln 50 55 60Leu Ala His Gln
Ser Asn Ser Thr Asn Ile Phe Phe Ser Pro Val Ser65 70 75 80Ile Ala
Thr Ala Phe Ala Met Leu Ser Leu Gly Thr Lys Ala Asp Thr 85 90 95His
Asp Glu Ile Leu Glu Gly Leu Asn Phe Asn Leu Thr Glu Ile Pro 100 105
110Glu Ala Gln Ile His Glu Gly Phe Gln Glu Leu Leu Arg Thr Leu Asn
115 120 125Gln Pro Asp Ser Gln Leu Gln Leu Thr Thr Gly Asn Gly Leu
Phe Leu 130 135 140Ser Glu Gly Leu Lys Leu Val Asp Lys Phe Leu Glu
Asp Val Lys Lys145 150 155 160Leu Tyr His Ser Glu Ala Phe Thr Val
Asn Phe Gly Asp Thr Glu Glu 165 170 175Ala Lys Lys Gln Ile Asn Asp
Tyr Val Glu Lys Gly Thr Gln Gly Lys 180 185 190Ile Val Asp Leu Val
Lys Glu Leu Asp Arg Asp Thr Val Phe Ala Leu 195 200 205Val Asn Tyr
Ile Phe Phe Lys Gly Lys Trp Glu Arg Pro Phe Glu Val 210 215 220Lys
Asp Thr Glu Glu Glu Asp Phe His Val Asp Gln Val Thr Thr Val225 230
235 240Lys Val Pro Met Met Lys Arg Leu Gly Met Phe Asn Ile Gln His
Cys 245 250 255Lys Lys Leu Ser Ser Trp Val Leu Leu Met Lys Tyr Leu
Gly Asn Ala 260 265 270Thr Ala Ile Phe Phe Leu Pro Asp Glu Gly Lys
Leu Gln His Leu Glu 275 280 285Asn Glu Leu Thr His Asp Ile Ile Thr
Lys Phe Leu Glu Asn Glu Asp 290 295 300Arg Arg Ser Ala Ser Leu His
Leu Pro Lys Leu Ser Ile Thr Gly Thr305 310 315 320Tyr Asp Leu Lys
Ser Val Leu Gly Gln Leu Gly Ile Thr Lys Val Phe 325 330 335Ser Asn
Gly Ala Asp Leu Ser Gly Val Thr Glu Glu Ala Pro Leu Lys 340 345
350Leu Ser Lys Ala Val His Lys Ala Val Leu Thr Ile Asp Glu Lys Gly
355 360 365Thr Glu Ala Ala Gly Ala Met Phe Leu Glu Ala Ile Pro Met
Ser Ile 370 375 380Pro Pro Glu Val Lys Phe Asn Lys Pro Phe Val Phe
Leu Met Ile Glu385 390 395 400Gln Asn Thr Lys Ser Pro Leu Phe Met
Gly Lys Val Val Asn Pro Thr 405 410 415Gln Lys3423PRTHomo sapiens
3Met Glu Arg Met Leu Pro Leu Leu Ala Leu Gly Leu Leu Ala Ala Gly1 5
10 15Phe Cys Pro Ala Val Leu Cys His Pro Asn Ser Pro Leu Asp Glu
Glu 20 25 30Asn Leu Thr Gln Glu Asn Gln Asp Arg Gly Thr His Val Asp
Leu Gly 35 40 45Leu Ala Ser Ala Asn Val Asp Phe Ala Phe Ser Leu Tyr
Lys Gln Leu 50 55 60Val Leu Lys Ala Pro Asp Lys Asn Val Ile Phe Ser
Pro Leu Ser Ile65 70 75 80Ser Thr Ala Leu Ala Phe Leu Ser Leu Gly
Ala His Asn Thr Thr Leu 85 90 95Thr Glu Ile Leu Lys Gly Leu Lys Phe
Asn Leu Thr Glu Thr Ser Glu 100 105 110Ala Glu Ile His Gln Ser Phe
Gln His Leu Leu Arg Thr Leu Asn Gln 115 120 125Ser Ser Asp Glu Leu
Gln Leu Ser Met Gly Asn Ala Met Phe Val Lys 130 135 140Glu Gln Leu
Ser Leu Leu Asp Arg Phe Thr Glu Asp Ala Lys Arg Leu145 150 155
160Tyr Gly Ser Glu Ala Phe Ala Thr Asp Phe Gln Asp Ser Ala Ala Ala
165 170 175Lys Lys Leu Ile Asn Asp Tyr Val Lys Asn Gly Thr Arg Gly
Lys Ile 180 185 190Thr Asp Leu Ile Lys Asp Leu Asp Ser Gln Thr Met
Met Val Leu Val 195 200 205Asn Tyr Ile Phe Phe Lys Ala Lys Trp Glu
Met Pro Phe Asp Pro Gln 210 215 220Asp Thr His Gln Ser Arg Phe Tyr
Leu Ser Lys Lys Lys Trp Val Met225 230 235 240Val Pro Met Met Ser
Leu His His Leu Thr Ile Pro Tyr Phe Arg Asp 245 250 255Glu Glu Leu
Ser Cys Thr Val Val Glu Leu Lys Tyr Thr Gly Asn Ala 260 265 270Ser
Ala Leu Phe Ile Leu Pro Asp Gln Asp Lys Met Glu Glu Val Glu 275 280
285Ala Met Leu Leu Pro Glu Thr Leu Lys Arg Trp Arg Asp Ser Leu Glu
290 295 300Phe Arg Glu Ile Gly Glu Leu Tyr Leu Pro Lys Phe Ser Ile
Ser Arg305 310 315 320Asp Tyr Asn Leu Asn Asp Ile Leu Leu Gln Leu
Gly Ile Glu Glu Ala 325 330 335Phe Thr Ser Lys Ala Asp Leu Ser Gly
Ile Thr Gly Ala Arg Asn Leu 340 345 350Ala Val Ser Gln Val Val His
Lys Ala Val Leu Asp Val Phe Glu Glu 355 360 365Gly Thr Glu Ala Ser
Ala Ala Thr Ala Val Lys Ile Thr Leu Leu Ser 370 375 380Ala Leu Val
Glu Thr Arg Thr Ile Val Arg Phe Asn Arg Pro Phe Leu385 390 395
400Met Ile Ile Val Pro Thr Asp Thr Gln Asn Ile Phe Phe Met Ser Lys
405 410 415Val Thr Asn Pro Lys Gln Ala 4204267PRTHomo sapiens 4Met
Lys Ala Ala Val Leu Thr Leu Ala Val Leu Phe Leu Thr Gly Ser1 5 10
15Gln Ala Arg His Phe Trp Gln Gln Asp Glu Pro Pro Gln Ser Pro Trp
20 25 30Asp Arg Val Lys Asp Leu Ala Thr Val Tyr Val Asp Val Leu Lys
Asp 35 40 45Ser Gly Arg Asp Tyr Val Ser Gln Phe Glu Gly Ser Ala Leu
Gly Lys 50 55 60Gln Leu Asn Leu Lys Leu Leu Asp Asn Trp Asp Ser Val
Thr Ser Thr65 70 75 80Phe Ser Lys Leu Arg Glu Gln Leu Gly Pro Val
Thr Gln Glu Phe Trp 85 90 95Asp Asn Leu Glu Lys Glu Thr Glu Gly Leu
Arg Gln Glu Met Ser Lys 100 105 110Asp Leu Glu Glu Val Lys Ala Lys
Val Gln Pro Tyr Leu Asp Asp Phe 115 120 125Gln Lys Lys Trp Gln Glu
Glu Met Glu Leu Tyr Arg Gln Lys Val Glu 130 135 140Pro Leu Arg Ala
Glu Leu Gln Glu Gly Ala Arg Gln Lys Leu His Glu145 150 155 160Leu
Gln Glu Lys Leu Ser Pro Leu Gly Glu Glu Met Arg Asp Arg Ala 165 170
175Arg Ala His Val Asp Ala Leu Arg Thr His Leu Ala Pro Tyr Ser Asp
180 185 190Glu Leu Arg Gln Arg Leu Ala Ala Arg Leu Glu Ala Leu Lys
Glu Asn 195 200 205Gly Gly Ala Arg Leu Ala Glu Tyr His Ala Lys Ala
Thr Glu His Leu 210 215 220Ser Thr Leu Ser Glu Lys Ala Lys Pro Ala
Leu Glu Asp Leu Arg Gln225 230 235 240Gly Leu Leu Pro Val Leu Glu
Ser Phe Lys Val Ser Phe Leu Ser Ala 245 250 255Leu Glu Glu Tyr Thr
Lys Lys Leu Asn Thr Gln 260 2655412PRTHomo sapiens 5Met Gln Pro Ser
Ser Leu Leu Pro Leu Ala Leu Cys Leu Leu Ala Ala1 5 10 15Pro Ala Ser
Ala Leu Val Arg Ile Pro Leu His Lys Phe Thr Ser Ile 20 25 30Arg Arg
Thr Met Ser Glu Val Gly Gly Ser Val Glu Asp Leu Ile Ala 35 40 45Lys
Gly Pro Val Ser Lys Tyr Ser Gln Ala Val Pro Ala Val Thr Glu 50 55
60Gly Pro Ile Pro Glu Val Leu Lys Asn Tyr Met Asp Ala Gln Tyr Tyr65
70 75 80Gly Glu Ile Gly Ile Gly Thr Pro Pro Gln Cys Phe Thr Val Val
Phe 85 90 95Asp Thr Gly Ser Ser Asn Leu Trp Val Pro Ser Ile His Cys
Lys Leu 100 105 110Leu Asp Ile Ala Cys Trp Ile His His Lys Tyr Asn
Ser Asp Lys Ser 115 120 125Ser Thr Tyr Val Lys Asn Gly Thr Ser Phe
Asp Ile His Tyr Gly Ser 130 135 140Gly Ser Leu Ser Gly Tyr Leu Ser
Gln Asp Thr Val Ser Val Pro Cys145 150 155 160Gln Ser Ala Ser Ser
Ala Ser Ala Leu Gly Gly Val Lys Val Glu Arg 165 170 175Gln Val Phe
Gly Glu Ala Thr Lys Gln Pro Gly Ile Thr Phe Ile Ala 180 185 190Ala
Lys Phe Asp Gly Ile Leu Gly Met Ala Tyr Pro Arg Ile Ser Val 195 200
205Asn Asn Val Leu Pro Val Phe Asp Asn Leu Met Gln Gln Lys Leu Val
210 215 220Asp Gln Asn Ile Phe Ser Phe Tyr Leu Ser Arg Asp Pro Asp
Ala Gln225 230 235 240Pro Gly Gly Glu Leu Met Leu Gly Gly Thr Asp
Ser Lys Tyr Tyr Lys 245 250 255Gly Ser Leu Ser Tyr Leu Asn Val Thr
Arg Lys Ala Tyr Trp Gln Val 260 265 270His Leu Asp Gln Val Glu Val
Ala Ser Gly Leu Thr Leu Cys Lys Glu 275 280 285Gly Cys Glu Ala Ile
Val Asp Thr Gly Thr Ser Leu Met Val Gly Pro 290 295 300Val Asp Glu
Val Arg Glu Leu Gln Lys Ala Ile Gly Ala Val Pro Leu305 310 315
320Ile Gln Gly Glu Tyr Met Ile Pro Cys Glu Lys Val Ser Thr Leu Pro
325 330 335Ala Ile Thr Leu Lys Leu Gly Gly Lys Gly Tyr Lys Leu Ser
Pro Glu 340 345 350Asp Tyr Thr Leu Lys Val Ser Gln Ala Gly Lys Thr
Leu Cys Leu Ser 355 360 365Gly Phe Met Gly Met Asp Ile Pro Pro Pro
Ser Gly Pro Leu Trp Ile 370 375 380Leu Gly Asp Val Phe Ile Gly Arg
Tyr Tyr Thr Val Phe Asp Arg Asp385 390 395 400Asn Asn Arg Val Gly
Phe Ala Glu Ala Ala Arg Leu 405 4106252PRTHomo sapiens 6Met Gly Pro
Pro Ser Ala Ser Pro His Arg Glu Cys Ile Pro Trp Gln1 5 10 15Gly Leu
Leu Leu Thr Ala Ser Leu Leu Asn Phe Trp Asn Pro Pro Thr 20 25 30Thr
Ala Lys Leu Thr Ile Glu Ser Met Pro Leu Ser Val Ala Glu Gly 35 40
45Lys Glu Val Leu Leu Leu Val His Asn Leu Pro Gln His Leu Phe Gly
50 55 60Tyr Ser Trp Tyr Lys Gly Glu Arg Val Asp Gly Asn Ser Leu Ile
Val65 70 75 80Gly Tyr Val Ile Gly Thr Gln Gln Ala Thr Pro Gly Ala
Ala Tyr Ser 85 90 95Gly Arg Glu Thr Ile Tyr Thr Asn Ala Ser Leu Leu
Ile Gln Asn Val 100 105 110Thr Gln Asn Asp Ile Gly Phe Tyr Thr Leu
Gln Val Ile Lys Ser Asp 115 120 125Leu Val Asn Glu Glu Ala Thr Gly
Gln Phe His Val Tyr Gln Glu Asn 130 135 140Ala Pro Gly Leu Pro Val
Gly Ala Val Ala Gly Ile Val Thr Gly Val145 150 155 160Leu Val Gly
Val Ala Leu Val Ala Ala Leu Val Cys Phe Leu Leu Leu 165 170 175Ala
Lys Thr Gly Arg Thr Ser Ile Gln Arg Asp Leu Lys Glu Gln Gln 180 185
190Pro Gln Ala Leu Ala Pro Gly Arg Gly Pro Ser His Ser Ser Ala Phe
195 200 205Ser Met Ser Pro Leu Ser Thr Ala Gln Ala Pro Leu Pro Asn
Pro Arg 210 215 220Thr Ala Ala Ser Ile Tyr Glu Glu Leu Leu Lys His
Asp Thr Asn Ile225 230 235 240Tyr Cys Arg Met Asp His Lys Ala Glu
Val Ala Ser 245 2507449PRTHomo sapiens 7Met Met Lys Thr Leu Leu Leu
Phe Val Gly Leu Leu Leu Thr Trp Glu1 5 10 15Ser Gly Gln Val Leu Gly
Asp Gln Thr Val Ser Asp Asn Glu Leu Gln 20 25 30Glu Met Ser Asn Gln
Gly Ser Lys Tyr Val Asn Lys Glu Ile Gln Asn 35 40 45Ala Val Asn Gly
Val Lys Gln Ile Lys Thr Leu Ile Glu Lys Thr Asn 50 55 60Glu Glu Arg
Lys Thr Leu Leu Ser Asn Leu Glu Glu Ala Lys Lys Lys65 70 75 80Lys
Glu Asp Ala Leu Asn Glu Thr Arg Glu Ser Glu Thr Lys Leu Lys 85 90
95Glu Leu Pro Gly Val Cys Asn Glu Thr Met Met Ala Leu Trp Glu Glu
100 105 110Cys Lys Pro Cys Leu Lys Gln Thr Cys Met Lys Phe Tyr Ala
Arg Val 115 120 125Cys Arg Ser Gly Ser Gly Leu Val Gly Arg Gln Leu
Glu Glu Phe Leu 130 135 140Asn Gln Ser Ser Pro Phe Tyr Phe Trp Met
Asn Gly Asp Arg Ile Asp145 150 155 160Ser Leu Leu Glu Asn Asp Arg
Gln Gln Thr His Met Leu Asp Val Met 165 170 175Gln Asp His Phe Ser
Arg Ala Ser Ser Ile Ile Asp Glu Leu Phe Gln 180 185 190Asp Arg Phe
Phe Thr Arg Glu Pro Gln Asp Thr Tyr His Tyr Leu Pro 195 200 205Phe
Ser Leu Pro His Arg Arg Pro His Phe Phe Phe Pro Lys Ser Arg 210 215
220Ile Val Arg Ser Leu Met Pro Phe Ser Pro Tyr Glu Pro Leu Asn
Phe225 230 235 240His Ala Met Phe Gln Pro Phe Leu Glu Met Ile His
Glu Ala Gln Gln 245 250 255Ala Met Asp Ile His Phe His Ser Pro Ala
Phe Gln His Pro Pro Thr 260 265 270Glu Phe Ile Arg Glu Gly Asp Asp
Asp Arg Thr Val Cys Arg Glu Ile 275 280 285Arg His Asn Ser Thr Gly
Cys Leu Arg Met Lys Asp Gln Cys Asp Lys 290 295 300Cys Arg Glu Ile
Leu Ser Val Asp Cys Ser Thr Asn Asn Pro Ser Gln305 310 315 320Ala
Lys Leu Arg Arg Glu Leu Asp Glu Ser Leu Gln Val Ala Glu Arg 325 330
335Leu Thr Arg Lys Tyr Asn Glu Leu Leu Lys Ser Tyr Gln Trp Lys Met
340 345 350Leu Asn Thr Ser Ser Leu Leu Glu Gln Leu Asn Glu Gln Phe
Asn Trp 355 360 365Val Ser Arg Leu Ala Asn Leu Thr Gln Gly Glu Asp
Gln Tyr Tyr Leu 370 375 380Arg Val Thr Thr Val Ala Ser His Thr Ser
Asp Ser Asp Val Pro Ser385 390 395 400Gly Val Thr Glu Val Val Val
Lys Leu Phe Asp Ser Asp Pro Ile Thr 405 410 415Val Thr Val Pro Val
Glu Val Ser Arg Lys Asn Pro Lys Phe Met Glu 420 425 430Thr Val Ala
Glu Lys Ala Leu Gln Glu Tyr Arg Lys Lys His Arg Glu 435 440
445Glu81663PRTHomo sapiens 8Met Gly Pro Thr Ser Gly Pro Ser Leu Leu
Leu Leu Leu Leu Thr His1 5 10 15Leu Pro Leu Ala Leu Gly Ser Pro Met
Tyr Ser Ile Ile Thr Pro Asn 20 25 30Ile Leu Arg Leu Glu Ser Glu
Glu Thr Met Val Leu Glu Ala His Asp 35 40 45Ala Gln Gly Asp Val Pro
Val Thr Val Thr Val His Asp Phe Pro Gly 50 55 60Lys Lys Leu Val Leu
Ser Ser Glu Lys Thr Val Leu Thr Pro Ala Thr65 70 75 80Asn His Met
Gly Asn Val Thr Phe Thr Ile Pro Ala Asn Arg Glu Phe 85 90 95Lys Ser
Glu Lys Gly Arg Asn Lys Phe Val Thr Val Gln Ala Thr Phe 100 105
110Gly Thr Gln Val Val Glu Lys Val Val Leu Val Ser Leu Gln Ser Gly
115 120 125Tyr Leu Phe Ile Gln Thr Asp Lys Thr Ile Tyr Thr Pro Gly
Ser Thr 130 135 140Val Leu Tyr Arg Ile Phe Thr Val Asn His Lys Leu
Leu Pro Val Gly145 150 155 160Arg Thr Val Met Val Asn Ile Glu Asn
Pro Glu Gly Ile Pro Val Lys 165 170 175Gln Asp Ser Leu Ser Ser Gln
Asn Gln Leu Gly Val Leu Pro Leu Ser 180 185 190Trp Asp Ile Pro Glu
Leu Val Asn Met Gly Gln Trp Lys Ile Arg Ala 195 200 205Tyr Tyr Glu
Asn Ser Pro Gln Gln Val Phe Ser Thr Glu Phe Glu Val 210 215 220Lys
Glu Tyr Val Leu Pro Ser Phe Glu Val Ile Val Glu Pro Thr Glu225 230
235 240Lys Phe Tyr Tyr Ile Tyr Asn Glu Lys Gly Leu Glu Val Thr Ile
Thr 245 250 255Ala Arg Phe Leu Tyr Gly Lys Lys Val Glu Gly Thr Ala
Phe Val Ile 260 265 270Phe Gly Ile Gln Asp Gly Glu Gln Arg Ile Ser
Leu Pro Glu Ser Leu 275 280 285Lys Arg Ile Pro Ile Glu Asp Gly Ser
Gly Glu Val Val Leu Ser Arg 290 295 300Lys Val Leu Leu Asp Gly Val
Gln Asn Pro Arg Ala Glu Asp Leu Val305 310 315 320Gly Lys Ser Leu
Tyr Val Ser Ala Thr Val Ile Leu His Ser Gly Ser 325 330 335Asp Met
Val Gln Ala Glu Arg Ser Gly Ile Pro Ile Val Thr Ser Pro 340 345
350Tyr Gln Ile His Phe Thr Lys Thr Pro Lys Tyr Phe Lys Pro Gly Met
355 360 365Pro Phe Asp Leu Met Val Phe Val Thr Asn Pro Asp Gly Ser
Pro Ala 370 375 380Tyr Arg Val Pro Val Ala Val Gln Gly Glu Asp Thr
Val Gln Ser Leu385 390 395 400Thr Gln Gly Asp Gly Val Ala Lys Leu
Ser Ile Asn Thr His Pro Ser 405 410 415Gln Lys Pro Leu Ser Ile Thr
Val Arg Thr Lys Lys Gln Glu Leu Ser 420 425 430Glu Ala Glu Gln Ala
Thr Arg Thr Met Gln Ala Leu Pro Tyr Ser Thr 435 440 445Val Gly Asn
Ser Asn Asn Tyr Leu His Leu Ser Val Leu Arg Thr Glu 450 455 460Leu
Arg Pro Gly Glu Thr Leu Asn Val Asn Phe Leu Leu Arg Met Asp465 470
475 480Arg Ala His Glu Ala Lys Ile Arg Tyr Tyr Thr Tyr Leu Ile Met
Asn 485 490 495Lys Gly Arg Leu Leu Lys Ala Gly Arg Gln Val Arg Glu
Pro Gly Gln 500 505 510Asp Leu Val Val Leu Pro Leu Ser Ile Thr Thr
Asp Phe Ile Pro Ser 515 520 525Phe Arg Leu Val Ala Tyr Tyr Thr Leu
Ile Gly Ala Ser Gly Gln Arg 530 535 540Glu Val Val Ala Asp Ser Val
Trp Val Asp Val Lys Asp Ser Cys Val545 550 555 560Gly Ser Leu Val
Val Lys Ser Gly Gln Ser Glu Asp Arg Gln Pro Val 565 570 575Pro Gly
Gln Gln Met Thr Leu Lys Ile Glu Gly Asp His Gly Ala Arg 580 585
590Val Val Leu Val Ala Val Asp Lys Gly Val Phe Val Leu Asn Lys Lys
595 600 605Asn Lys Leu Thr Gln Ser Lys Ile Trp Asp Val Val Glu Lys
Ala Asp 610 615 620Ile Gly Cys Thr Pro Gly Ser Gly Lys Asp Tyr Ala
Gly Val Phe Ser625 630 635 640Asp Ala Gly Leu Thr Phe Thr Ser Ser
Ser Gly Gln Gln Thr Ala Gln 645 650 655Arg Ala Glu Leu Gln Cys Pro
Gln Pro Ala Ala Arg Arg Arg Arg Ser 660 665 670Val Gln Leu Thr Glu
Lys Arg Met Asp Lys Val Gly Lys Tyr Pro Lys 675 680 685Glu Leu Arg
Lys Cys Cys Glu Asp Gly Met Arg Glu Asn Pro Met Arg 690 695 700Phe
Ser Cys Gln Arg Arg Thr Arg Phe Ile Ser Leu Gly Glu Ala Cys705 710
715 720Lys Lys Val Phe Leu Asp Cys Cys Asn Tyr Ile Thr Glu Leu Arg
Arg 725 730 735Gln His Ala Arg Ala Ser His Leu Gly Leu Ala Arg Ser
Asn Leu Asp 740 745 750Glu Asp Ile Ile Ala Glu Glu Asn Ile Val Ser
Arg Ser Glu Phe Pro 755 760 765Glu Ser Trp Leu Trp Asn Val Glu Asp
Leu Lys Glu Pro Pro Lys Asn 770 775 780Gly Ile Ser Thr Lys Leu Met
Asn Ile Phe Leu Lys Asp Ser Ile Thr785 790 795 800Thr Trp Glu Ile
Leu Ala Val Ser Met Ser Asp Lys Lys Gly Ile Cys 805 810 815Val Ala
Asp Pro Phe Glu Val Thr Val Met Gln Asp Phe Phe Ile Asp 820 825
830Leu Arg Leu Pro Tyr Ser Val Val Arg Asn Glu Gln Val Glu Ile Arg
835 840 845Ala Val Leu Tyr Asn Tyr Arg Gln Asn Gln Glu Leu Lys Val
Arg Val 850 855 860Glu Leu Leu His Asn Pro Ala Phe Cys Ser Leu Ala
Thr Thr Lys Arg865 870 875 880Arg His Gln Gln Thr Val Thr Ile Pro
Pro Lys Ser Ser Leu Ser Val 885 890 895Pro Tyr Val Ile Val Pro Leu
Lys Thr Gly Leu Gln Glu Val Glu Val 900 905 910Lys Ala Ala Val Tyr
His His Phe Ile Ser Asp Gly Val Arg Lys Ser 915 920 925Leu Lys Val
Val Pro Glu Gly Ile Arg Met Asn Lys Thr Val Ala Val 930 935 940Arg
Thr Leu Asp Pro Glu Arg Leu Gly Arg Glu Gly Val Gln Lys Glu945 950
955 960Asp Ile Pro Pro Ala Asp Leu Ser Asp Gln Val Pro Asp Thr Glu
Ser 965 970 975Glu Thr Arg Ile Leu Leu Gln Gly Thr Pro Val Ala Gln
Met Thr Glu 980 985 990Asp Ala Val Asp Ala Glu Arg Leu Lys His Leu
Ile Val Thr Pro Ser 995 1000 1005Gly Cys Gly Glu Gln Asn Met Ile
Gly Met Thr Pro Thr Val Ile 1010 1015 1020Ala Val His Tyr Leu Asp
Glu Thr Glu Gln Trp Glu Lys Phe Gly 1025 1030 1035Leu Glu Lys Arg
Gln Gly Ala Leu Glu Leu Ile Lys Lys Gly Tyr 1040 1045 1050Thr Gln
Gln Leu Ala Phe Arg Gln Pro Ser Ser Ala Phe Ala Ala 1055 1060
1065Phe Val Lys Arg Ala Pro Ser Thr Trp Leu Thr Ala Tyr Val Val
1070 1075 1080Lys Val Phe Ser Leu Ala Val Asn Leu Ile Ala Ile Asp
Ser Gln 1085 1090 1095Val Leu Cys Gly Ala Val Lys Trp Leu Ile Leu
Glu Lys Gln Lys 1100 1105 1110Pro Asp Gly Val Phe Gln Glu Asp Ala
Pro Val Ile His Gln Glu 1115 1120 1125Met Ile Gly Gly Leu Arg Asn
Asn Asn Glu Lys Asp Met Ala Leu 1130 1135 1140Thr Ala Phe Val Leu
Ile Ser Leu Gln Glu Ala Lys Asp Ile Cys 1145 1150 1155Glu Glu Gln
Val Asn Ser Leu Pro Gly Ser Ile Thr Lys Ala Gly 1160 1165 1170Asp
Phe Leu Glu Ala Asn Tyr Met Asn Leu Gln Arg Ser Tyr Thr 1175 1180
1185Val Ala Ile Ala Gly Tyr Ala Leu Ala Gln Met Gly Arg Leu Lys
1190 1195 1200Gly Pro Leu Leu Asn Lys Phe Leu Thr Thr Ala Lys Asp
Lys Asn 1205 1210 1215Arg Trp Glu Asp Pro Gly Lys Gln Leu Tyr Asn
Val Glu Ala Thr 1220 1225 1230Ser Tyr Ala Leu Leu Ala Leu Leu Gln
Leu Lys Asp Phe Asp Phe 1235 1240 1245Val Pro Pro Val Val Arg Trp
Leu Asn Glu Gln Arg Tyr Tyr Gly 1250 1255 1260Gly Gly Tyr Gly Ser
Thr Gln Ala Thr Phe Met Val Phe Gln Ala 1265 1270 1275Leu Ala Gln
Tyr Gln Lys Asp Ala Pro Asp His Gln Glu Leu Asn 1280 1285 1290Leu
Asp Val Ser Leu Gln Leu Pro Ser Arg Ser Ser Lys Ile Thr 1295 1300
1305His Arg Ile His Trp Glu Ser Ala Ser Leu Leu Arg Ser Glu Glu
1310 1315 1320Thr Lys Glu Asn Glu Gly Phe Thr Val Thr Ala Glu Gly
Lys Gly 1325 1330 1335Gln Gly Thr Leu Ser Val Val Thr Met Tyr His
Ala Lys Ala Lys 1340 1345 1350Asp Gln Leu Thr Cys Asn Lys Phe Asp
Leu Lys Val Thr Ile Lys 1355 1360 1365Pro Ala Pro Glu Thr Glu Lys
Arg Pro Gln Asp Ala Lys Asn Thr 1370 1375 1380Met Ile Leu Glu Ile
Cys Thr Arg Tyr Arg Gly Asp Gln Asp Ala 1385 1390 1395Thr Met Ser
Ile Leu Asp Ile Ser Met Met Thr Gly Phe Ala Pro 1400 1405 1410Asp
Thr Asp Asp Leu Lys Gln Leu Ala Asn Gly Val Asp Arg Tyr 1415 1420
1425Ile Ser Lys Tyr Glu Leu Asp Lys Ala Phe Ser Asp Arg Asn Thr
1430 1435 1440Leu Ile Ile Tyr Leu Asp Lys Val Ser His Ser Glu Asp
Asp Cys 1445 1450 1455Leu Ala Phe Lys Val His Gln Tyr Phe Asn Val
Glu Leu Ile Gln 1460 1465 1470Pro Gly Ala Val Lys Val Tyr Ala Tyr
Tyr Asn Leu Glu Glu Ser 1475 1480 1485Cys Thr Arg Phe Tyr His Pro
Glu Lys Glu Asp Gly Lys Leu Asn 1490 1495 1500Lys Leu Cys Arg Asp
Glu Leu Cys Arg Cys Ala Glu Glu Asn Cys 1505 1510 1515Phe Ile Gln
Lys Ser Asp Asp Lys Val Thr Leu Glu Glu Arg Leu 1520 1525 1530Asp
Lys Ala Cys Glu Pro Gly Val Asp Tyr Val Tyr Lys Thr Arg 1535 1540
1545Leu Val Lys Val Gln Leu Ser Asn Asp Phe Asp Glu Tyr Ile Met
1550 1555 1560Ala Ile Glu Gln Thr Ile Lys Ser Gly Ser Asp Glu Val
Gln Val 1565 1570 1575Gly Gln Gln Arg Thr Phe Ile Ser Pro Ile Lys
Cys Arg Glu Ala 1580 1585 1590Leu Lys Leu Glu Glu Lys Lys His Tyr
Leu Met Trp Gly Leu Ser 1595 1600 1605Ser Asp Phe Trp Gly Glu Lys
Pro Asn Leu Ser Tyr Ile Ile Gly 1610 1615 1620Lys Asp Thr Trp Val
Glu His Trp Pro Glu Glu Asp Glu Cys Gln 1625 1630 1635Asp Glu Glu
Asn Gln Lys Gln Cys Gln Asp Leu Gly Ala Phe Thr 1640 1645 1650Glu
Ser Met Val Val Phe Gly Cys Pro Asn 1655 16609559PRTHomo sapiens
9Met Ser Ala Cys Arg Ser Phe Ala Val Ala Ile Cys Ile Leu Glu Ile1 5
10 15Ser Ile Leu Thr Ala Gln Tyr Thr Thr Ser Tyr Asp Pro Glu Leu
Thr 20 25 30Glu Ser Ser Gly Ser Ala Ser His Ile Asp Cys Arg Met Ser
Pro Trp 35 40 45Ser Glu Trp Ser Gln Cys Asp Pro Cys Leu Arg Gln Met
Phe Arg Ser 50 55 60Arg Ser Ile Glu Val Phe Gly Gln Phe Asn Gly Lys
Arg Cys Thr Asp65 70 75 80Ala Val Gly Asp Arg Arg Gln Cys Val Pro
Thr Glu Pro Cys Glu Asp 85 90 95Ala Glu Asp Asp Cys Gly Asn Asp Phe
Gln Cys Ser Thr Gly Arg Cys 100 105 110Ile Lys Met Arg Leu Arg Cys
Asn Gly Asp Asn Asp Cys Gly Asp Phe 115 120 125Ser Asp Glu Asp Asp
Cys Glu Ser Glu Pro Arg Pro Pro Cys Arg Asp 130 135 140Arg Val Val
Glu Glu Ser Glu Leu Ala Arg Thr Ala Gly Tyr Gly Ile145 150 155
160Asn Ile Leu Gly Met Asp Pro Leu Ser Thr Pro Phe Asp Asn Glu Phe
165 170 175Tyr Asn Gly Leu Cys Asn Arg Asp Arg Asp Gly Asn Thr Leu
Thr Tyr 180 185 190Tyr Arg Arg Pro Trp Asn Val Ala Ser Leu Ile Tyr
Glu Thr Lys Gly 195 200 205Glu Lys Asn Phe Arg Thr Glu His Tyr Glu
Glu Gln Ile Glu Ala Phe 210 215 220Lys Ser Ile Ile Gln Glu Lys Thr
Ser Asn Phe Asn Ala Ala Ile Ser225 230 235 240Leu Lys Phe Thr Pro
Thr Glu Thr Asn Lys Ala Glu Gln Cys Cys Glu 245 250 255Glu Thr Ala
Ser Ser Ile Ser Leu His Gly Lys Gly Ser Phe Arg Phe 260 265 270Ser
Tyr Ser Lys Asn Glu Thr Tyr Gln Leu Phe Leu Ser Tyr Ser Ser 275 280
285Lys Lys Glu Lys Met Phe Leu His Val Lys Gly Glu Ile His Leu Gly
290 295 300Arg Phe Val Met Arg Asn Arg Asp Val Val Leu Thr Thr Thr
Phe Val305 310 315 320Asp Asp Ile Lys Ala Leu Pro Thr Thr Tyr Glu
Lys Gly Glu Tyr Phe 325 330 335Ala Phe Leu Glu Thr Tyr Gly Thr His
Tyr Ser Ser Ser Gly Ser Leu 340 345 350Gly Gly Leu Tyr Glu Leu Ile
Tyr Val Leu Asp Lys Ala Ser Met Lys 355 360 365Arg Lys Gly Val Glu
Leu Lys Asp Ile Lys Arg Cys Leu Gly Tyr His 370 375 380Leu Asp Val
Ser Leu Ala Phe Ser Glu Ile Ser Val Gly Ala Glu Phe385 390 395
400Asn Lys Asp Asp Cys Val Lys Arg Gly Glu Gly Arg Ala Val Asn Ile
405 410 415Thr Ser Glu Asn Leu Ile Asp Asp Val Val Ser Leu Ile Arg
Gly Gly 420 425 430Thr Arg Lys Tyr Ala Phe Glu Leu Lys Glu Lys Leu
Leu Arg Gly Thr 435 440 445Val Ile Asp Val Thr Asp Phe Val Asn Trp
Ala Ser Ser Ile Asn Asp 450 455 460Ala Pro Val Leu Ile Ser Gln Lys
Leu Ser Pro Ile Tyr Asn Leu Val465 470 475 480Pro Val Lys Met Lys
Asn Ala His Leu Lys Lys Gln Asn Leu Glu Arg 485 490 495Ala Ile Glu
Asp Tyr Ile Asn Glu Phe Ser Val Arg Lys Cys His Thr 500 505 510Cys
Gln Asn Gly Gly Thr Val Ile Leu Met Asp Gly Lys Cys Leu Cys 515 520
525Ala Cys Pro Phe Lys Phe Glu Gly Ile Ala Cys Glu Ile Ser Lys Gln
530 535 540Lys Ile Ser Glu Gly Leu Pro Ala Leu Glu Phe Pro Asn Glu
Lys545 550 55510224PRTHomo sapiens 10Met Glu Lys Leu Leu Cys Phe
Leu Val Leu Thr Ser Leu Ser His Ala1 5 10 15Phe Gly Gln Thr Asp Met
Ser Arg Lys Ala Phe Val Phe Pro Lys Glu 20 25 30Ser Asp Thr Ser Tyr
Val Ser Leu Lys Ala Pro Leu Thr Lys Pro Leu 35 40 45Lys Ala Phe Thr
Val Cys Leu His Phe Tyr Thr Glu Leu Ser Ser Thr 50 55 60Arg Gly Tyr
Ser Ile Phe Ser Tyr Ala Thr Lys Arg Gln Asp Asn Glu65 70 75 80Ile
Leu Ile Phe Trp Ser Lys Asp Ile Gly Tyr Ser Phe Thr Val Gly 85 90
95Gly Ser Glu Ile Leu Phe Glu Val Pro Glu Val Thr Val Ala Pro Val
100 105 110His Ile Cys Thr Ser Trp Glu Ser Ala Ser Gly Ile Val Glu
Phe Trp 115 120 125Val Asp Gly Lys Pro Arg Val Arg Lys Ser Leu Lys
Lys Gly Tyr Thr 130 135 140Val Gly Ala Glu Ala Ser Ile Ile Leu Gly
Gln Glu Gln Asp Ser Phe145 150 155 160Gly Gly Asn Phe Glu Gly Ser
Gln Ser Leu Val Gly Asp Ile Gly Asn 165 170 175Val Asn Met Trp Asp
Phe Val Leu Ser Pro Asp Glu Ile Asn Thr Ile 180 185 190Tyr Leu Gly
Gly Pro Phe Ser Pro Asn Val Leu Asn Trp Arg Ala Leu 195 200 205Lys
Tyr Glu Val Gln Gly Glu Val Phe Thr Lys Pro Gln Leu Trp Pro 210 215
22011491PRTHomo sapiens 11Met Lys Arg Met Val Ser Trp Ser Phe His
Lys Leu Lys Thr Met Lys1 5 10 15His Leu Leu Leu Leu Leu Leu Cys Val
Phe Leu Val Lys Ser Gln Gly 20 25 30Val Asn Asp Asn Glu Glu Gly Phe
Phe Ser Ala Arg Gly His Arg Pro 35 40
45Leu Asp Lys Lys Arg Glu Glu Ala Pro Ser Leu Arg Pro Ala Pro Pro
50 55 60Pro Ile Ser Gly Gly Gly Tyr Arg Ala Arg Pro Ala Lys Ala Ala
Ala65 70 75 80Thr Gln Lys Lys Val Glu Arg Lys Ala Pro Asp Ala Gly
Gly Cys Leu 85 90 95His Ala Asp Pro Asp Leu Gly Val Leu Cys Pro Thr
Gly Cys Gln Leu 100 105 110Gln Glu Ala Leu Leu Gln Gln Glu Arg Pro
Ile Arg Asn Ser Val Asp 115 120 125Glu Leu Asn Asn Asn Val Glu Ala
Val Ser Gln Thr Ser Ser Ser Ser 130 135 140Phe Gln Tyr Met Tyr Leu
Leu Lys Asp Leu Trp Gln Lys Arg Gln Lys145 150 155 160Gln Val Lys
Asp Asn Glu Asn Val Val Asn Glu Tyr Ser Ser Glu Leu 165 170 175Glu
Lys His Gln Leu Tyr Ile Asp Glu Thr Val Asn Ser Asn Ile Pro 180 185
190Thr Asn Leu Arg Val Leu Arg Ser Ile Leu Glu Asn Leu Arg Ser Lys
195 200 205Ile Gln Lys Leu Glu Ser Asp Val Ser Ala Gln Met Glu Tyr
Cys Arg 210 215 220Thr Pro Cys Thr Val Ser Cys Asn Ile Pro Val Val
Ser Gly Lys Glu225 230 235 240Cys Glu Glu Ile Ile Arg Lys Gly Gly
Glu Thr Ser Glu Met Tyr Leu 245 250 255Ile Gln Pro Asp Ser Ser Val
Lys Pro Tyr Arg Val Tyr Cys Asp Met 260 265 270Asn Thr Glu Asn Gly
Gly Trp Thr Val Ile Gln Asn Arg Gln Asp Gly 275 280 285Ser Val Asp
Phe Gly Arg Lys Trp Asp Pro Tyr Lys Gln Gly Phe Gly 290 295 300Asn
Val Ala Thr Asn Thr Asp Gly Lys Asn Tyr Cys Gly Leu Pro Gly305 310
315 320Glu Tyr Trp Leu Gly Asn Asp Lys Ile Ser Gln Leu Thr Arg Met
Gly 325 330 335Pro Thr Glu Leu Leu Ile Glu Met Glu Asp Trp Lys Gly
Asp Lys Val 340 345 350Lys Ala His Tyr Gly Gly Phe Thr Val Gln Asn
Glu Ala Asn Lys Tyr 355 360 365Gln Ile Ser Val Asn Lys Tyr Arg Gly
Thr Ala Gly Asn Ala Leu Met 370 375 380Asp Gly Ala Ser Gln Leu Met
Gly Glu Asn Arg Thr Met Thr Ile His385 390 395 400Asn Gly Met Phe
Phe Ser Thr Tyr Asp Arg Asp Asn Asp Gly Trp Leu 405 410 415Thr Ser
Asp Pro Arg Lys Gln Cys Ser Lys Glu Asp Gly Gly Gly Trp 420 425
430Trp Tyr Asn Arg Cys His Ala Ala Asn Pro Asn Gly Arg Tyr Tyr Trp
435 440 445Gly Gly Gln Tyr Thr Trp Asp Met Ala Lys His Gly Thr Asp
Asp Gly 450 455 460Val Val Trp Met Asn Trp Lys Gly Ser Trp Tyr Ser
Met Arg Lys Met465 470 475 480Ser Met Lys Ile Arg Pro Phe Phe Pro
Gln Gln 485 49012453PRTHomo sapiens 12Met Ser Trp Ser Leu His Pro
Arg Asn Leu Ile Leu Tyr Phe Tyr Ala1 5 10 15Leu Leu Phe Leu Ser Ser
Thr Cys Val Ala Tyr Val Ala Thr Arg Asp 20 25 30Asn Cys Cys Ile Leu
Asp Glu Arg Phe Gly Ser Tyr Cys Pro Thr Thr 35 40 45Cys Gly Ile Ala
Asp Phe Leu Ser Thr Tyr Gln Thr Lys Val Asp Lys 50 55 60Asp Leu Gln
Ser Leu Glu Asp Ile Leu His Gln Val Glu Asn Lys Thr65 70 75 80Ser
Glu Val Lys Gln Leu Ile Lys Ala Ile Gln Leu Thr Tyr Asn Pro 85 90
95Asp Glu Ser Ser Lys Pro Asn Met Ile Asp Ala Ala Thr Leu Lys Ser
100 105 110Arg Lys Met Leu Glu Glu Ile Met Lys Tyr Glu Ala Ser Ile
Leu Thr 115 120 125His Asp Ser Ser Ile Arg Tyr Leu Gln Glu Ile Tyr
Asn Ser Asn Asn 130 135 140Gln Lys Ile Val Asn Leu Lys Glu Lys Val
Ala Gln Leu Glu Ala Gln145 150 155 160Cys Gln Glu Pro Cys Lys Asp
Thr Val Gln Ile His Asp Ile Thr Gly 165 170 175Lys Asp Cys Gln Asp
Ile Ala Asn Lys Gly Ala Lys Gln Ser Gly Leu 180 185 190Tyr Phe Ile
Lys Pro Leu Lys Ala Asn Gln Gln Phe Leu Val Tyr Cys 195 200 205Glu
Ile Asp Gly Ser Gly Asn Gly Trp Thr Val Phe Gln Lys Arg Leu 210 215
220Asp Gly Ser Val Asp Phe Lys Lys Asn Trp Ile Gln Tyr Lys Glu
Gly225 230 235 240Phe Gly His Leu Ser Pro Thr Gly Thr Thr Glu Phe
Trp Leu Gly Asn 245 250 255Glu Lys Ile His Leu Ile Ser Thr Gln Ser
Ala Ile Pro Tyr Ala Leu 260 265 270Arg Val Glu Leu Glu Asp Trp Asn
Gly Arg Thr Ser Thr Ala Asp Tyr 275 280 285Ala Met Phe Lys Val Gly
Pro Glu Ala Asp Lys Tyr Arg Leu Thr Tyr 290 295 300Ala Tyr Phe Ala
Gly Gly Asp Ala Gly Asp Ala Phe Asp Gly Phe Asp305 310 315 320Phe
Gly Asp Asp Pro Ser Asp Lys Phe Phe Thr Ser His Asn Gly Met 325 330
335Gln Phe Ser Thr Trp Asp Asn Asp Asn Asp Lys Phe Glu Gly Asn Cys
340 345 350Ala Glu Gln Asp Gly Ser Gly Trp Trp Met Asn Lys Cys His
Ala Gly 355 360 365His Leu Asn Gly Val Tyr Tyr Gln Gly Gly Thr Tyr
Ser Lys Ala Ser 370 375 380Thr Pro Asn Gly Tyr Asp Asn Gly Ile Ile
Trp Ala Thr Trp Lys Thr385 390 395 400Arg Trp Tyr Ser Met Lys Lys
Thr Thr Met Lys Ile Ile Pro Phe Asn 405 410 415Arg Leu Thr Ile Gly
Glu Gly Gln Gln His His Leu Gly Gly Ala Lys 420 425 430Gln Val Arg
Pro Glu His Pro Ala Glu Thr Glu Tyr Asp Ser Leu Tyr 435 440 445Pro
Glu Asp Asp Leu 45013739PRTHomo sapiens 13Met Pro Ser Pro Arg Pro
Val Leu Leu Arg Gly Ala Arg Ala Ala Leu1 5 10 15Leu Leu Leu Leu Pro
Pro Arg Leu Leu Ala Arg Pro Ser Leu Leu Leu 20 25 30Arg Arg Ser Leu
Ser Ala Ala Ser Cys Pro Pro Ile Ser Leu Pro Ala 35 40 45Ala Ala Ser
Arg Ser Ser Met Asp Gly Ala Gly Ala Glu Glu Val Leu 50 55 60Ala Pro
Leu Arg Leu Ala Val Arg Gln Gln Gly Asp Leu Val Arg Lys65 70 75
80Leu Lys Glu Asp Lys Ala Pro Gln Val Asp Val Asp Lys Ala Val Ala
85 90 95Glu Leu Lys Ala Arg Lys Arg Val Leu Glu Ala Lys Glu Leu Ala
Leu 100 105 110Gln Pro Lys Asp Asp Ile Val Asp Arg Ala Lys Met Glu
Asp Thr Leu 115 120 125Lys Arg Arg Phe Phe Tyr Asp Gln Ala Phe Ala
Ile Tyr Gly Gly Val 130 135 140Ser Gly Leu Tyr Asp Phe Gly Pro Val
Gly Cys Ala Leu Lys Asn Asn145 150 155 160Ile Ile Gln Thr Trp Arg
Gln His Phe Ile Gln Glu Glu Gln Ile Leu 165 170 175Glu Ile Asp Cys
Thr Met Leu Thr Pro Glu Pro Val Leu Lys Thr Ser 180 185 190Gly His
Val Asp Lys Phe Ala Asp Phe Met Val Lys Asp Val Lys Asn 195 200
205Gly Glu Cys Phe Arg Ala Asp His Leu Leu Lys Ala His Leu Gln Lys
210 215 220Leu Met Ser Asp Lys Lys Cys Ser Val Glu Lys Lys Ser Glu
Met Glu225 230 235 240Ser Val Leu Ala Gln Leu Asp Asn Tyr Gly Gln
Gln Glu Leu Ala Asp 245 250 255Leu Phe Val Asn Tyr Asn Val Lys Ser
Pro Ile Thr Gly Asn Asp Leu 260 265 270Ser Pro Pro Val Ser Phe Asn
Leu Met Phe Lys Thr Phe Ile Gly Pro 275 280 285Gly Gly Asn Met Pro
Gly Tyr Leu Arg Pro Glu Thr Ala Gln Gly Ile 290 295 300Phe Leu Asn
Phe Lys Arg Leu Leu Glu Phe Asn Gln Gly Lys Leu Pro305 310 315
320Phe Ala Ala Ala Gln Ile Gly Asn Ser Phe Arg Asn Glu Ile Ser Pro
325 330 335Arg Ser Gly Leu Ile Arg Val Arg Glu Phe Thr Met Ala Glu
Ile Glu 340 345 350His Phe Val Asp Pro Ser Glu Lys Asp His Pro Lys
Phe Gln Asn Val 355 360 365Ala Asp Leu His Leu Tyr Leu Tyr Ser Ala
Lys Ala Gln Val Ser Gly 370 375 380Gln Ser Ala Arg Lys Met Arg Leu
Gly Asp Ala Val Glu Gln Gly Val385 390 395 400Ile Asn Asn Thr Val
Leu Gly Tyr Phe Ile Gly Arg Ile Tyr Leu Tyr 405 410 415Leu Thr Lys
Val Gly Ile Ser Pro Asp Lys Leu Arg Phe Arg Gln His 420 425 430Met
Glu Asn Glu Met Ala His Tyr Ala Cys Asp Cys Trp Asp Ala Glu 435 440
445Ser Lys Thr Ser Tyr Gly Trp Ile Glu Ile Val Gly Cys Ala Asp Arg
450 455 460Ser Cys Tyr Asp Leu Ser Cys His Ala Arg Ala Thr Lys Val
Pro Leu465 470 475 480Val Ala Glu Lys Pro Leu Lys Glu Pro Lys Thr
Val Asn Val Val Gln 485 490 495Phe Glu Pro Ser Lys Gly Ala Ile Gly
Lys Ala Tyr Lys Lys Asp Ala 500 505 510Lys Leu Val Met Glu Tyr Leu
Ala Ile Cys Asp Glu Cys Tyr Ile Thr 515 520 525Glu Met Glu Met Leu
Leu Asn Glu Lys Gly Glu Phe Thr Ile Glu Thr 530 535 540Glu Gly Lys
Thr Phe Gln Leu Thr Lys Asp Met Ile Asn Val Lys Arg545 550 555
560Phe Gln Lys Thr Leu Tyr Val Glu Glu Val Val Pro Asn Val Ile Glu
565 570 575Pro Ser Phe Gly Leu Gly Arg Ile Met Tyr Thr Val Phe Glu
His Thr 580 585 590Phe His Val Arg Glu Gly Asp Glu Gln Arg Thr Phe
Phe Ser Phe Pro 595 600 605Ala Val Val Ala Pro Phe Lys Cys Ser Val
Leu Pro Leu Ser Gln Asn 610 615 620Gln Glu Phe Met Pro Phe Val Lys
Glu Leu Ser Glu Ala Leu Thr Arg625 630 635 640His Gly Val Ser His
Lys Val Asp Asp Ser Ser Gly Ser Ile Gly Arg 645 650 655Arg Tyr Ala
Arg Thr Asp Glu Ile Gly Val Ala Phe Gly Val Thr Ile 660 665 670Asp
Phe Asp Thr Val Asn Lys Thr Pro His Thr Ala Thr Leu Arg Asp 675 680
685Arg Asp Ser Met Arg Gln Ile Arg Ala Glu Ile Ser Glu Leu Pro Ser
690 695 700Ile Val Gln Asp Leu Ala Asn Gly Asn Ile Thr Trp Ala Asp
Val Glu705 710 715 720Ala Arg Tyr Pro Leu Phe Glu Gly Gln Glu Thr
Gly Lys Lys Glu Thr 725 730 735Ile Glu Glu14782PRTHomo sapiens
14Met Ala Pro His Arg Pro Ala Pro Ala Leu Leu Cys Ala Leu Ser Leu1
5 10 15Ala Leu Cys Ala Leu Ser Leu Pro Val Arg Ala Ala Thr Ala Ser
Arg 20 25 30Gly Ala Ser Gln Ala Gly Ala Pro Gln Gly Arg Val Pro Glu
Ala Arg 35 40 45Pro Asn Ser Met Val Val Glu His Pro Glu Phe Leu Lys
Ala Gly Lys 50 55 60Glu Pro Gly Leu Gln Ile Trp Arg Val Glu Lys Phe
Asp Leu Val Pro65 70 75 80Val Pro Thr Asn Leu Tyr Gly Asp Phe Phe
Thr Gly Asp Ala Tyr Val 85 90 95Ile Leu Lys Thr Val Gln Leu Arg Asn
Gly Asn Leu Gln Tyr Asp Leu 100 105 110His Tyr Trp Leu Gly Asn Glu
Cys Ser Gln Asp Glu Ser Gly Ala Ala 115 120 125Ala Ile Phe Thr Val
Gln Leu Asp Asp Tyr Leu Asn Gly Arg Ala Val 130 135 140Gln His Arg
Glu Val Gln Gly Phe Glu Ser Ala Thr Phe Leu Gly Tyr145 150 155
160Phe Lys Ser Gly Leu Lys Tyr Lys Lys Gly Gly Val Ala Ser Gly Phe
165 170 175Lys His Val Val Pro Asn Glu Val Val Val Gln Arg Leu Phe
Gln Val 180 185 190Lys Gly Arg Arg Val Val Arg Ala Thr Glu Val Pro
Val Ser Trp Glu 195 200 205Ser Phe Asn Asn Gly Asp Cys Phe Ile Leu
Asp Leu Gly Asn Asn Ile 210 215 220His Gln Trp Cys Gly Ser Asn Ser
Asn Arg Tyr Glu Arg Leu Lys Ala225 230 235 240Thr Gln Val Ser Lys
Gly Ile Arg Asp Asn Glu Arg Ser Gly Arg Ala 245 250 255Arg Val His
Val Ser Glu Glu Gly Thr Glu Pro Glu Ala Met Leu Gln 260 265 270Val
Leu Gly Pro Lys Pro Ala Leu Pro Ala Gly Thr Glu Asp Thr Ala 275 280
285Lys Glu Asp Ala Ala Asn Arg Lys Leu Ala Lys Leu Tyr Lys Val Ser
290 295 300Asn Gly Ala Gly Thr Met Ser Val Ser Leu Val Ala Asp Glu
Asn Pro305 310 315 320Phe Ala Gln Gly Ala Leu Lys Ser Glu Asp Cys
Phe Ile Leu Asp His 325 330 335Gly Lys Asp Gly Lys Ile Phe Val Trp
Lys Gly Lys Gln Ala Asn Thr 340 345 350Glu Glu Arg Lys Ala Ala Leu
Lys Thr Ala Ser Asp Phe Ile Thr Lys 355 360 365Met Asp Tyr Pro Lys
Gln Thr Gln Val Ser Val Leu Pro Glu Gly Gly 370 375 380Glu Thr Pro
Leu Phe Lys Gln Phe Phe Lys Asn Trp Arg Asp Pro Asp385 390 395
400Gln Thr Asp Gly Leu Gly Leu Ser Tyr Leu Ser Ser His Ile Ala Asn
405 410 415Val Glu Arg Val Pro Phe Asp Ala Ala Thr Leu His Thr Ser
Thr Ala 420 425 430Met Ala Ala Gln His Gly Met Asp Asp Asp Gly Thr
Gly Gln Lys Gln 435 440 445Ile Trp Arg Ile Glu Gly Ser Asn Lys Val
Pro Val Asp Pro Ala Thr 450 455 460Tyr Gly Gln Phe Tyr Gly Gly Asp
Ser Tyr Ile Ile Leu Tyr Asn Tyr465 470 475 480Arg His Gly Gly Arg
Gln Gly Gln Ile Ile Tyr Asn Trp Gln Gly Ala 485 490 495Gln Ser Thr
Gln Asp Glu Val Ala Ala Ser Ala Ile Leu Thr Ala Gln 500 505 510Leu
Asp Glu Glu Leu Gly Gly Thr Pro Val Gln Ser Arg Val Val Gln 515 520
525Gly Lys Glu Pro Ala His Leu Met Ser Leu Phe Gly Gly Lys Pro Met
530 535 540Ile Ile Tyr Lys Gly Gly Thr Ser Arg Glu Gly Gly Gln Thr
Ala Pro545 550 555 560Ala Ser Thr Arg Leu Phe Gln Val Arg Ala Asn
Ser Ala Gly Ala Thr 565 570 575Arg Ala Val Glu Val Leu Pro Lys Ala
Gly Ala Leu Asn Ser Asn Asp 580 585 590Ala Phe Val Leu Lys Thr Pro
Ser Ala Ala Tyr Leu Trp Val Gly Thr 595 600 605Gly Ala Ser Glu Ala
Glu Lys Thr Gly Ala Gln Glu Leu Leu Arg Val 610 615 620Leu Arg Ala
Gln Pro Val Gln Val Ala Glu Gly Ser Glu Pro Asp Gly625 630 635
640Phe Trp Glu Ala Leu Gly Gly Lys Ala Ala Tyr Arg Thr Ser Pro Arg
645 650 655Leu Lys Asp Lys Lys Met Asp Ala His Pro Pro Arg Leu Phe
Ala Cys 660 665 670Ser Asn Lys Ile Gly Arg Phe Val Ile Glu Glu Val
Pro Gly Glu Leu 675 680 685Met Gln Glu Asp Leu Ala Thr Asp Asp Val
Met Leu Leu Asp Thr Trp 690 695 700Asp Gln Val Phe Val Trp Val Gly
Lys Asp Ser Gln Glu Glu Glu Lys705 710 715 720Thr Glu Ala Leu Thr
Ser Ala Lys Arg Tyr Ile Glu Thr Asp Pro Ala 725 730 735Asn Arg Asp
Arg Arg Thr Pro Ile Thr Val Val Lys Gln Gly Phe Glu 740 745 750Pro
Pro Ser Phe Val Gly Trp Phe Leu Gly Trp Asp Asp Asp Tyr Trp 755 760
765Ser Val Asp Pro Leu Asp Arg Ala Met Ala Glu Leu Ala Ala 770 775
78015406PRTHomo sapiens 15Met Ser Ala Leu Gly Ala Val Ile Ala Leu
Leu Leu Trp Gly Gln Leu1 5 10 15Phe Ala Val Asp Ser Gly Asn Asp Val
Thr Asp Ile Ala Asp Asp Gly 20 25 30Cys Pro Lys Pro Pro Glu Ile Ala
His Gly Tyr Val Glu His Ser Val 35 40
45Arg Tyr Gln Cys Lys Asn Tyr Tyr Lys Leu Arg Thr Glu Gly Asp Gly
50 55 60Val Tyr Thr Leu Asn Asp Lys Lys Gln Trp Ile Asn Lys Ala Val
Gly65 70 75 80Asp Lys Leu Pro Glu Cys Glu Ala Asp Asp Gly Cys Pro
Lys Pro Pro 85 90 95Glu Ile Ala His Gly Tyr Val Glu His Ser Val Arg
Tyr Gln Cys Lys 100 105 110Asn Tyr Tyr Lys Leu Arg Thr Glu Gly Asp
Gly Val Tyr Thr Leu Asn 115 120 125Asn Glu Lys Gln Trp Ile Asn Lys
Ala Val Gly Asp Lys Leu Pro Glu 130 135 140Cys Glu Ala Val Cys Gly
Lys Pro Lys Asn Pro Ala Asn Pro Val Gln145 150 155 160Arg Ile Leu
Gly Gly His Leu Asp Ala Lys Gly Ser Phe Pro Trp Gln 165 170 175Ala
Lys Met Val Ser His His Asn Leu Thr Thr Gly Ala Thr Leu Ile 180 185
190Asn Glu Gln Trp Leu Leu Thr Thr Ala Lys Asn Leu Phe Leu Asn His
195 200 205Ser Glu Asn Ala Thr Ala Lys Asp Ile Ala Pro Thr Leu Thr
Leu Tyr 210 215 220Val Gly Lys Lys Gln Leu Val Glu Ile Glu Lys Val
Val Leu His Pro225 230 235 240Asn Tyr Ser Gln Val Asp Ile Gly Leu
Ile Lys Leu Lys Gln Lys Val 245 250 255Ser Val Asn Glu Arg Val Met
Pro Ile Cys Leu Pro Ser Lys Asp Tyr 260 265 270Ala Glu Val Gly Arg
Val Gly Tyr Val Ser Gly Trp Gly Arg Asn Ala 275 280 285Asn Phe Lys
Phe Thr Asp His Leu Lys Tyr Val Met Leu Pro Val Ala 290 295 300Asp
Gln Asp Gln Cys Ile Arg His Tyr Glu Gly Ser Thr Val Pro Glu305 310
315 320Lys Lys Thr Pro Lys Ser Pro Val Gly Val Gln Pro Ile Leu Asn
Glu 325 330 335His Thr Phe Cys Ala Gly Met Ser Lys Tyr Gln Glu Asp
Thr Cys Tyr 340 345 350Gly Asp Ala Gly Ser Ala Phe Ala Val His Asp
Leu Glu Glu Asp Thr 355 360 365Trp Tyr Ala Thr Gly Ile Leu Ser Phe
Asp Lys Ser Cys Ala Val Ala 370 375 380Glu Tyr Gly Val Tyr Val Lys
Val Thr Ser Ile Gln Asp Trp Val Gln385 390 395 400Lys Thr Ile Ala
Glu Asn 40516115PRTHomo sapiens 16Met Pro Met Phe Ile Val Asn Thr
Asn Val Pro Arg Ala Ser Val Pro1 5 10 15Asp Gly Phe Leu Ser Glu Leu
Thr Gln Gln Leu Ala Gln Ala Thr Gly 20 25 30Lys Pro Pro Gln Tyr Ile
Ala Val His Val Val Pro Asp Gln Leu Met 35 40 45Ala Phe Gly Gly Ser
Ser Glu Pro Cys Ala Leu Cys Ser Leu His Ser 50 55 60Ile Gly Lys Ile
Gly Gly Ala Gln Asn Arg Ser Tyr Ser Lys Leu Leu65 70 75 80Cys Gly
Leu Leu Ala Glu Arg Leu Arg Ile Ser Pro Asp Arg Val Tyr 85 90 95Ile
Asn Tyr Tyr Asp Met Asn Ala Ala Asn Val Gly Trp Asn Asn Ser 100 105
110Thr Phe Ala 11517314PRTHomo sapiens 17Met Arg Ile Ala Val Ile
Cys Phe Cys Leu Leu Gly Ile Thr Cys Ala1 5 10 15Ile Pro Val Lys Gln
Ala Asp Ser Gly Ser Ser Glu Glu Lys Gln Leu 20 25 30Tyr Asn Lys Tyr
Pro Asp Ala Val Ala Thr Trp Leu Asn Pro Asp Pro 35 40 45Ser Gln Lys
Gln Asn Leu Leu Ala Pro Gln Asn Ala Val Ser Ser Glu 50 55 60Glu Thr
Asn Asp Phe Lys Gln Glu Thr Leu Pro Ser Lys Ser Asn Glu65 70 75
80Ser His Asp His Met Asp Asp Met Asp Asp Glu Asp Asp Asp Asp His
85 90 95Val Asp Ser Gln Asp Ser Ile Asp Ser Asn Asp Ser Asp Asp Val
Asp 100 105 110Asp Thr Asp Asp Ser His Gln Ser Asp Glu Ser His His
Ser Asp Glu 115 120 125Ser Asp Glu Leu Val Thr Asp Phe Pro Thr Asp
Leu Pro Ala Thr Glu 130 135 140Val Phe Thr Pro Val Val Pro Thr Val
Asp Thr Tyr Asp Gly Arg Gly145 150 155 160Asp Ser Val Val Tyr Gly
Leu Arg Ser Lys Ser Lys Lys Phe Arg Arg 165 170 175Pro Asp Ile Gln
Tyr Pro Asp Ala Thr Asp Glu Asp Ile Thr Ser His 180 185 190Met Glu
Ser Glu Glu Leu Asn Gly Ala Tyr Lys Ala Ile Pro Val Ala 195 200
205Gln Asp Leu Asn Ala Pro Ser Asp Trp Asp Ser Arg Gly Lys Asp Ser
210 215 220Tyr Glu Thr Ser Gln Leu Asp Asp Gln Ser Ala Glu Thr His
Ser His225 230 235 240Lys Gln Ser Arg Leu Tyr Lys Arg Lys Ala Asn
Asp Glu Ser Asn Glu 245 250 255His Ser Asp Val Ile Asp Ser Gln Glu
Leu Ser Lys Val Ser Arg Glu 260 265 270Phe His Ser His Glu Phe His
Ser His Glu Asp Met Leu Val Val Asp 275 280 285Pro Lys Ser Lys Glu
Glu Asp Lys His Leu Lys Phe Arg Ile Ser His 290 295 300Glu Leu Asp
Ser Ala Ser Ser Glu Val Asn305 31018199PRTHomo sapiens 18Met Ser
Ser Gly Asn Ala Lys Ile Gly His Pro Ala Pro Asn Phe Lys1 5 10 15Ala
Thr Ala Val Met Pro Asp Gly Gln Phe Lys Asp Ile Ser Leu Ser 20 25
30Asp Tyr Lys Gly Lys Tyr Val Val Phe Phe Phe Tyr Pro Leu Asp Phe
35 40 45Thr Phe Val Cys Pro Thr Glu Ile Ile Ala Phe Ser Asp Arg Ala
Glu 50 55 60Glu Phe Lys Lys Leu Asn Cys Gln Val Ile Gly Ala Ser Val
Asp Ser65 70 75 80His Phe Cys His Leu Ala Trp Val Asn Thr Pro Lys
Lys Gln Gly Gly 85 90 95Leu Gly Pro Met Asn Ile Pro Leu Val Ser Asp
Pro Lys Arg Thr Ile 100 105 110Ala Gln Asp Tyr Gly Val Leu Lys Ala
Asp Glu Gly Ile Ser Phe Arg 115 120 125Gly Leu Phe Ile Ile Asp Asp
Lys Gly Ile Leu Arg Gln Ile Thr Val 130 135 140Asn Asp Leu Pro Val
Gly Arg Ser Val Asp Glu Thr Leu Arg Leu Val145 150 155 160Gln Ala
Phe Gln Phe Thr Asp Lys His Gly Glu Val Cys Pro Ala Gly 165 170
175Trp Lys Pro Gly Ser Asp Thr Ile Lys Pro Asp Val Gln Lys Ser Lys
180 185 190Glu Tyr Phe Ser Lys Gln Lys 19519412PRTHomo sapiens
19Met Pro Leu Gln Leu Leu Leu Leu Leu Ile Leu Leu Gly Pro Gly Asn1
5 10 15Ser Leu Gln Leu Trp Asp Thr Trp Ala Asp Glu Ala Glu Lys Ala
Leu 20 25 30Gly Pro Leu Leu Ala Arg Asp Arg Arg Gln Ala Thr Glu Tyr
Glu Tyr 35 40 45Leu Asp Tyr Asp Phe Leu Pro Glu Thr Glu Pro Pro Glu
Met Leu Arg 50 55 60Asn Ser Thr Asp Thr Thr Pro Leu Thr Gly Pro Gly
Thr Pro Glu Ser65 70 75 80Thr Thr Val Glu Pro Ala Ala Arg Arg Ser
Thr Gly Leu Asp Ala Gly 85 90 95Gly Ala Val Thr Glu Leu Thr Thr Glu
Leu Ala Asn Met Gly Asn Leu 100 105 110Ser Thr Asp Ser Ala Ala Met
Glu Ile Gln Thr Thr Gln Pro Ala Ala 115 120 125Thr Glu Ala Gln Thr
Thr Gln Pro Val Pro Thr Glu Ala Gln Thr Thr 130 135 140Pro Leu Ala
Ala Thr Glu Ala Gln Thr Thr Arg Leu Thr Ala Thr Glu145 150 155
160Ala Gln Thr Thr Pro Leu Ala Ala Thr Glu Ala Gln Thr Thr Pro Pro
165 170 175Ala Ala Thr Glu Ala Gln Thr Thr Gln Pro Thr Gly Leu Glu
Ala Gln 180 185 190Thr Thr Ala Pro Ala Ala Met Glu Ala Gln Thr Thr
Ala Pro Ala Ala 195 200 205Met Glu Ala Gln Thr Thr Pro Pro Ala Ala
Met Glu Ala Gln Thr Thr 210 215 220Gln Thr Thr Ala Met Glu Ala Gln
Thr Thr Ala Pro Glu Ala Thr Glu225 230 235 240Ala Gln Thr Thr Gln
Pro Thr Ala Thr Glu Ala Gln Thr Thr Pro Leu 245 250 255Ala Ala Met
Glu Ala Leu Ser Thr Glu Pro Ser Ala Thr Glu Ala Leu 260 265 270Ser
Met Glu Pro Thr Thr Lys Arg Gly Leu Phe Ile Pro Phe Ser Val 275 280
285Ser Ser Val Thr His Lys Gly Ile Pro Met Ala Ala Ser Asn Leu Ser
290 295 300Val Asn Tyr Pro Val Gly Ala Pro Asp His Ile Ser Val Lys
Gln Cys305 310 315 320Leu Leu Ala Ile Leu Ile Leu Ala Leu Val Ala
Thr Ile Phe Phe Val 325 330 335Cys Thr Val Val Leu Ala Val Arg Leu
Ser Arg Lys Gly His Met Tyr 340 345 350Pro Val Arg Asn Tyr Ser Pro
Thr Glu Met Val Cys Ile Ser Ser Leu 355 360 365Leu Pro Asp Gly Gly
Glu Gly Pro Ser Ala Thr Ala Asn Gly Gly Leu 370 375 380Ser Lys Ala
Lys Ser Pro Gly Leu Thr Pro Glu Pro Arg Glu Asp Arg385 390 395
400Glu Gly Asp Asp Leu Thr Leu His Ser Phe Leu Pro 405
4102093PRTHomo sapiens 20Met Leu Thr Glu Leu Glu Lys Ala Leu Asn
Ser Ile Ile Asp Val Tyr1 5 10 15His Lys Tyr Ser Leu Ile Lys Gly Asn
Phe His Ala Val Tyr Arg Asp 20 25 30Asp Leu Lys Lys Leu Leu Glu Thr
Glu Cys Pro Gln Tyr Ile Arg Lys 35 40 45Lys Gly Ala Asp Val Trp Phe
Lys Glu Leu Asp Ile Asn Thr Asp Gly 50 55 60Ala Val Asn Phe Gln Glu
Phe Leu Ile Leu Val Ile Lys Met Gly Val65 70 75 80Ala Ala His Lys
Lys Ser His Glu Glu Ser His Lys Glu 85 9021114PRTHomo sapiens 21Met
Thr Cys Lys Met Ser Gln Leu Glu Arg Asn Ile Glu Thr Ile Ile1 5 10
15Asn Thr Phe His Gln Tyr Ser Val Lys Leu Gly His Pro Asp Thr Leu
20 25 30Asn Gln Gly Glu Phe Lys Glu Leu Val Arg Lys Asp Leu Gln Asn
Phe 35 40 45Leu Lys Lys Glu Asn Lys Asn Glu Lys Val Ile Glu His Ile
Met Glu 50 55 60Asp Leu Asp Thr Asn Ala Asp Lys Gln Leu Ser Phe Glu
Glu Phe Ile65 70 75 80Met Leu Met Ala Arg Leu Thr Trp Ala Ser His
Glu Lys Met His Glu 85 90 95Gly Asp Glu Gly Pro Gly His His His Lys
Pro Gly Leu Gly Glu Gly 100 105 110Thr Pro22122PRTHomo sapiens
22Met Lys Leu Leu Thr Gly Leu Val Phe Cys Ser Leu Val Leu Gly Val1
5 10 15Ser Ser Arg Ser Phe Phe Ser Phe Leu Gly Glu Ala Phe Asp Gly
Ala 20 25 30Arg Asp Met Trp Arg Ala Tyr Ser Asp Met Arg Glu Ala Asn
Tyr Ile 35 40 45Gly Ser Asp Lys Tyr Phe His Ala Arg Gly Asn Tyr Asp
Ala Ala Lys 50 55 60Arg Gly Pro Gly Gly Val Trp Ala Ala Glu Ala Ile
Ser Asp Ala Arg65 70 75 80Glu Asn Ile Gln Arg Phe Phe Gly His Gly
Ala Glu Asp Ser Leu Ala 85 90 95Asp Gln Ala Ala Asn Glu Trp Gly Arg
Ser Gly Lys Asp Pro Asn His 100 105 110Phe Arg Pro Ala Gly Leu Pro
Glu Lys Tyr 115 12023472PRTHomo sapiens 23Met Ala Thr Lys Cys Gly
Asn Cys Gly Pro Gly Tyr Ser Thr Pro Leu1 5 10 15Glu Ala Met Lys Gly
Pro Arg Glu Glu Ile Val Tyr Leu Pro Cys Ile 20 25 30Tyr Arg Asn Thr
Gly Thr Glu Ala Pro Asp Tyr Leu Ala Thr Val Asp 35 40 45Val Asp Pro
Lys Ser Pro Gln Tyr Cys Gln Val Ile His Arg Leu Pro 50 55 60Met Pro
Asn Leu Lys Asp Glu Leu His His Ser Gly Trp Asn Thr Cys65 70 75
80Ser Ser Cys Phe Gly Asp Ser Thr Lys Ser Arg Thr Lys Leu Val Leu
85 90 95Pro Ser Leu Ile Ser Ser Arg Ile Tyr Val Val Asp Val Gly Ser
Glu 100 105 110Pro Arg Ala Pro Lys Leu His Lys Val Ile Glu Pro Lys
Asp Ile His 115 120 125Ala Lys Cys Glu Leu Ala Phe Leu His Thr Ser
His Cys Leu Ala Ser 130 135 140Gly Glu Val Met Ile Ser Ser Leu Gly
Asp Val Lys Gly Asn Gly Lys145 150 155 160Gly Gly Phe Val Leu Leu
Asp Gly Glu Thr Phe Glu Val Lys Gly Thr 165 170 175Trp Glu Arg Pro
Gly Gly Ala Ala Pro Leu Gly Tyr Asp Phe Trp Tyr 180 185 190Gln Pro
Arg His Asn Val Met Ile Ser Thr Glu Trp Ala Ala Pro Asn 195 200
205Val Leu Arg Asp Gly Phe Asn Pro Ala Asp Val Glu Ala Gly Leu Tyr
210 215 220Gly Ser His Leu Tyr Val Trp Asp Trp Gln Arg His Glu Ile
Val Gln225 230 235 240Thr Leu Ser Leu Lys Asp Gly Leu Ile Pro Leu
Glu Ile Arg Phe Leu 245 250 255His Asn Pro Asp Ala Ala Gln Gly Phe
Val Gly Cys Ala Leu Ser Ser 260 265 270Thr Ile Gln Arg Phe Tyr Lys
Asn Glu Gly Gly Thr Trp Ser Val Glu 275 280 285Lys Val Ile Gln Val
Pro Pro Lys Lys Val Lys Gly Trp Leu Leu Pro 290 295 300Glu Met Pro
Gly Leu Ile Thr Asp Ile Leu Leu Ser Leu Asp Asp Arg305 310 315
320Phe Leu Tyr Phe Ser Asn Trp Leu His Gly Asp Leu Arg Gln Tyr Asp
325 330 335Ile Ser Asp Pro Gln Arg Pro Arg Leu Thr Gly Gln Leu Phe
Leu Gly 340 345 350Gly Ser Ile Val Lys Gly Gly Pro Val Gln Val Leu
Glu Asp Glu Glu 355 360 365Leu Lys Ser Gln Pro Glu Pro Leu Val Val
Lys Gly Lys Arg Val Ala 370 375 380Gly Gly Pro Gln Met Ile Gln Leu
Ser Leu Asp Gly Lys Arg Leu Tyr385 390 395 400Ile Thr Thr Ser Leu
Tyr Ser Ala Trp Asp Lys Gln Phe Tyr Pro Asp 405 410 415Leu Ile Arg
Glu Gly Ser Val Met Leu Gln Val Asp Val Asp Thr Val 420 425 430Lys
Gly Gly Leu Lys Leu Asn Pro Asn Phe Leu Val Asp Phe Gly Lys 435 440
445Glu Pro Leu Gly Pro Ala Leu Ala His Glu Leu Arg Tyr Pro Gly Gly
450 455 460Asp Cys Ser Ser Asp Ile Trp Ile465 47024760PRTHomo
sapiens 24Met Lys Thr Trp Val Lys Ile Val Phe Gly Val Ala Thr Ser
Ala Val1 5 10 15Leu Ala Leu Leu Val Met Cys Ile Val Leu Arg Pro Ser
Arg Val His 20 25 30Asn Ser Glu Glu Asn Thr Met Arg Ala Leu Thr Leu
Lys Asp Ile Leu 35 40 45Asn Gly Thr Phe Ser Tyr Lys Thr Phe Phe Pro
Asn Trp Ile Ser Gly 50 55 60Gln Glu Tyr Leu His Gln Ser Ala Asp Asn
Asn Ile Val Leu Tyr Asn65 70 75 80Ile Glu Thr Gly Gln Ser Tyr Thr
Ile Leu Ser Asn Arg Thr Met Lys 85 90 95Ser Val Asn Ala Ser Asn Tyr
Gly Leu Ser Pro Asp Arg Gln Phe Val 100 105 110Tyr Leu Glu Ser Asp
Tyr Ser Lys Leu Trp Arg Tyr Ser Tyr Thr Ala 115 120 125Thr Tyr Tyr
Ile Tyr Asp Leu Ser Asn Gly Glu Phe Val Arg Gly Asn 130 135 140Glu
Leu Pro Arg Pro Ile Gln Tyr Leu Cys Trp Ser Pro Val Gly Ser145 150
155 160Lys Leu Ala Tyr Val Tyr Gln Asn Asn Ile Tyr Leu Lys Gln Arg
Pro 165 170 175Gly Asp Pro Pro Phe Gln Ile Thr Phe Asn Gly Arg Glu
Asn Lys Ile 180 185 190Phe Asn Gly Ile Pro Asp Trp Val Tyr Glu Glu
Glu Met Leu Ala Thr 195 200 205Lys Tyr Ala Leu Trp Trp Ser Pro Asn
Gly Lys Phe Leu Ala Tyr Ala 210 215 220Glu Phe Asn Asp Thr Asp Ile
Pro Val Ile Ala Tyr Ser Tyr Tyr Gly225 230 235 240Asp Glu Gln Tyr
Pro Arg Thr Ile Asn Ile Pro Tyr Pro Lys Ala Gly 245 250 255Ala Lys
Asn Pro Val Val Arg Ile Phe Ile
Ile Asp Thr Thr Tyr Pro 260 265 270Ala Tyr Val Gly Pro Gln Glu Val
Pro Val Pro Ala Met Ile Ala Ser 275 280 285Ser Asp Tyr Tyr Phe Ser
Trp Leu Thr Trp Val Thr Asp Glu Arg Val 290 295 300Cys Leu Gln Trp
Leu Lys Arg Val Gln Asn Val Ser Val Leu Ser Ile305 310 315 320Cys
Asp Phe Arg Glu Asp Trp Gln Thr Trp Asp Cys Pro Lys Thr Gln 325 330
335Glu His Ile Glu Glu Ser Arg Thr Gly Trp Ala Gly Gly Phe Phe Val
340 345 350Ser Thr Pro Val Phe Ser Tyr Asp Ala Ile Ser Tyr Tyr Lys
Ile Phe 355 360 365Ser Asp Lys Asp Gly Tyr Lys His Ile His Tyr Ile
Lys Asp Thr Val 370 375 380Glu Asn Ala Ile Gln Ile Thr Ser Gly Lys
Trp Glu Ala Ile Asn Ile385 390 395 400Phe Arg Val Thr Gln Asp Ser
Leu Phe Tyr Ser Ser Asn Glu Phe Glu 405 410 415Glu Tyr Pro Gly Arg
Arg Asn Ile Tyr Arg Ile Ser Ile Gly Ser Tyr 420 425 430Pro Pro Ser
Lys Lys Cys Val Thr Cys His Leu Arg Lys Glu Arg Cys 435 440 445Gln
Tyr Tyr Thr Ala Ser Phe Ser Asp Tyr Ala Lys Tyr Tyr Ala Leu 450 455
460Val Cys Tyr Gly Pro Gly Ile Pro Ile Ser Thr Leu His Asp Gly
Arg465 470 475 480Thr Asp Gln Glu Ile Lys Ile Leu Glu Glu Asn Lys
Glu Leu Glu Asn 485 490 495Ala Leu Lys Asn Ile Gln Leu Pro Lys Glu
Glu Ile Lys Lys Leu Glu 500 505 510Val Asp Glu Ile Thr Leu Trp Tyr
Lys Met Ile Leu Pro Pro Gln Phe 515 520 525Asp Arg Ser Lys Lys Tyr
Pro Leu Leu Ile Gln Val Tyr Gly Gly Pro 530 535 540Cys Ser Gln Ser
Val Arg Ser Val Phe Ala Val Asn Trp Ile Ser Tyr545 550 555 560Leu
Ala Ser Lys Glu Gly Met Val Ile Ala Leu Val Asp Gly Arg Gly 565 570
575Thr Ala Phe Gln Gly Asp Lys Leu Leu Tyr Ala Val Tyr Arg Lys Leu
580 585 590Gly Val Tyr Glu Val Glu Asp Gln Ile Thr Ala Val Arg Lys
Phe Ile 595 600 605Glu Met Gly Phe Ile Asp Glu Lys Arg Ile Ala Ile
Trp Gly Trp Ser 610 615 620Tyr Gly Gly Tyr Val Ser Ser Leu Ala Leu
Ala Ser Gly Thr Gly Leu625 630 635 640Phe Lys Cys Gly Ile Ala Val
Ala Pro Val Ser Ser Trp Glu Tyr Tyr 645 650 655Ala Ser Val Tyr Thr
Glu Arg Phe Met Gly Leu Pro Thr Lys Asp Asp 660 665 670Asn Leu Glu
His Tyr Lys Asn Ser Thr Val Met Ala Arg Ala Glu Tyr 675 680 685Phe
Arg Asn Val Asp Tyr Leu Leu Ile His Gly Thr Ala Asp Asp Asn 690 695
700Val His Phe Gln Asn Ser Ala Gln Ile Ala Lys Ala Leu Val Asn
Ala705 710 715 720Gln Val Asp Phe Gln Ala Met Trp Tyr Ser Asp Gln
Asn His Gly Leu 725 730 735Ser Gly Leu Ser Thr Asn His Leu Tyr Thr
His Met Thr His Phe Leu 740 745 750Lys Gln Cys Phe Ser Leu Ser Asp
755 76025760PRTHomo sapiens 25Met Met Asp Gln Ala Arg Ser Ala Phe
Ser Asn Leu Phe Gly Gly Glu1 5 10 15Pro Leu Ser Tyr Thr Arg Phe Ser
Leu Ala Arg Gln Val Asp Gly Asp 20 25 30Asn Ser His Val Glu Met Lys
Leu Ala Val Asp Glu Glu Glu Asn Ala 35 40 45Asp Asn Asn Thr Lys Ala
Asn Val Thr Lys Pro Lys Arg Cys Ser Gly 50 55 60Ser Ile Cys Tyr Gly
Thr Ile Ala Val Ile Val Phe Phe Leu Ile Gly65 70 75 80Phe Met Ile
Gly Tyr Leu Gly Tyr Cys Lys Gly Val Glu Pro Lys Thr 85 90 95Glu Cys
Glu Arg Leu Ala Gly Thr Glu Ser Pro Val Arg Glu Glu Pro 100 105
110Gly Glu Asp Phe Pro Ala Ala Arg Arg Leu Tyr Trp Asp Asp Leu Lys
115 120 125Arg Lys Leu Ser Glu Lys Leu Asp Ser Thr Asp Phe Thr Gly
Thr Ile 130 135 140Lys Leu Leu Asn Glu Asn Ser Tyr Val Pro Arg Glu
Ala Gly Ser Gln145 150 155 160Lys Asp Glu Asn Leu Ala Leu Tyr Val
Glu Asn Gln Phe Arg Glu Phe 165 170 175Lys Leu Ser Lys Val Trp Arg
Asp Gln His Phe Val Lys Ile Gln Val 180 185 190Lys Asp Ser Ala Gln
Asn Ser Val Ile Ile Val Asp Lys Asn Gly Arg 195 200 205Leu Val Tyr
Leu Val Glu Asn Pro Gly Gly Tyr Val Ala Tyr Ser Lys 210 215 220Ala
Ala Thr Val Thr Gly Lys Leu Val His Ala Asn Phe Gly Thr Lys225 230
235 240Lys Asp Phe Glu Asp Leu Tyr Thr Pro Val Asn Gly Ser Ile Val
Ile 245 250 255Val Arg Ala Gly Lys Ile Thr Phe Ala Glu Lys Val Ala
Asn Ala Glu 260 265 270Ser Leu Asn Ala Ile Gly Val Leu Ile Tyr Met
Asp Gln Thr Lys Phe 275 280 285Pro Ile Val Asn Ala Glu Leu Ser Phe
Phe Gly His Ala His Leu Gly 290 295 300Thr Gly Asp Pro Tyr Thr Pro
Gly Phe Pro Ser Phe Asn His Thr Gln305 310 315 320Phe Pro Pro Ser
Arg Ser Ser Gly Leu Pro Asn Ile Pro Val Gln Thr 325 330 335Ile Ser
Arg Ala Ala Ala Glu Lys Leu Phe Gly Asn Met Glu Gly Asp 340 345
350Cys Pro Ser Asp Trp Lys Thr Asp Ser Thr Cys Arg Met Val Thr Ser
355 360 365Glu Ser Lys Asn Val Lys Leu Thr Val Ser Asn Val Leu Lys
Glu Ile 370 375 380Lys Ile Leu Asn Ile Phe Gly Val Ile Lys Gly Phe
Val Glu Pro Asp385 390 395 400His Tyr Val Val Val Gly Ala Gln Arg
Asp Ala Trp Gly Pro Gly Ala 405 410 415Ala Lys Ser Gly Val Gly Thr
Ala Leu Leu Leu Lys Leu Ala Gln Met 420 425 430Phe Ser Asp Met Val
Leu Lys Asp Gly Phe Gln Pro Ser Arg Ser Ile 435 440 445Ile Phe Ala
Ser Trp Ser Ala Gly Asp Phe Gly Ser Val Gly Ala Thr 450 455 460Glu
Trp Leu Glu Gly Tyr Leu Ser Ser Leu His Leu Lys Ala Phe Thr465 470
475 480Tyr Ile Asn Leu Asp Lys Ala Val Leu Gly Thr Ser Asn Phe Lys
Val 485 490 495Ser Ala Ser Pro Leu Leu Tyr Thr Leu Ile Glu Lys Thr
Met Gln Asn 500 505 510Val Lys His Pro Val Thr Gly Gln Phe Leu Tyr
Gln Asp Ser Asn Trp 515 520 525Ala Ser Lys Val Glu Lys Leu Thr Leu
Asp Asn Ala Ala Phe Pro Phe 530 535 540Leu Ala Tyr Ser Gly Ile Pro
Ala Val Ser Phe Cys Phe Cys Glu Asp545 550 555 560Thr Asp Tyr Pro
Tyr Leu Gly Thr Thr Met Asp Thr Tyr Lys Glu Leu 565 570 575Ile Glu
Arg Ile Pro Glu Leu Asn Lys Val Ala Arg Ala Ala Ala Glu 580 585
590Val Ala Gly Gln Phe Val Ile Lys Leu Thr His Asp Val Glu Leu Asn
595 600 605Leu Asp Tyr Glu Arg Tyr Asn Ser Gln Leu Leu Ser Phe Val
Arg Asp 610 615 620Leu Asn Gln Tyr Arg Ala Asp Ile Lys Glu Met Gly
Leu Ser Leu Gln625 630 635 640Trp Leu Tyr Ser Ala Arg Gly Asp Phe
Phe Arg Ala Thr Ser Arg Leu 645 650 655Thr Thr Asp Phe Gly Asn Ala
Glu Lys Thr Asp Arg Phe Val Met Lys 660 665 670Lys Leu Asn Asp Arg
Val Met Arg Val Glu Tyr His Phe Leu Ser Pro 675 680 685Tyr Val Ser
Pro Lys Glu Ser Pro Phe Arg His Val Phe Trp Gly Ser 690 695 700Gly
Ser His Thr Leu Pro Ala Leu Leu Glu Asn Leu Lys Leu Arg Lys705 710
715 720Gln Asn Asn Gly Ala Phe Asn Glu Thr Leu Phe Arg Asn Gln Leu
Ala 725 730 735Leu Ala Thr Trp Thr Ile Gln Gly Ala Ala Asn Ala Leu
Ser Gly Asp 740 745 750Val Trp Asp Ile Asp Asn Glu Phe 755
76026308PRTHomo sapiens 26Met Pro Gly Gln Glu Leu Arg Thr Val Asn
Gly Ser Gln Met Leu Leu1 5 10 15Val Leu Leu Val Leu Ser Trp Leu Pro
His Gly Gly Ala Leu Ser Leu 20 25 30Ala Glu Ala Ser Arg Ala Ser Phe
Pro Gly Pro Ser Glu Leu His Ser 35 40 45Glu Asp Ser Arg Phe Arg Glu
Leu Arg Lys Arg Tyr Glu Asp Leu Leu 50 55 60Thr Arg Leu Arg Ala Asn
Gln Ser Trp Glu Asp Ser Asn Thr Asp Leu65 70 75 80Val Pro Ala Pro
Ala Val Arg Ile Leu Thr Pro Glu Val Arg Leu Gly 85 90 95Ser Gly Gly
His Leu His Leu Arg Ile Ser Arg Ala Ala Leu Pro Glu 100 105 110Gly
Leu Pro Glu Ala Ser Arg Leu His Arg Ala Leu Phe Arg Leu Ser 115 120
125Pro Thr Ala Ser Arg Ser Trp Asp Val Thr Arg Pro Leu Arg Arg Gln
130 135 140Leu Ser Leu Ala Arg Pro Gln Ala Pro Ala Leu His Leu Arg
Leu Ser145 150 155 160Pro Pro Pro Ser Gln Ser Asp Gln Leu Leu Ala
Glu Ser Ser Ser Ala 165 170 175Arg Pro Gln Leu Glu Leu His Leu Arg
Pro Gln Ala Ala Arg Gly Arg 180 185 190Arg Arg Ala Arg Ala Arg Asn
Gly Asp His Cys Pro Leu Gly Pro Gly 195 200 205Arg Cys Cys Arg Leu
His Thr Val Arg Ala Ser Leu Glu Asp Leu Gly 210 215 220Trp Ala Asp
Trp Val Leu Ser Pro Arg Glu Val Gln Val Thr Met Cys225 230 235
240Ile Gly Ala Cys Pro Ser Gln Phe Arg Ala Ala Asn Met His Ala Gln
245 250 255Ile Lys Thr Ser Leu His Arg Leu Lys Pro Asp Thr Val Pro
Ala Pro 260 265 270Cys Cys Val Pro Ala Ser Tyr Asn Pro Met Val Leu
Ile Gln Lys Thr 275 280 285Asp Thr Gly Val Ser Leu Gln Thr Tyr Asp
Asp Leu Leu Ala Lys Asp 290 295 300Cys His Cys
Ile3052715PRTArtificial Sequencesource/note="Description of
Artificial Sequence Synthetic peptide" 27Ile Ala Glu Leu Leu Ser
Pro Gly Ser Val Asp Pro Leu Thr Arg1 5 10 15284PRTArtificial
Sequencesource/note="Description of Artificial Sequence Synthetic
peptide" 28Ile Ala Glu Leu1295PRTArtificial
Sequencesource/note="Description of Artificial Sequence Synthetic
peptide" 29Ile Ala Glu Leu Leu1 5306PRTArtificial
Sequencesource/note="Description of Artificial Sequence Synthetic
peptide" 30Ile Ala Glu Leu Leu Ser1 5317PRTArtificial
Sequencesource/note="Description of Artificial Sequence Synthetic
peptide" 31Ile Ala Glu Leu Leu Ser Pro1 5328PRTArtificial
Sequencesource/note="Description of Artificial Sequence Synthetic
peptide" 32Ile Ala Glu Leu Leu Ser Pro Gly1 5339PRTArtificial
Sequencesource/note="Description of Artificial Sequence Synthetic
peptide" 33Ile Ala Glu Leu Leu Ser Pro Gly Ser1 53410PRTArtificial
Sequencesource/note="Description of Artificial Sequence Synthetic
peptide" 34Ile Ala Glu Leu Leu Ser Pro Gly Ser Val1 5
103511PRTArtificial Sequencesource/note="Description of Artificial
Sequence Synthetic peptide" 35Ile Ala Glu Leu Leu Ser Pro Gly Ser
Val Asp1 5 103612PRTArtificial Sequencesource/note="Description of
Artificial Sequence Synthetic peptide" 36Ile Ala Glu Leu Leu Ser
Pro Gly Ser Val Asp Pro1 5 103713PRTArtificial
Sequencesource/note="Description of Artificial Sequence Synthetic
peptide" 37Ile Ala Glu Leu Leu Ser Pro Gly Ser Val Asp Pro Leu1 5
103814PRTArtificial Sequencesource/note="Description of Artificial
Sequence Synthetic peptide" 38Ile Ala Glu Leu Leu Ser Pro Gly Ser
Val Asp Pro Leu Thr1 5 103913PRTArtificial
Sequencesource/note="Description of Artificial Sequence Synthetic
peptide" 39Glu Leu Leu Ser Pro Gly Ser Val Asp Pro Leu Thr Arg1 5
104012PRTArtificial Sequencesource/note="Description of Artificial
Sequence Synthetic peptide" 40Leu Leu Ser Pro Gly Ser Val Asp Pro
Leu Thr Arg1 5 104111PRTArtificial Sequencesource/note="Description
of Artificial Sequence Synthetic peptide" 41Leu Ser Pro Gly Ser Val
Asp Pro Leu Thr Arg1 5 104210PRTArtificial
Sequencesource/note="Description of Artificial Sequence Synthetic
peptide" 42Ser Pro Gly Ser Val Asp Pro Leu Thr Arg1 5
10439PRTArtificial Sequencesource/note="Description of Artificial
Sequence Synthetic peptide" 43Pro Gly Ser Val Asp Pro Leu Thr Arg1
5448PRTArtificial Sequencesource/note="Description of Artificial
Sequence Synthetic peptide" 44Gly Ser Val Asp Pro Leu Thr Arg1
5457PRTArtificial Sequencesource/note="Description of Artificial
Sequence Synthetic peptide" 45Ser Val Asp Pro Leu Thr Arg1
5466PRTArtificial Sequencesource/note="Description of Artificial
Sequence Synthetic peptide" 46Val Asp Pro Leu Thr Arg1
5475PRTArtificial Sequencesource/note="Description of Artificial
Sequence Synthetic peptide" 47Asp Pro Leu Thr Arg1
5484PRTArtificial Sequencesource/note="Description of Artificial
Sequence Synthetic peptide" 48Pro Leu Thr Arg14910PRTArtificial
Sequencesource/note="Description of Artificial Sequence Synthetic
peptide" 49Ala Asp Leu Ser Gly Ile Thr Gly Ala Arg1 5
105012PRTArtificial Sequencesource/note="Description of Artificial
Sequence Synthetic peptide" 50Thr Glu His Tyr Glu Glu Gln Ile Glu
Ala Phe Lys1 5 105110PRTArtificial Sequencesource/note="Description
of Artificial Sequence Synthetic peptide" 51Glu Ser Asp Thr Ser Tyr
Val Ser Leu Lys1 5 105210PRTArtificial
Sequencesource/note="Description of Artificial Sequence Synthetic
peptide" 52Gly Tyr Ser Ile Phe Ser Tyr Ala Thr Lys1 5
10537PRTArtificial Sequencesource/note="Description of Artificial
Sequence Synthetic peptide" 53Lys Ala Phe Val Phe Pro Lys1
55413PRTArtificial Sequencesource/note="Description of Artificial
Sequence Synthetic peptide" 54Ala Gly Ala Leu Asn Ser Asn Asp Ala
Phe Val Leu Lys1 5 105511PRTArtificial
Sequencesource/note="Description of Artificial Sequence Synthetic
peptide" 55Ala Leu Asn Ser Ile Ile Asp Val Tyr His Lys1 5
10567PRTArtificial Sequencesource/note="Description of Artificial
Sequence Synthetic peptide" 56Gly Ala Asp Val Trp Phe Lys1
5577PRTArtificial Sequencesource/note="Description of Artificial
Sequence Synthetic peptide" 57Asp Leu Gln Asn Phe Leu Lys1
55813PRTArtificial Sequencesource/note="Description of Artificial
Sequence Synthetic peptide" 58Leu Gly His Pro Asp Thr Leu Asn Gln
Gly Glu Phe Lys1 5 10598PRTArtificial
Sequencesource/note="Description of Artificial Sequence Synthetic
peptide" 59Gly Lys Ile Thr Asp Leu Ile Lys1 5
* * * * *