U.S. patent application number 17/204892 was filed with the patent office on 2021-08-19 for cell-free dna for assessing and/or treating cancer.
The applicant listed for this patent is The Johns Hopkins University. Invention is credited to Vilmos Adleff, Stephen Cristiano, Jacob Fiksel, Alessandro Leal, Jillian A. Phallen, Robert B. Scharpf, Victor E. Velculescu.
Application Number | 20210254152 17/204892 |
Document ID | / |
Family ID | 1000005504704 |
Filed Date | 2021-08-19 |
United States Patent
Application |
20210254152 |
Kind Code |
A1 |
Velculescu; Victor E. ; et
al. |
August 19, 2021 |
CELL-FREE DNA FOR ASSESSING AND/OR TREATING CANCER
Abstract
This document relates to methods and materials for assessed,
monitored, and/or treated mammals (e.g., humans) having cancer. For
example, methods and materials for identifying a mammal as having
cancer (e.g., a localized cancer) are provided. For example,
methods and materials for assessing, monitoring, and/or treating a
mammal having cancer are provided.
Inventors: |
Velculescu; Victor E.;
(Dayton, MD) ; Cristiano; Stephen; (Baltimore,
MD) ; Leal; Alessandro; (Baltimore, MD) ;
Phallen; Jillian A.; (Baltimore, MD) ; Fiksel;
Jacob; (Baltimore, MD) ; Adleff; Vilmos;
(Baltimore, MD) ; Scharpf; Robert B.; (Baltimore,
MD) |
|
Applicant: |
Name |
City |
State |
Country |
Type |
The Johns Hopkins University |
Baltimore |
MD |
US |
|
|
Family ID: |
1000005504704 |
Appl. No.: |
17/204892 |
Filed: |
March 17, 2021 |
Related U.S. Patent Documents
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Application
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Filing Date |
Patent Number |
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16730938 |
Dec 30, 2019 |
10982279 |
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17204892 |
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PCT/US19/32914 |
May 17, 2019 |
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16730938 |
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62795900 |
Jan 23, 2019 |
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62673516 |
May 18, 2018 |
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Current U.S.
Class: |
1/1 |
Current CPC
Class: |
G16B 50/20 20190201;
G16B 30/00 20190201; G06F 17/18 20130101; G16B 40/00 20190201; G16B
40/30 20190201; C12Q 1/6874 20130101; C12Q 2600/156 20130101; C12Q
1/6886 20130101; G16B 40/20 20190201 |
International
Class: |
C12Q 1/6874 20060101
C12Q001/6874; G16B 40/00 20060101 G16B040/00; G16B 30/00 20060101
G16B030/00; C12Q 1/6886 20060101 C12Q001/6886 |
Goverment Interests
STATEMENT REGARDING FEDERAL FUNDING
[0002] This invention was made with U.S. government support under
grant No. CA121113 from the National Institutes of Health. The U.S.
government has certain rights in the invention.
Claims
1-67. (canceled)
68. A system for determining a cell free DNA (cfDNA) fragmentation
profile of a subject comprising: processing cfDNA fragments
obtained from a sample obtained from the subject into sequencing
libraries; subjecting the sequencing libraries to whole genome
sequencing to obtain sequenced fragments, wherein genome coverage
is from about 0.1.times. to 9.times.; mapping the sequenced
fragments to a genome to obtain genomic intervals of mapped
sequences; analyzing the genomic intervals of mapped sequences to
determine cfDNA fragment lengths; and determining a cfDNA
fragmentation profile for the subject.
69. The system of claim 68, wherein the system is a machine
learning system.
70. The system of claim 69, wherein the machine learning system is
a gradient tree boosting machine learning system.
71. The system of claim 68, wherein a cfDNA fragmentation profile
in the subject that is more variable than a reference cfDNA
fragmentation profile is indicative of the subject as having or at
risk of having cancer.
72. The system of claim 68, wherein a cfDNA fragmentation profile
in the subject that is less or equally variable than a reference
cfDNA fragmentation profile is indicative of the subject as being
healthy.
73. The system of claim 71, wherein the reference cfDNA
fragmentation profile is a reference nucleosome cfDNA fragmentation
profile.
74. The system of claim 68, wherein determining the cfDNA
fragmentation profile distinguishes circulating tumor DNA (ctDNA)
from non-cancer-associated white blood cell DNA in the blood.
75. The system of claim 68, wherein the mapped sequences comprise
tens or hundreds to thousands of genomic intervals.
76. The system of claim 68, wherein the genomic intervals are
non-overlapping.
77. The system of claim 68, wherein the genomic intervals each
comprise thousands to millions of base pairs.
78. The system of claim 68, wherein a cfDNA fragmentation profile
is determined within each genomic interval.
79. The system of claim 68, wherein a cfDNA fragmentation profile
comprises a median fragment size.
80. The system of claim 68, wherein a cfDNA fragmentation profile
comprises a fragment size distribution.
81. The system of claim 68, wherein a cfDNA fragmentation profile
is determined over the whole genome or a subgenomic interval.
82. The system of claim 68, wherein cfDNA fragmentation profiles
provide over 20,000 reads per genomic intervals.
83. The system of claim 68, wherein the genomic coverage is about
0.1.times., 0.2.times., 0.5.times., 1.times. or 2.times..
84. The system of claim 68, wherein the cfDNA fragmentation profile
further predicts the tissue of origin of the cancer in a subject
having or at risk of having cancer.
85. The system of claim 68, wherein the cancer is selected from the
group consisting of: colorectal cancer, lung cancer, breast cancer,
gastric cancer, pancreatic cancer, bile duct cancer, and ovarian
cancer.
86. The system of claim 68, wherein the cancer is treated with or
has previously been treated with a treatment comprising
administering to the subject a cancer treatment selected from the
group consisting of surgery, adjuvant chemotherapy, neoadjuvant
chemotherapy, radiation therapy, hormone therapy, cytotoxic
therapy, immunotherapy, adoptive T cell therapy, targeted therapy
and combination thereof.
87. The system of claim 68, wherein cfDNA fragments are nucleosome
protected DNA fragments.
88. The system of claim 68, wherein the sample is a blood, serum,
plasma, amnion, tissue, urine, cerebrospinal fluid, saliva, sputum,
broncho-alveolar lavage, bile, lymphatic fluid, cyst fluid, stool,
ascites, pap smear, breast milk or exhaled breath condensate
sample.
89. A method of predicting a cell free DNA (cfDNA) fragmentation
profile of a subject comprising: determining a cfDNA fragmentation
profile prediction for the subject based on a DNA evaluation of
fragments for early interception (DELFI) classifier score, using
the system of claim 68, thereby predicting a cfDNA fragmentation
profile of the subject.
90. A method of predicting a cancer status in a subject comprising:
determining a cfDNA fragmentation profile prediction for the
subject using the system of claim 68; and classifying the subject
as a healthy subject or a subject having or at risk of having
cancer based on variability of the cfDNA fragmentation profile in
the subject, thereby predicting a cancer status in the subject.
91. A method of detecting and/or monitoring the status of cancer in
a subject comprising: determining a first cfDNA fragmentation
profile of the subject at a first time using the system of claim
68; and classifying the subject as a healthy subject or a subject
having or at risk of having cancer based on the cfDNA fragmentation
profile of the subject, thereby detecting cancer in the
subject.
92. The method of claim 91, further comprising determining a second
cfDNA fragmentation profile of the subject at a second time and
comparing the first cfDNA fragmentation profile to the second cfDNA
fragmentation profile to monitor the status of cancer in the
subject.
93. The method of claim 92, wherein the first and/or the second
cfDNA fragmentation profiles are determined before, during and/or
after the course of a cancer treatment.
94. The method of claim 93, wherein determining the first and/or
the second cfDNA fragmentation profiles over the course of a cancer
treatment indicates responsiveness to the cancer treatment.
95. The method of claim 92, wherein a second cfDNA fragmentation
profile that is less or equally variable than a reference cfDNA
fragmentation profile obtained in a healthy subject indicates a
response to the cancer treatment in the subject.
96. The method of claim 92, wherein a second cfDNA fragmentation
profile that is more variable than a reference cfDNA fragmentation
profile obtained in a healthy subject indicates an absence of
response to the cancer treatment in the subject.
97. The method of claim 91, wherein determining the cfDNA
fragmentation profile is indicative of a change in tumor size,
and/or change in tumor localization.
Description
CROSS-REFERENCE TO RELATED APPLICATIONS
[0001] This application claims the benefit of U.S. Patent
Application Ser. No. 62/673,516, filed on May 18, 2018, and claims
the benefit of U.S. Patent Application Ser. No. 62/795,900, filed
on Jan. 23, 2019. The disclosure of the prior applications are
considered part of (and are incorporated by reference in) the
disclosure of this application.
BACKGROUND
I. Technical Field
[0003] This document relates to methods and materials for assessing
and/or treating mammals (e.g., humans) having cancer. For example,
this document provides methods and materials for identifying a
mammal as having cancer (e.g., a localized cancer). For example,
this document provides methods and materials for monitoring and/or
treating a mammal having cancer.
2. Background Information
[0004] Much of the morbidity and mortality of human cancers
world-wide is a result of the late diagnosis of these diseases,
where treatments are less effective (Torre et al., 2015 CA Cancer J
Clin 65:87; and World Health Organization, 2017 Guide to Cancer
Early Diagnosis). Unfortunately, clinically proven biomarkers that
can be used to broadly diagnose and treat patients are not widely
available (Mazzucchelli, 2000 Advances in clinical pathology 4:111;
Ruibal Morell, 1992 The International journal of biological markers
7:160; Galli et al., 2013 Clinical chemistry and laboratory
medicine 51:1369; Sikaris, 2011 Heart, lung &circulation
20:634; Lin et al., 2016 in Screening for Colorectal Cancer: A
Systematic Review for the U.S. Preventive Services Task Force.
(Rockville, Md.); Wanebo et al., 1978 N Engl J Med 299:448; and
Zauber, 2015 Dig Dis Sci 60:681).
SUMMARY
[0005] Recent analyses of cell-free DNA suggests that such
approaches may provide new avenues for early diagnosis (Phallen et
al., 2017 Sci Transl Med 9; Cohen et al., 2018 Science 359:926;
Alix-Panabieres et al., 2016 Cancer discovery 6:479; Siravegna et
al., 2017 Nature reviews. Clinical oncology 14:531; Haber et al.,
2014 Cancer discovery 4:650; Husain et al., 2017 JAMA 318:1272; and
Wan et al., 2017 Nat Rev Cancer 17:223).
[0006] This document provides methods and materials for determining
a cell free DNA (cfDNA) fragmentation profile in a mammal (e.g., in
a sample obtained from a mammal). In some cases, determining a
cfDNA fragmentation profile in a mammal can be used for identifying
a mammal as having cancer. For example, cfDNA fragments obtained
from a mammal (e.g., from a sample obtained from a mammal) can be
subjected to low coverage whole-genome sequencing, and the
sequenced fragments can be mapped to the genome (e.g., in
non-overlapping windows) and assessed to determine a cfDNA
fragmentation profile. This document also provides methods and
materials for assessing and/or treating mammals (e.g., humans)
having, or suspected of having, cancer. In some cases, this
document provides methods and materials for identifying a mammal as
having cancer. For example, a sample (e.g., a blood sample)
obtained from a mammal can be assessed to determine if the mammal
has cancer based, at least in part, on the cfDNA fragmentation
profile. In some cases, this document provides methods and
materials for monitoring and/or treating a mammal having cancer.
For example, one or more cancer treatments can be administered to a
mammal identified as having cancer (e.g., based, at least in part,
on a cfDNA fragmentation profile) to treat the mammal.
[0007] Described herein is a non-invasive method for the early
detection and localization of cancer. cfDNA in the blood can
provide a non-invasive diagnostic avenue for patients with cancer.
As demonstrated herein, DNA Evaluation of Fragments for early
Interception (DELFI) was developed and used to evaluate genome-wide
fragmentation patterns of cfDNA of 236 patients with breast,
colorectal, lung, ovarian, pancreatic, gastric, or bile duct
cancers as well as 245 healthy individuals. These analyses revealed
that cfDNA profiles of healthy individuals reflected nucleosomal
fragmentation patterns of white blood cells, while patients with
cancer had altered fragmentation profiles. DELFI had sensitivities
of detection ranging from 57% to >99% among the seven cancer
types at 98% specificity and identified the tissue of origin of the
cancers to a limited number of sites in 75% of cases. Assessing
cfDNA (e.g., using DELFI) can provide a screening approach for
early detection of cancer, which can increase the chance for
successful treatment of a patient having cancer. Assessing cfDNA
(e.g., using DELFI) can also provide an approach for monitoring
cancer, which can increase the chance for successful treatment and
improved outcome of a patient having cancer. In addition, a cfDNA
fragmentation profile can be obtained from limited amounts of cfDNA
and using inexpensive reagents and/or instruments.
[0008] In general, one aspect of this document features methods for
determining a cfDNA fragmentation profile of a mammal. The methods
can include, or consist essentially of, processing cfDNA fragments
obtained from a sample obtained from the mammal into sequencing
libraries, subjecting the sequencing libraries to whole genome
sequencing (e.g., low-coverage whole genome sequencing) to obtain
sequenced fragments, mapping the sequenced fragments to a genome to
obtain windows of mapped sequences, and analyzing the windows of
mapped sequences to determine cfDNA fragment lengths. The mapped
sequences can include tens to thousands of windows. The windows of
mapped sequences can be non-overlapping windows. The windows of
mapped sequences can each include about 5 million base pairs. The
cfDNA fragmentation profile can be determined within each window.
The cfDNA fragmentation profile can include a median fragment size.
The cfDNA fragmentation profile can include a fragment size
distribution. The cfDNA fragmentation profile can include a ratio
of small cfDNA fragments to large cfDNA fragments in the windows of
mapped sequences. The cfDNA fragmentation profile can be over the
whole genome. The cfDNA fragmentation profile can be over a
subgenomic interval (e.g., an interval in a portion of a
chromosome).
[0009] In another aspect, this document features methods for
identifying a mammal as having cancer. The methods can include, or
consist essentially of, determining a cfDNA fragmentation profile
in a sample obtained from a mammal, comparing the cfDNA
fragmentation profile to a reference cfDNA fragmentation profile,
and identifying the mammal as having cancer when the cfDNA
fragmentation profile in the sample obtained from the mammal is
different from the reference cfDNA fragmentation profile. The
reference cfDNA fragmentation profile can be a cfDNA fragmentation
profile of a healthy mammal. The reference cfDNA fragmentation
profile can be generated by determining a cfDNA fragmentation
profile in a sample obtained from the healthy mammal. The reference
DNA fragmentation pattern can be a reference nucleosome cfDNA
fragmentation profile. The cfDNA fragmentation profiles can include
a median fragment size, and a median fragment size of the cfDNA
fragmentation profile can be shorter than a median fragment size of
the reference cfDNA fragmentation profile. The cfDNA fragmentation
profiles can include a fragment size distribution, and a fragment
size distribution of the cfDNA fragmentation profile can differ by
at least 10 nucleotides as compared to a fragment size distribution
of the reference cfDNA fragmentation profile. The cfDNA
fragmentation profiles can include position dependent differences
in fragmentation patterns, including a ratio of small cfDNA
fragments to large cfDNA fragments, where a small cfDNA fragment
can be 100 base pairs (bp) to 150 bp in length and a large cfDNA
fragments can be 151 bp to 220 bp in length, and where a
correlation of fragment ratios in the cfDNA fragmentation profile
can be lower than a correlation of fragment ratios of the reference
cfDNA fragmentation profile. The cfDNA fragmentation profiles can
include sequence coverage of small cfDNA fragments, large cfDNA
fragments, or of both small and large cfDNA fragments, across the
genome. The cancer can be colorectal cancer, lung cancer, breast
cancer, bile duct cancer, pancreatic cancer, gastric cancer, or
ovarian cancer. The step of comparing can include comparing the
cfDNA fragmentation profile to a reference cfDNA fragmentation
profile in windows across the whole genome. The step of comparing
can include comparing the cfDNA fragmentation profile to a
reference cfDNA fragmentation profile over a subgenomic interval
(e.g., an interval in a portion of a chromosome). The mammal can
have been previously administered a cancer treatment to treat the
cancer. The cancer treatment can be surgery, adjuvant chemotherapy,
neoadjuvant chemotherapy, radiation therapy, hormone therapy,
cytotoxic therapy, immunotherapy, adoptive T cell therapy, targeted
therapy, or any combinations thereof. The method also can include
administering to the mammal a cancer treatment (e.g., surgery,
adjuvant chemotherapy, neoadjuvant chemotherapy, radiation therapy,
hormone therapy, cytotoxic therapy, immunotherapy, adoptive T cell
therapy, targeted therapy, or any combinations thereof). The mammal
can be monitored for the presence of cancer after administration of
the cancer treatment.
[0010] In another aspect, this document features methods for
treating a mammal having cancer. The methods can include, or
consist essentially of, identifying the mammal as having cancer,
where the identifying includes determining a cfDNA fragmentation
profile in a sample obtained from the mammal, comparing the cfDNA
fragmentation profile to a reference cfDNA fragmentation profile,
and identifying the mammal as having cancer when the cfDNA
fragmentation profile obtained from the mammal is different from
the reference cfDNA fragmentation profile; and administering a
cancer treatment to the mammal. The mammal can be a human. The
cancer can be colorectal cancer, lung cancer, breast cancer,
gastric cancers, pancreatic cancers, bile duct cancers, or ovarian
cancer. The cancer treatment can be surgery, adjuvant chemotherapy,
neoadjuvant chemotherapy, radiation therapy, hormone therapy,
cytotoxic therapy, immunotherapy, adoptive T cell therapy, targeted
therapy, or combinations thereof. The reference cfDNA fragmentation
profile can be a cfDNA fragmentation profile of a healthy mammal.
The reference cfDNA fragmentation profile can be generated by
determining a cfDNA fragmentation profile in a sample obtained from
a healthy mammal. The reference DNA fragmentation pattern can be a
reference nucleosome cfDNA fragmentation profile. The cfDNA
fragmentation profile can include a median fragment size, where a
median fragment size of the cfDNA fragmentation profile is shorter
than a median fragment size of the reference cfDNA fragmentation
profile. The cfDNA fragmentation profile can include a fragment
size distribution, where a fragment size distribution of the cfDNA
fragmentation profile differs by at least 10 nucleotides as
compared to a fragment size distribution of the reference cfDNA
fragmentation profile. The cfDNA fragmentation profile can include
a ratio of small cfDNA fragments to large cfDNA fragments in the
windows of mapped sequences, where a small cfDNA fragment is 100 bp
to 150 bp in length, where a large cfDNA fragments is 151 bp to 220
bp in length, and where a correlation of fragment ratios in the
cfDNA fragmentation profile is lower than a correlation of fragment
ratios of the reference cfDNA fragmentation profile. The cfDNA
fragmentation profile can include the sequence coverage of small
cfDNA fragments in windows across the genome. The cfDNA
fragmentation profile can include the sequence coverage of large
cfDNA fragments in windows across the genome. The cfDNA
fragmentation profile can include the sequence coverage of small
and large cfDNA fragments in windows across the genome. The step of
comparing can include comparing the cfDNA fragmentation profile to
a reference cfDNA fragmentation profile over the whole genome. The
step of comparing can include comparing the cfDNA fragmentation
profile to a reference cfDNA fragmentation profile over a
subgenomic interval. The mammal can have previously been
administered a cancer treatment to treat the cancer. The cancer
treatment can be surgery, adjuvant chemotherapy, neoadjuvant
chemotherapy, radiation therapy, hormone therapy, cytotoxic
therapy, immunotherapy, adoptive T cell therapy, targeted therapy,
or combinations thereof. The method also can include monitoring the
mammal for the presence of cancer after administration of the
cancer treatment.
[0011] Unless otherwise defined, all technical and scientific terms
used herein have the same meaning as commonly understood by one of
ordinary skill in the art to which this invention pertains.
Although methods and materials similar or equivalent to those
described herein can be used to practice the invention, suitable
methods and materials are described below. All publications, patent
applications, patents, and other references mentioned herein are
incorporated by reference in their entirety. In case of conflict,
the present specification, including definitions, will control. In
addition, the materials, methods, and examples are illustrative
only and not intended to be limiting.
[0012] The details of one or more embodiments of the invention are
set forth in the accompanying drawings and the description below.
Other features, objects, and advantages of the invention will be
apparent from the description and drawings, and from the
claims.
DESCRIPTION OF THE DRAWINGS
[0013] FIG. 1. Schematic of an exemplary DELFI approach. Blood is
collected from a cohort of healthy individuals and patients with
cancer. Nucleosome protected cfDNA is extracted from the plasma
fraction, processed into sequencing libraries, examined through
whole genome sequencing, mapped to the genome, and analyzed to
determine cfDNA fragment profiles in different windows across the
genome. Machine learning approaches are used to categorize
individuals as healthy or as having cancer and to identify the
tumor tissue of origin using genome-wide cfDNA fragmentation
patterns.
[0014] FIG. 2. Simulations of non-invasive cancer detection based
on number of alterations analyzed and tumor-derived cfDNA fragment
distributions. Monte Carlo simulations were performed using
different numbers of tumor-specific alterations to evaluate the
probability of detecting cancer alterations in cfDNA at the
indicated fraction of tumor-derived molecules. The simulations were
performed assuming an average of 2000 genome equivalents of cfDNA
and the requirement of five or more observations of any alteration.
These analyses indicate that increasing the number of
tumor-specific alterations improves the sensitivity of detection of
circulating tumor DNA.
[0015] FIG. 3. Tumor-derived cfDNA fragment distributions.
Cumulative density functions of cfDNA fragment lengths of 42 loci
containing tumor-specific alterations from 30 patients with breast,
colorectal, lung, or ovarian cancer are shown with 95% confidence
bands (blue). Lengths of mutant cfDNA fragments were significantly
different in size compared to wild-type cfDNA fragments (red) at
these loci.
[0016] FIGS. 4A and 4B. Tumor-derived cfDNA GC content and fragment
length. A, GC content was similar for mutated and non-mutated
fragments. B, GC content was not correlated to fragment length.
[0017] FIG. 5. Germline cfDNA fragment distributions. Cumulative
density functions of fragment lengths of 44 loci containing
germline alterations (non-tumor derived) from 38 patients with
breast, colorectal, lung, or ovarian cancer are shown with 95%
confidence bands. Fragments with germline mutations (blue) were
comparable in length to wild-type cfDNA fragment lengths (red).
[0018] FIG. 6. Hematopoietic cfDNA fragment distributions.
Cumulative density functions of fragment lengths of 41 loci
containing hematopoietic alterations (non-tumor derived) from 28
patients with breast, colorectal, lung, or ovarian cancer are shown
with 95% confidence bands. After correction for multiple testing,
there were no significant differences (.alpha.=0.05) in the size
distributions of mutated hematopoietic ctDNA fragments (blue) and
wild-type cfDNA fragments (red).
[0019] FIGS. 7A-7F. cfDNA fragmentation profiles in healthy
individuals and patients with cancer. A, Genome-wide cfDNA
fragmentation profiles (defined as the ratio of short to long
fragments) from .about.9.times. whole genome sequencing are shown
in 5 Mb bins for 30 healthy individuals (top) and 8 lung cancer
patients (bottom). B, An analysis of healthy cfDNA (top), lung
cancer cfDNA (middle), and healthy lymphocyte (bottom)
fragmentation profiles and lymphocyte profiles from chromosome 1 at
1 Mb resolution. The healthy lymphocyte profiles were scaled with a
standard deviation equal to that of the median healthy cfDNA
profiles. Healthy cfDNA patterns closely mirrored those in healthy
lymphocytes while lung cancer cfDNA profiles were more varied and
differed from both healthy and lymphocyte profiles. C, Smoothed
median distances between adjacent nucleosome centered at zero using
100 kb bins from healthy cfDNA (top) and nuclease-digested healthy
lymphocytes (middle) are depicted together with the first
eigenvector for the genome contact matrix obtained through
previously reported Hi-C analyses of lymphoblastoid cells (bottom).
Healthy cfDNA nucleosome distances closely mirrored those in
nuclease-digested lymphocytes as well as those from lymphoblastoid
Hi-C analyses. cfDNA fragmentation profiles from healthy
individuals (n=30) had high correlations while patients with lung
cancer had lower correlations to median fragmentation profiles of
lymphocytes (D), healthy cfDNA (E), and lymphocyte nucleosome (F)
distances.
[0020] FIG. 8. Density of cfDNA fragment lengths in healthy
individuals and patients with lung cancer. cfDNA fragments lengths
are shown for healthy individuals (n=30, gray) and patients with
lung cancer (n=8, blue).
[0021] FIGS. 9A and 9B. Subsampling of whole genome sequence data
for analysis of cfDNA fragmentation profiles. A, High coverage
(9.times.) whole-genome sequencing data were subsampled to
2.times., 1.times., 0.5.times., 0.2.times., and 0.1.times. fold
coverage. Mean centered genome-wide fragmentation profiles in 5 Mb
bins for 30 healthy individuals and 8 patients with lung cancer are
depicted for each subsampled fold coverage with median profiles
shown in blue. B, Pearson correlation of subsampled profiles to
initial profile at 9.times. coverage for healthy individuals and
patients with lung cancer.
[0022] FIG. 10. cfDNA fragmentation profiles and sequence
alterations during therapy. Detection and monitoring of cancer in
serial blood draws from NSCLC patients (n=19) undergoing treatment
with targeted tyrosine kinase inhibitors (black arrows) was
performed using targeted sequencing (top) and genome-wide
fragmentation profiles (bottom). For each case, the vertical axis
of the lower panel displays -1 times the correlation of each sample
to the median healthy cfDNA fragmentation profile. Error bars
depict confidence intervals from binomial tests for mutant allele
fractions and confidence intervals calculated using Fisher
transformation for genome-wide fragmentation profiles. Although the
approaches analyze different aspects of cfDNA (whole genome
compared to specific alterations) the targeted sequencing and
fragmentation profiles were similar for patients responding to
therapy as well as those with stable or progressive disease. As
fragmentation profiles reflect both genomic and epigenomic
alterations, while mutant allele fractions only reflect individual
mutations, mutant allele fractions alone may not reflect the
absolute level of correlation of fragmentation profiles to healthy
individuals.
[0023] FIGS. 11A-11C. cfDNA fragmentation profiles in healthy
individuals and patients with cancer. A, Fragmentation profiles
(bottom) in the context of tumor copy number changes (top) in a
colorectal cancer patient where parallel analyses of tumor tissue
were performed. The distribution of segment means and integer copy
numbers are shown at top right in the indicated colors. Altered
fragmentation profiles were present in regions of the genome that
were copy neutral and were further affected in regions with copy
number changes. B, GC adjusted fragmentation profiles from
1-2.times. whole genome sequencing for healthy individuals and
patients with cancer are depicted per cancer type using 5 Mb
windows. The median healthy profile is indicated in black and the
98% confidence band is shown in gray. For patients with cancer,
individual profiles are colored based on their correlation to the
healthy median. C, Windows are indicated in orange if more than 10%
of the cancer samples had a fragment ratio more than three standard
deviations from the median healthy fragment ratio. These analyses
highlight the multitude of position dependent alterations across
the genome in cfDNA of individuals with cancer.
[0024] FIGS. 12A and 12B. Profiles of cfDNA fragment lengths in
copy neutral regions in healthy individuals and one patient with
colorectal cancer. A, The fragmentation profile in 211 copy neutral
windows in chromosomes 1-6 for 25 randomly selected healthy
individuals (gray). For a patient with colorectal cancer (CGCRC291)
with an estimated mutant allele fraction of 20%, the cancer
fragment length profile was diluted to an approximate 10% tumor
contribution (blue). A and B, While the marginal densities of the
fragment profiles for the healthy samples and cancer patient show
substantial overlap (A, right), the fragmentation profiles are
different as can be seen visualization of the fragmentation
profiles (A, left) and by the separation of the colorectal cancer
patient from the healthy samples in a principal component analysis
(B).
[0025] FIGS. 13A and 13B. Genome-wide GC correction of cfDNA
fragments. To estimate and control for the effects of GC content on
sequencing coverage, coverage in non-overlapping 100 kb genomic
windows was calculated across the autosomes. For each window, the
average GC of the aligned fragments was calculated. A, Loess
smoothing of raw coverage (top row) for two randomly selected
healthy subjects (CGPLH189 and CGPLH380) and two cancer patients
(CGPLLU161 and CGPLBR24) with undetectable aneuploidy (PA score
<2.35). After subtracting the average coverage predicted by the
loess model, the residuals were resealed to the median autosomal
coverage (bottom row). As fragment length may also result in
coverage biases, this GC correction procedure was performed
separately for short (.ltoreq.150 bp) and long (.gtoreq.151 bp)
fragments. While the 100 kb bins on chromosome 19 (blue points)
consistently have less coverage than predicted by the loess model,
we did not implement a chromosome-specific correction as such an
approach would remove the effects of chromosomal copy number on
coverage. B, Overall, a limited correlation was found between short
or long fragment coverage and GC content after correction among
healthy subjects and cancer patients with a PA score <3.
[0026] FIG. 14. Schematic of machine learning model. Gradient tree
boosting machine learning was used to examine whether cfDNA can be
categorized as having characteristics of a cancer patient or
healthy individual. The machine learning model included
fragmentation size and coverage characteristics in windows
throughout the genome, as well as chromosomal arm and mitochondrial
DNA copy numbers. A 10-fold cross validation approach was employed
in which each sample is randomly assigned to a fold and 9 of the
folds (90% of the data) are used for training and one fold (10% of
the data) is used for testing. The prediction accuracy from a
single cross validation is an average over the 10 possible
combinations of test and training sets. As this prediction accuracy
can reflect bias from the initial randomization of patients, the
entire procedure was repeat, including the randomization of
patients to folds, 10 times. For all cases, feature selection and
model estimation were performed on training data and were validated
on test data and the test data were never used for feature
selection. Ultimately, a DELFI score was obtained that could be
used to classify individuals as likely healthy or having
cancer.
[0027] FIG. 15. Distribution of AUCs across the repeated 10-fold
cross-validation. The 25.sup.th, 50.sup.th, and 75.sup.th
percentiles of the 100 AUCs for the cohort of 215 healthy
individuals and 208 patients with cancer are indicated by dashed
lines.
[0028] FIGS. 16A and 16B. Whole-genome analyses of chromosomal arm
copy number changes and mitochondrial genome representation. A, Z
scores for each autosome arm are depicted for healthy individuals
(n=215) and patients with cancer (n=208). The vertical axis depicts
normal copy at zero with positive and negative values indicating
arm gains and losses, respectively. Z scores greater than 50 or
less than -50 are thresholded at the indicated values. B, The
fraction of reads mapping to the mitochondrial genome is depicted
for healthy individuals and patients with cancer.
[0029] FIGS. 17A and 17B. Detection of cancer using DELFI. A,
Receiver operator characteristics for detection of cancer using
cfDNA fragmentation profiles and other genome-wide features in a
machine learning approach are depicted for a cohort of 215 healthy
individuals and 208 patients with cancer (DELFI, AUC=0.94), with
.gtoreq.95% specificity shaded in blue. Machine learning analyses
of chromosomal arm copy number (Chr copy number (ML)), and
mitochondrial genome copy number (mtDNA), are shown in the
indicated colors. B, Analyses of individual cancers types using the
DELFI-combined approach had AUCs ranging from 0.86 to >0.99.
[0030] FIG. 18. DELFI detection of cancer by stage. Receiver
operator characteristics for detection of cancer using cfDNA
fragmentation profiles and other genome-wide features in a machine
learning approach are depicted for a cohort of 215 healthy
individuals and each stage of 208 patients with cancer with >95%
specificity shaded in blue.
[0031] FIG. 19. DELFI tissue of origin prediction. Receiver
operator characteristics for DELFI tissue prediction of bile duct,
breast, colorectal, gastric, lung, ovarian, and pancreatic cancers
are depicted. In order to increase sample sizes within cancer type
classes, cases detected with a 90% specificity were included, and
the lung cancer cohort was supplemented with the addition of
baseline cfDNA data from 18 lung cancer patients with prior
treatment (see, e.g., Shen et al., 2018 Nature, 563:579-583).
[0032] FIG. 20. Detection of cancer using DELFI and mutation-based
cfDNA approaches. DELFI (green) and targeted sequencing for
mutation identification (blue) were performed independently in a
cohort of 126 patients with breast, bile duct, colorectal, gastric,
lung, or ovarian cancers. The number of individuals detected by
each approach and in combination are indicated for DELFI detection
with a specificity of 98%, targeted sequencing specificity at
>99%, and a combined specificity of 98%. ND indicates not
detected.
DETAILED DESCRIPTION
[0033] This document provides methods and materials for determining
a cfDNA fragmentation profile in a mammal (e.g., in a sample
obtained from a mammal). As used herein, the terms "fragmentation
profile," "position dependent differences in fragmentation
patterns," and "differences in fragment size and coverage in a
position dependent manner across the genome" are equivalent and can
be used interchangeably. In some cases, determining a cfDNA
fragmentation profile in a mammal can be used for identifying a
mammal as having cancer. For example, cfDNA fragments obtained from
a mammal (e.g., from a sample obtained from a mammal) can be
subjected to low coverage whole-genome sequencing, and the
sequenced fragments can be mapped to the genome (e.g., in
non-overlapping windows) and assessed to determine a cfDNA
fragmentation profile. As described herein, a cfDNA fragmentation
profile of a mammal having cancer is more heterogeneous (e.g., in
fragment lengths) than a cfDNA fragmentation profile of a healthy
mammal (e.g., a mammal not having cancer). As such, this document
also provides methods and materials for assessing, monitoring,
and/or treating mammals (e.g., humans) having, or suspected of
having, cancer. In some cases, this document provides methods and
materials for identifying a mammal as having cancer. For example, a
sample (e.g., a blood sample) obtained from a mammal can be
assessed to determine the presence and, optionally, the tissue of
origin of the cancer in the mammal based, at least in part, on the
cfDNA fragmentation profile of the mammal. In some cases, this
document provides methods and materials for monitoring a mammal as
having cancer. For example, a sample (e.g., a blood sample)
obtained from a mammal can be assessed to determine the presence of
the cancer in the mammal based, at least in part, on the cfDNA
fragmentation profile of the mammal. In some cases, this document
provides methods and materials for identifying a mammal as having
cancer, and administering one or more cancer treatments to the
mammal to treat the mammal. For example, a sample (e.g., a blood
sample) obtained from a mammal can be assessed to determine if the
mammal has cancer based, at least in part, on the cfDNA
fragmentation profile of the mammal, and one or more cancer
treatments can be administered to the mammal.
[0034] A cfDNA fragmentation profile can include one or more cfDNA
fragmentation patterns. A cfDNA fragmentation pattern can include
any appropriate cfDNA fragmentation pattern. Examples of cfDNA
fragmentation patterns include, without limitation, median fragment
size, fragment size distribution, ratio of small cfDNA fragments to
large cfDNA fragments, and the coverage of cfDNA fragments. In some
cases, a cfDNA fragmentation pattern includes two or more (e.g.,
two, three, or four) of median fragment size, fragment size
distribution, ratio of small cfDNA fragments to large cfDNA
fragments, and the coverage of cfDNA fragments. In some cases,
cfDNA fragmentation profile can be a genome-wide cfDNA profile
(e.g., a genome-wide cfDNA profile in windows across the genome).
In some cases, cfDNA fragmentation profile can be a targeted region
profile. A targeted region can be any appropriate portion of the
genome (e.g., a chromosomal region). Examples of chromosomal
regions for which a cfDNA fragmentation profile can be determined
as described herein include, without limitation, a portion of a
chromosome (e.g., a portion of 2q, 4p, 5p, 6q, 7p, 8q, 9q, 10q,
11q, 12q, and/or 14q) and a chromosomal arm (e.g., a chromosomal
arm of 8q, 13q, 11q, and/or 3p). In some cases, a cfDNA
fragmentation profile can include two or more targeted region
profiles.
[0035] In some cases, a cfDNA fragmentation profile can be used to
identify changes (e.g., alterations) in cfDNA fragment lengths. An
alteration can be a genome-wide alteration or an alteration in one
or more targeted regions/loci. A target region can be any region
containing one or more cancer-specific alterations. Examples of
cancer-specific alterations, and their chromosomal locations,
include, without limitation, those shown in Table 3 (Appendix C)
and those shown in Table 6 (Appendix F). In some cases, a cfDNA
fragmentation profile can be used to identify (e.g., simultaneously
identify) from about 10 alterations to about 500 alterations (e.g.,
from about 25 to about 500, from about 50 to about 500, from about
100 to about 500, from about 200 to about 500, from about 300 to
about 500, from about 10 to about 400, from about 10 to about 300,
from about 10 to about 200, from about 10 to about 100, from about
10 to about 50, from about 20 to about 400, from about 30 to about
300, from about 40 to about 200, from about 50 to about 100, from
about 20 to about 100, from about 25 to about 75, from about 50 to
about 250, or from about 100 to about 200, alterations).
[0036] In some cases, a cfDNA fragmentation profile can be used to
detect tumor-derived DNA. For example, a cfDNA fragmentation
profile can be used to detect tumor-derived DNA by comparing a
cfDNA fragmentation profile of a mammal having, or suspected of
having, cancer to a reference cfDNA fragmentation profile (e.g., a
cfDNA fragmentation profile of a healthy mammal and/or a
nucleosomal DNA fragmentation profile of healthy cells from the
mammal having, or suspected of having, cancer). In some cases, a
reference cfDNA fragmentation profile is a previously generated
profile from a healthy mammal. For example, methods provided herein
can be used to determine a reference cfDNA fragmentation profile in
a healthy mammal, and that reference cfDNA fragmentation profile
can be stored (e.g., in a computer or other electronic storage
medium) for future comparison to a test cfDNA fragmentation profile
in mammal having, or suspected of having, cancer. In some cases, a
reference cfDNA fragmentation profile (e.g., a stored cfDNA
fragmentation profile) of a healthy mammal is determined over the
whole genome. In some cases, a reference cfDNA fragmentation
profile (e.g., a stored cfDNA fragmentation profile) of a healthy
mammal is determined over a subgenomic interval.
[0037] In some cases, a cfDNA fragmentation profile can be used to
identify a mammal (e.g., a human) as having cancer (e.g., a
colorectal cancer, a lung cancer, a breast cancer, a gastric
cancer, a pancreatic cancer, a bile duct cancer, and/or an ovarian
cancer).
[0038] A cfDNA fragmentation profile can include a cfDNA fragment
size pattern. cfDNA fragments can be any appropriate size. For
example, cfDNA fragment can be from about 50 base pairs (bp) to
about 400 bp in length. As described herein, a mammal having cancer
can have a cfDNA fragment size pattern that contains a shorter
median cfDNA fragment size than the median cfDNA fragment size in a
healthy mammal. A healthy mammal (e.g., a mammal not having cancer)
can have cfDNA fragment sizes having a median cfDNA fragment size
from about 166.6 bp to about 167.2 bp (e.g., about 166.9 bp). In
some cases, a mammal having cancer can have cfDNA fragment sizes
that are, on average, about 1.28 bp to about 2.49 bp (e.g., about
1.88 bp) shorter than cfDNA fragment sizes in a healthy mammal. For
example, a mammal having cancer can have cfDNA fragment sizes
having a median cfDNA fragment size of about 164.11 bp to about
165.92 bp (e.g., about 165.02 bp).
[0039] A cfDNA fragmentation profile can include a cfDNA fragment
size distribution. As described herein, a mammal having cancer can
have a cfDNA size distribution that is more variable than a cfDNA
fragment size distribution in a healthy mammal. In some case, a
size distribution can be within a targeted region. A healthy mammal
(e.g., a mammal not having cancer) can have a targeted region cfDNA
fragment size distribution of about 1 or less than about 1. In some
cases, a mammal having cancer can have a targeted region cfDNA
fragment size distribution that is longer (e.g., 10, 15, 20, 25,
30, 35, 40, 45, 50 or more bp longer, or any number of base pairs
between these numbers) than a targeted region cfDNA fragment size
distribution in a healthy mammal. In some cases, a mammal having
cancer can have a targeted region cfDNA fragment size distribution
that is shorter (e.g., 10, 15, 20, 25, 30, 35, 40, 45, 50 or more
bp shorter, or any number of base pairs between these numbers) than
a targeted region cfDNA fragment size distribution in a healthy
mammal. In some cases, a mammal having cancer can have a targeted
region cfDNA fragment size distribution that is about 47 bp smaller
to about 30 bp longer than a targeted region cfDNA fragment size
distribution in a healthy mammal. In some cases, a mammal having
cancer can have a targeted region cfDNA fragment size distribution
of, on average, a 10, 11, 12, 13, 14, 15, 15, 17, 18, 19, 20 or
more bp difference in lengths of cfDNA fragments. For example, a
mammal having cancer can have a targeted region cfDNA fragment size
distribution of, on average, about a 13 bp difference in lengths of
cfDNA fragments. In some case, a size distribution can be a
genome-wide size distribution. A healthy mammal (e.g., a mammal not
having cancer) can have very similar distributions of short and
long cfDNA fragments genome-wide. In some cases, a mammal having
cancer can have, genome-wide, one or more alterations (e.g.,
increases and decreases) in cfDNA fragment sizes. The one or more
alterations can be any appropriate chromosomal region of the
genome. For example, an alteration can be in a portion of a
chromosome. Examples of portions of chromosomes that can contain
one or more alterations in cfDNA fragment sizes include, without
limitation, portions of 2q, 4p, 5p, 6q, 7p, 8q, 9q, 10q, 11q, 12q,
and 14q. For example, an alteration can be across a chromosome arm
(e.g., an entire chromosome arm).
[0040] A cfDNA fragmentation profile can include a ratio of small
cfDNA fragments to large cfDNA fragments and a correlation of
fragment ratios to reference fragment ratios. As used herein, with
respect to ratios of small cfDNA fragments to large cfDNA
fragments, a small cfDNA fragment can be from about 100 bp in
length to about 150 bp in length. As used herein, with respect to
ratios of small cfDNA fragments to large cfDNA fragments, a large
cfDNA fragment can be from about 151 bp in length to 220 bp in
length. As described herein, a mammal having cancer can have a
correlation of fragment ratios (e.g., a correlation of cfDNA
fragment ratios to reference DNA fragment ratios such as DNA
fragment ratios from one or more healthy mammals) that is lower
(e.g., 2-fold lower, 3-fold lower, 4-fold lower, 5-fold lower,
6-fold lower, 7-fold lower, 8-fold lower, 9-fold lower, 10-fold
lower, or more) than in a healthy mammal. A healthy mammal (e.g., a
mammal not having cancer) can have a correlation of fragment ratios
(e.g., a correlation of cfDNA fragment ratios to reference DNA
fragment ratios such as DNA fragment ratios from one or more
healthy mammals) of about 1 (e.g., about 0.96). In some cases, a
mammal having cancer can have a correlation of fragment ratios
(e.g., a correlation of cfDNA fragment ratios to reference DNA
fragment ratios such as DNA fragment ratios from one or more
healthy mammals) that is, on average, about 0.19 to about 0.30
(e.g., about 0.25) lower than a correlation of fragment ratios
(e.g., a correlation of cfDNA fragment ratios to reference DNA
fragment ratios such as DNA fragment ratios from one or more
healthy mammals) in a healthy mammal.
[0041] A cfDNA fragmentation profile can include coverage of all
fragments. Coverage of all fragments can include windows (e.g.,
non-overlapping windows) of coverage. In some cases, coverage of
all fragments can include windows of small fragments (e.g.,
fragments from about 100 bp to about 150 bp in length). In some
cases, coverage of all fragments can include windows of large
fragments (e.g., fragments from about 151 bp to about 220 bp in
length).
[0042] In some cases, a cfDNA fragmentation profile can be used to
identify the tissue of origin of a cancer (e.g., a colorectal
cancer, a lung cancer, a breast cancer, a gastric cancer, a
pancreatic cancer, a bile duct cancer, or an ovarian cancer). For
example, a cfDNA fragmentation profile can be used to identify a
localized cancer. When a cfDNA fragmentation profile includes a
targeted region profile, one or more alterations described herein
(e.g., in Table 3 (Appendix C) and/or in Table 6 (Appendix F)) can
be used to identify the tissue of origin of a cancer. In some
cases, one or more alterations in chromosomal regions can be used
to identify the tissue of origin of a cancer.
[0043] A cfDNA fragmentation profile can be obtained using any
appropriate method. In some cases, cfDNA from a mammal (e.g., a
mammal having, or suspected of having, cancer) can be processed
into sequencing libraries which can be subjected to whole genome
sequencing (e.g., low-coverage whole genome sequencing), mapped to
the genome, and analyzed to determine cfDNA fragment lengths.
Mapped sequences can be analyzed in non-overlapping windows
covering the genome. Windows can be any appropriate size. For
example, windows can be from thousands to millions of bases in
length. As one non-limiting example, a window can be about 5
megabases (Mb) long. Any appropriate number of windows can be
mapped. For example, tens to thousands of windows can be mapped in
the genome. For example, hundreds to thousands of windows can be
mapped in the genome. A cfDNA fragmentation profile can be
determined within each window. In some cases, a cfDNA fragmentation
profile can be obtained as described in Example 1. In some cases, a
cfDNA fragmentation profile can be obtained as shown in FIG. 1.
[0044] In some cases, methods and materials described herein also
can include machine learning. For example, machine learning can be
used for identifying an altered fragmentation profile (e.g., using
coverage of cfDNA fragments, fragment size of cfDNA fragments,
coverage of chromosomes, and mtDNA).
[0045] In some cases, methods and materials described herein can be
the sole method used to identify a mammal (e.g., a human) as having
cancer (e.g., a colorectal cancer, a lung cancer, a breast cancer,
a gastric cancer, a pancreatic cancer, a bile duct cancer, and/or
an ovarian cancer). For example, determining a cfDNA fragmentation
profile can be the sole method used to identify a mammal as having
cancer.
[0046] In some cases, methods and materials described herein can be
used together with one or more additional methods used to identify
a mammal (e.g., a human) as having cancer (e.g., a colorectal
cancer, a lung cancer, a breast cancer, a gastric cancer, a
pancreatic cancer, a bile duct cancer, and/or an ovarian cancer).
Examples of methods used to identify a mammal as having cancer
include, without limitation, identifying one or more
cancer-specific sequence alterations, identifying one or more
chromosomal alterations (e.g., aneuploidies and rearrangements),
and identifying other cfDNA alterations. For example, determining a
cfDNA fragmentation profile can be used together with identifying
one or more cancer-specific mutations in a mammal's genome to
identify a mammal as having cancer. For example, determining a
cfDNA fragmentation profile can be used together with identifying
one or more aneuploidies in a mammal's genome to identify a mammal
as having cancer.
[0047] In some aspects, this document also provides methods and
materials for assessing, monitoring, and/or treating mammals (e.g.,
humans) having, or suspected of having, cancer. In some cases, this
document provides methods and materials for identifying a mammal as
having cancer. For example, a sample (e.g., a blood sample)
obtained from a mammal can be assessed to determine if the mammal
has cancer based, at least in part, on the cfDNA fragmentation
profile of the mammal. In some cases, this document provides
methods and materials for identifying the location (e.g., the
anatomic site or tissue of origin) of a cancer in a mammal. For
example, a sample (e.g., a blood sample) obtained from a mammal can
be assessed to determine the tissue of origin of the cancer in the
mammal based, at least in part, on the cfDNA fragmentation profile
of the mammal. In some cases, this document provides methods and
materials for identifying a mammal as having cancer, and
administering one or more cancer treatments to the mammal to treat
the mammal. For example, a sample (e.g., a blood sample) obtained
from a mammal can be assessed to determine if the mammal has cancer
based, at least in part, on the cfDNA fragmentation profile of the
mammal, and administering one or more cancer treatments to the
mammal. In some cases, this document provides methods and materials
for treating a mammal having cancer. For example, one or more
cancer treatments can be administered to a mammal identified as
having cancer (e.g., based, at least in part, on the cfDNA
fragmentation profile of the mammal) to treat the mammal. In some
cases, during or after the course of a cancer treatment (e.g., any
of the cancer treatments described herein), a mammal can undergo
monitoring (or be selected for increased monitoring) and/or further
diagnostic testing. In some cases, monitoring can include assessing
mammals having, or suspected of having, cancer by, for example,
assessing a sample (e.g., a blood sample) obtained from the mammal
to determine the cfDNA fragmentation profile of the mammal as
described herein, and changes in the cfDNA fragmentation profiles
over time can be used to identify response to treatment and/or
identify the mammal as having cancer (e.g., a residual cancer).
[0048] Any appropriate mammal can be assessed, monitored, and/or
treated as described herein. A mammal can be a mammal having
cancer. A mammal can be a mammal suspected of having cancer.
Examples of mammals that can be assessed, monitored, and/or treated
as described herein include, without limitation, humans, primates
such as monkeys, dogs, cats, horses, cows, pigs, sheep, mice, and
rats. For example, a human having, or suspected of having, cancer
can be assessed to determine a cfDNA fragmentation profiled as
described herein and, optionally, can be treated with one or more
cancer treatments as described herein.
[0049] Any appropriate sample from a mammal can be assessed as
described herein (e.g., assessed for a DNA fragmentation pattern).
In some cases, a sample can include DNA (e.g., genomic DNA). In
some cases, a sample can include cfDNA (e.g., circulating tumor DNA
(ctDNA)). In some cases, a sample can be fluid sample (e.g., a
liquid biopsy). Examples of samples that can contain DNA and/or
polypeptides include, without limitation, blood (e.g., whole blood,
serum, or plasma), amnion, tissue, urine, cerebrospinal fluid,
saliva, sputum, broncho-alveolar lavage, bile, lymphatic fluid,
cyst fluid, stool, ascites, pap smears, breast milk, and exhaled
breath condensate. For example, a plasma sample can be assessed to
determine a cfDNA fragmentation profiled as described herein.
[0050] A sample from a mammal to be assessed as described herein
(e.g., assessed for a DNA fragmentation pattern) can include any
appropriate amount of cfDNA. In some cases, a sample can include a
limited amount of DNA. For example, a cfDNA fragmentation profile
can be obtained from a sample that includes less DNA than is
typically required for other cfDNA analysis methods, such as those
described in, for example, Phallen et al., 2017 Sci Transl Med 9;
Cohen et al., 2018 Science 359:926; Newman et al., 2014 Nat Med
20:548; and Newman et al., 2016 Nat Biotechnol 34:547).
[0051] In some cases, a sample can be processed (e.g., to isolate
and/or purify DNA and/or polypeptides from the sample). For
example, DNA isolation and/or purification can include cell lysis
(e.g., using detergents and/or surfactants), protein removal (e.g.,
using a protease), and/or RNA removal (e.g., using an RNase). As
another example, polypeptide isolation and/or purification can
include cell lysis (e.g., using detergents and/or surfactants), DNA
removal (e.g., using a DNase), and/or RNA removal (e.g., using an
RNase).
[0052] A mammal having, or suspected of having, any appropriate
type of cancer can be assessed (e.g., to determine a cfDNA
fragmentation profile) and/or treated (e.g., by administering one
or more cancer treatments to the mammal) using the methods and
materials described herein. A cancer can be any stage cancer. In
some cases, a cancer can be an early stage cancer. In some cases, a
cancer can be an asymptomatic cancer. In some cases, a cancer can
be a residual disease and/or a recurrence (e.g., after surgical
resection and/or after cancer therapy). A cancer can be any type of
cancer. Examples of types of cancers that can be assessed,
monitored, and/or treated as described herein include, without
limitation, colorectal cancers, lung cancers, breast cancers,
gastric cancers, pancreatic cancers, bile duct cancers, and ovarian
cancers.
[0053] When treating a mammal having, or suspected of having,
cancer as described herein, the mammal can be administered one or
more cancer treatments. A cancer treatment can be any appropriate
cancer treatment. One or more cancer treatments described herein
can be administered to a mammal at any appropriate frequency (e.g.,
once or multiple times over a period of time ranging from days to
weeks). Examples of cancer treatments include, without limitation
adjuvant chemotherapy, neoadjuvant chemotherapy, radiation therapy,
hormone therapy, cytotoxic therapy, immunotherapy, adoptive T cell
therapy (e.g., chimeric antigen receptors and/or T cells having
wild-type or modified T cell receptors), targeted therapy such as
administration of kinase inhibitors (e.g., kinase inhibitors that
target a particular genetic lesion, such as a translocation or
mutation), (e.g. a kinase inhibitor, an antibody, a bispecific
antibody), signal transduction inhibitors, bispecific antibodies or
antibody fragments (e.g., BiTEs), monoclonal antibodies, immune
checkpoint inhibitors, surgery (e.g., surgical resection), or any
combination of the above. In some cases, a cancer treatment can
reduce the severity of the cancer, reduce a symptom of the cancer,
and/or to reduce the number of cancer cells present within the
mammal.
[0054] In some cases, a cancer treatment can include an immune
checkpoint inhibitor. Non-limiting examples of immune checkpoint
inhibitors include nivolumab (Opdivo), pembrolizumab (Keytruda),
atezolizumab (tecentriq), avelumab (bavencio), durvalumab
(imfinzi), ipilimumab (yervoy). See, e.g., Pardoll (2012) Nat. Rev
Cancer 12: 252-264; Sun et al. (2017) Eur Rev Med Pharmacol Sci
21(6): 1198-1205; Hamanishi et al. (2015) J. Clin. Oncol. 33(34):
4015-22; Brahmer et al. (2012) N Engl J Med 366(26): 2455-65;
Ricciuti et al. (2017) J. Thorac Oncol. 12(5): e51-e55; Ellis et
al. (2017) Clin Lung Cancer pii: S1525-7304(17)30043-8; Zou and
Awad (2017) Ann Oncol 28(4): 685-687; Sorscher (2017) N Engl J Med
376(10: 996-7; Hui et al. (2017) Ann Oncol 28(4): 874-881;
Vansteenkiste et al. (2017) Expert Opin Biol Ther 17(6): 781-789;
Hellmann et al. (2017) Lancet Oncol. 18(1): 31-41, Chen (2017) J.
Chin Med Assoc 80(1): 7-14.
[0055] In some cases, a cancer treatment can be an adoptive T cell
therapy (e.g., chimeric antigen receptors and/or T cells having
wild-type or modified T cell receptors). See, e.g., Rosenberg and
Restifo (2015) Science 348(6230): 62-68; Chang and Chen (2017)
Trends Mol Med 23(5): 430-450; Yee and Lizee (2016) Cancer J.
23(2): 144-148; Chen et al. (2016) Oncoimmunology 6(2): e1273302;
US 2016/0194404; US 2014/0050788; US 2014/0271635; U.S. Pat. No.
9,233,125; incorporated by reference in their entirety herein.
[0056] In some cases, a cancer treatment can be a chemotherapeutic
agent. Non-limiting examples of chemotherapeutic agents include:
amsacrine, azacitidine, axathioprine, bevacizumab (or an
antigen-binding fragment thereof), bleomycin, busulfan,
carboplatin, capecitabine, chlorambucil, cisplatin,
cyclophosphamide, cytarabine, dacarbazine, daunorubicin, docetaxel,
doxifluridine, doxorubicin, epirubicin, erlotinib hydrochlorides,
etoposide, fiudarabine, floxuridine, fludarabine, fluorouracil,
gemcitabine, hydroxyurea, idarubicin, ifosfamide, irinotecan,
lomustine, mechlorethamine, melphalan, mercaptopurine, methotrxate,
mitomycin, mitoxantrone, oxaliplatin, paclitaxel, pemetrexed,
procarbazine, all-trans retinoic acid, streptozocin, tafluposide,
temozolomide, teniposide, tioguanine, topotecan, uramustine,
valrubicin, vinblastine, vincristine, vindesine, vinorelbine, and
combinations thereof. Additional examples of anti-cancer therapies
are known in the art; see, e.g. the guidelines for therapy from the
American Society of Clinical Oncology (ASCO), European Society for
Medical Oncology (ESMO), or National Comprehensive Cancer Network
(NCCN).
[0057] When monitoring a mammal having, or suspected of having,
cancer as described herein (e.g., based, at least in part, on the
cfDNA fragmentation profile of the mammal), the monitoring can be
before, during, and/or after the course of a cancer treatment.
Methods of monitoring provided herein can be used to determine the
efficacy of one or more cancer treatments and/or to select a mammal
for increased monitoring. In some cases, the monitoring can include
identifying a cfDNA fragmentation profile as described herein. For
example, a cfDNA fragmentation profile can be obtained before
administering one or more cancer treatments to a mammal having, or
suspected or having, cancer, one or more cancer treatments can be
administered to the mammal, and one or more cfDNA fragmentation
profiles can be obtained during the course of the cancer treatment.
In some cases, a cfDNA fragmentation profile can change during the
course of cancer treatment (e.g., any of the cancer treatments
described herein). For example, a cfDNA fragmentation profile
indicative that the mammal has cancer can change to a cfDNA
fragmentation profile indicative that the mammal does not have
cancer. Such a cfDNA fragmentation profile change can indicate that
the cancer treatment is working. Conversely, a cfDNA fragmentation
profile can remain static (e.g., the same or approximately the
same) during the course of cancer treatment (e.g., any of the
cancer treatments described herein). Such a static cfDNA
fragmentation profile can indicate that the cancer treatment is not
working. In some cases, the monitoring can include conventional
techniques capable of monitoring one or more cancer treatments
(e.g., the efficacy of one or more cancer treatments). In some
cases, a mammal selected for increased monitoring can be
administered a diagnostic test (e.g., any of the diagnostic tests
disclosed herein) at an increased frequency compared to a mammal
that has not been selected for increased monitoring. For example, a
mammal selected for increased monitoring can be administered a
diagnostic test at a frequency of twice daily, daily, bi-weekly,
weekly, bi-monthly, monthly, quarterly, semi-annually, annually, or
any at frequency therein. In some cases, a mammal selected for
increased monitoring can be administered a one or more additional
diagnostic tests compared to a mammal that has not been selected
for increased monitoring. For example, a mammal selected for
increased monitoring can be administered two diagnostic tests,
whereas a mammal that has not been selected for increased
monitoring is administered only a single diagnostic test (or no
diagnostic tests). In some cases, a mammal that has been selected
for increased monitoring can also be selected for further
diagnostic testing. Once the presence of a tumor or a cancer (e.g.,
a cancer cell) has been identified (e.g., by any of the variety of
methods disclosed herein), it may be beneficial for the mammal to
undergo both increased monitoring (e.g., to assess the progression
of the tumor or cancer in the mammal and/or to assess the
development of one or more cancer biomarkers such as mutations),
and further diagnostic testing (e.g., to determine the size and/or
exact location (e.g., tissue of origin) of the tumor or the
cancer). In some cases, one or more cancer treatments can be
administered to the mammal that is selected for increased
monitoring after a cancer biomarker is detected and/or after the
cfDNA fragmentation profile of the mammal has not improved or
deteriorated. Any of the cancer treatments disclosed herein or
known in the art can be administered. For example, a mammal that
has been selected for increased monitoring can be further
monitored, and a cancer treatment can be administered if the
presence of the cancer cell is maintained throughout the increased
monitoring period. Additionally or alternatively, a mammal that has
been selected for increased monitoring can be administered a cancer
treatment, and further monitored as the cancer treatment
progresses. In some cases, after a mammal that has been selected
for increased monitoring has been administered a cancer treatment,
the increased monitoring will reveal one or more cancer biomarkers
(e.g., mutations). In some cases, such one or more cancer
biomarkers will provide cause to administer a different cancer
treatment (e.g., a resistance mutation may arise in a cancer cell
during the cancer treatment, which cancer cell harboring the
resistance mutation is resistant to the original cancer
treatment).
[0058] When a mammal is identified as having cancer as described
herein (e.g., based, at least in part, on the cfDNA fragmentation
profile of the mammal), the identifying can be before and/or during
the course of a cancer treatment. Methods of identifying a mammal
as having cancer provided herein can be used as a first diagnosis
to identify the mammal (e.g., as having cancer before any course of
treatment) and/or to select the mammal for further diagnostic
testing. In some cases, once a mammal has been determined to have
cancer, the mammal may be administered further tests and/or
selected for further diagnostic testing. In some cases, methods
provided herein can be used to select a mammal for further
diagnostic testing at a time period prior to the time period when
conventional techniques are capable of diagnosing the mammal with
an early-stage cancer. For example, methods provided herein for
selecting a mammal for further diagnostic testing can be used when
a mammal has not been diagnosed with cancer by conventional methods
and/or when a mammal is not known to harbor a cancer. In some
cases, a mammal selected for further diagnostic testing can be
administered a diagnostic test (e.g., any of the diagnostic tests
disclosed herein) at an increased frequency compared to a mammal
that has not been selected for further diagnostic testing. For
example, a mammal selected for further diagnostic testing can be
administered a diagnostic test at a frequency of twice daily,
daily, bi-weekly, weekly, bi-monthly, monthly, quarterly,
semi-annually, annually, or any at frequency therein. In some
cases, a mammal selected for further diagnostic testing can be
administered a one or more additional diagnostic tests compared to
a mammal that has not been selected for further diagnostic testing.
For example, a mammal selected for further diagnostic testing can
be administered two diagnostic tests, whereas a mammal that has not
been selected for further diagnostic testing is administered only a
single diagnostic test (or no diagnostic tests). In some cases, the
diagnostic testing method can determine the presence of the same
type of cancer (e.g., having the same tissue or origin) as the
cancer that was originally detected (e.g., based, at least in part,
on the cfDNA fragmentation profile of the mammal). Additionally or
alternatively, the diagnostic testing method can determine the
presence of a different type of cancer as the cancer that was
original detected. In some cases, the diagnostic testing method is
a scan. In some cases, the scan is a computed tomography (CT), a CT
angiography (CTA), a esophagram (a Barium swallom), a Barium enema,
a magnetic resonance imaging (MRI), a PET scan, an ultrasound
(e.g., an endobronchial ultrasound, an endoscopic ultrasound), an
X-ray, a DEXA scan. In some cases, the diagnostic testing method is
a physical examination, such as an anoscopy, a bronchoscopy (e.g.,
an autofluorescence bronchoscopy, a white-light bronchoscopy, a
navigational bronchoscopy), a colonoscopy, a digital breast
tomosynthesis, an endoscopic retrograde cholangiopancreatography
(ERCP), an ensophagogastroduodenoscopy, a mammography, a Pap smear,
a pelvic exam, a positron emission tomography and computed
tomography (PET-CT) scan. In some cases, a mammal that has been
selected for further diagnostic testing can also be selected for
increased monitoring. Once the presence of a tumor or a cancer
(e.g., a cancer cell) has been identified (e.g., by any of the
variety of methods disclosed herein), it may be beneficial for the
mammal to undergo both increased monitoring (e.g., to assess the
progression of the tumor or cancer in the mammal and/or to assess
the development of one or more cancer biomarkers such as
mutations), and further diagnostic testing (e.g., to determine the
size and/or exact location of the tumor or the cancer). In some
cases, a cancer treatment is administered to the mammal that is
selected for further diagnostic testing after a cancer biomarker is
detected and/or after the cfDNA fragmentation profile of the mammal
has not improved or deteriorated. Any of the cancer treatments
disclosed herein or known in the art can be administered. For
example, a mammal that has been selected for further diagnostic
testing can be administered a further diagnostic test, and a cancer
treatment can be administered if the presence of the tumor or the
cancer is confirmed. Additionally or alternatively, a mammal that
has been selected for further diagnostic testing can be
administered a cancer treatment, and can be further monitored as
the cancer treatment progresses. In some cases, after a mammal that
has been selected for further diagnostic testing has been
administered a cancer treatment, the additional testing will reveal
one or more cancer biomarkers (e.g., mutations). In some cases,
such one or more cancer biomarkers (e.g., mutations) will provide
cause to administer a different cancer treatment (e.g., a
resistance mutation may arise in a cancer cell during the cancer
treatment, which cancer cell harboring the resistance mutation is
resistant to the original cancer treatment).
[0059] The invention will be further described in the following
examples, which do not limit the scope of the invention described
in the claims.
EXAMPLES
Example 1: Cell-Free DIVA Fragmentation in Patients with Cancer
[0060] Analyses of cell free DNA have largely focused on targeted
sequencing of specific genes. Such studies permit detection of a
small number of tumor-specific alterations in patients with cancer
and not all patients, especially those with early stage disease,
have detectable changes. Whole genome sequencing of cell-free DNA
can identify chromosomal abnormalities and rearrangements in cancer
patients but detection of such alterations has been challenging in
part due to the difficulty in distinguishing a small number of
abnormal from normal chromosomal changes (Leary et al., 2010 Sci
Transl Med 2:20ra14; and Leary et al., 2012 Sci Transl Med
4:162ra154). Other efforts have suggested nucleosome patterns and
chromatin structure may be different between cancer and normal
tissues, and that cfDNA in patients with cancer may result in
abnormal cfDNA fragment size as well as position (Snyder et al.,
2016 Cell 164:57; Jahr et al., 2001 Cancer Res 61:1659; Ivanov et
al., 2015 BMC Genomics 16(Suppl 13):S1). However, the amount of
sequencing needed for nucleosome footprint analyses of cfDNA is
impractical for routine analyses.
[0061] The sensitivity of any cell-free DNA approach depends on the
number of potential alterations examined as well as the technical
and biological limitations of detecting such changes. As a typical
blood sample contains .about.2000 genome equivalents of cfDNA per
milliliter of plasma (Phallen et al., 2017 Sci Transl Med 9), the
theoretical limit of detection of a single alteration can be no
better than one in a few thousand mutant to wild-type molecules. An
approach that detects a larger number of alterations in the same
number of genome equivalents would be more sensitive for detecting
cancer in the circulation. Monte Carlo simulations show that
increasing the number of potential abnormalities detected from only
a few to tens or hundreds can potentially improve the limit of
detection by orders of magnitude, similar to recent probability
analyses of multiple methylation changes in cfDNA (FIG. 2).
[0062] This study presents a novel method called DELFI for
detection of cancer and further identification of tissue of origin
using whole genome sequencing (FIG. 1). The approach uses cfDNA
fragmentation profiles and machine learning to distinguish patterns
of healthy blood cell DNA from tumor-derived DNA and to identify
the primary tumor tissue. DELFI was used for a retrospective
analysis of cfDNA from 245 healthy individuals and 236 patients
with breast, colorectal, lung, ovarian, pancreatic, gastric, or
bile duct cancers, with most patients exhibiting localized disease.
Assuming this approach had sensitivity .gtoreq.0.80 for
discriminating cancer patients from healthy individuals while
maintaining a specificity of 0.95, a study of at least 200 cancer
patients would enable estimation of the true sensitivity with a
margin of error of 0.06 at the desired specificity of 0.95 or
greater.
Materials and Methods
Patient and Sample Characteristics
[0063] Plasma samples from healthy individuals and plasma and
tissue samples from patients with breast, lung, ovarian,
colorectal, bile duct, or gastric cancer were obtained from
ILSBio/Bioreclamation, Aarhus University, Herlev Hospital of the
University of Copenhagen, Hvidovre Hospital, the University Medical
Center of the University of Utrecht, the Academic Medical Center of
the University of Amsterdam, the Netherlands Cancer Institute, and
the University of California, San Diego. All samples were obtained
under Institutional Review Board approved protocols with informed
consent for research use at participating institutions. Plasma
samples from healthy individuals were obtained at the time of
routine screening, including for colonoscopies or Pap smears.
Individuals were considered healthy if they had no previous history
of cancer and negative screening results.
[0064] Plasma samples from individuals with breast, colorectal,
gastric, lung, ovarian, pancreatic, and bile duct cancer were
obtained at the time of diagnosis, prior to tumor resection or
therapy. Nineteen lung cancer patients analyzed for change in cfDNA
fragmentation profiles across multiple time points were undergoing
treatment with anti-EGFR or anti-ERBB2 therapy (see, e.g., Phallen
et al., 2019 Cancer Research 15, 1204-1213). Clinical data for all
patients included in this study are listed in Table 1 (Appendix A).
Gender was confirmed through genomic analyses of X and Y chromosome
representation. Pathologic staging of gastric cancer patients was
performed after neoadjuvant therapy. Samples where the tumor stage
was unknown were indicated as stage X or unknown.
Nucleosomal DNA Purification
[0065] Viably frozen lymphocytes were elutriated from leukocytes
obtained from a healthy male (C0618) and female (D0808-L) (Advanced
Biotechnologies Inc., Eldersburg, Md.). Aliquots of
1.times.10.sup.6 cells were used for nucleosomal DNA purification
using EZ Nucleosomal DNA Prep Kit (Zymo Research, Irvine, Calif.).
Cells were initially treated with 100 .mu.l of Nuclei Prep Buffer
and incubated on ice for 5 minutes. After centrifugation at 200 g
for 5 minutes, supernatant was discarded and pelleted nuclei were
treated twice with 1000 of Atlantis Digestion Buffer or with 100
.mu.l of micrococcal nuclease (MN) Digestion Buffer. Finally,
cellular nucleic DNA was fragmented with 0.5 U of Atlantis dsDNase
at 42.degree. C. for 20 minutes or 1.5 U of MNase at 37.degree. C.
for 20 minutes. Reactions were stopped using 5.times.MN Stop Buffer
and DNA was purified using Zymo-Spin.TM. IIC Columns. Concentration
and quality of eluted cellular nucleic DNA were analyzed using the
Bioanalyzer 2100 (Agilent Technologies, Santa Clara, Calif.).
Sample Preparation and Sequencing of cfDNA
[0066] Whole blood was collected in EDTA tubes and processed
immediately or within one day after storage at 4.degree. C., or was
collected in Streck tubes and processed within two days of
collection for three cancer patients who were part of the
monitoring analysis. Plasma and cellular components were separated
by centrifugation at 800 g for 10 min at 4.degree. C. Plasma was
centrifuged a second time at 18,000 g at room temperature to remove
any remaining cellular debris and stored at -80.degree. C. until
the time of DNA extraction. DNA was isolated from plasma using the
Qiagen Circulating Nucleic Acids Kit (Qiagen GmbH) and eluted in
LoBind tubes (Eppendorf AG). Concentration and quality of cfDNA
were assessed using the Bioanalyzer 2100 (Agilent
Technologies).
[0067] NGS cfDNA libraries were prepared for whole genome
sequencing and targeted sequencing using 5 to 250 ng of cfDNA as
described elsewhere (see, e.g., Phallen et al, 2017 Sci Transl Med
9:eaan2415). Briefly, genomic libraries were prepared using the
NEBNext DNA Library Prep Kit for Illumina [New England Biolabs
(NEB)] with four main modifications to the manufacturer's
guidelines: (i) The library purification steps used the on-bead
AMPure XP approach to minimize sample loss during elution and tube
transfer steps (see, e.g., Fisher et al., 2011 Genome Biol 12:R1);
(ii) NEBNext End Repair, A-tailing, and adapter ligation enzyme and
buffer volumes were adjusted as appropriate to accommodate the
on-bead AMPure XP purification strategy; (iii) a pool of eight
unique Illumina dual index adapters with 8-base pair (bp) barcodes
was used in the ligation reaction instead of the standard Illumina
single or dual index adapters with 6- or 8-bp barcodes,
respectively; and (iv) cfDNA libraries were amplified with Phusion
Hot Start Polymerase.
[0068] Whole genome libraries were sequenced directly. For targeted
libraries, capture was performed using Agilent SureSelect reagents
and a custom set of hybridization probes targeting 58 genes (see,
e.g., Phallen et al., 2017 Sci Transl Med 9:eaan2415) per the
manufacturer's guidelines. The captured library was amplified with
Phusion Hot Start Polymerase (NEB). Concentration and quality of
captured cfDNA libraries were assessed on the Bioanalyzer 2100
using the DNA1000 Kit (Agilent Technologies). Targeted libraries
were sequenced using 100-bp paired-end runs on the Illumina HiSeq
2000/2500 (Illumina).
Analyses of Targeted Sequencing Data from cfDNA
[0069] Analyses of targeted NGS data for cfDNA samples was
performed as described elsewhere (see, e.g., Phallen et al., 2017
Sci Transl Med 9:eaan2415). Briefly, primary processing was
completed using Illumina CASAVA (Consensus Assessment of Sequence
and Variation) software (version 1.8), including demultiplexing and
masking of dual-index adapter sequences. Sequence reads were
aligned against the human reference genome (version hg18 or hg19)
using NovoAlign with additional realignment of select regions using
the Needleman-Wunsch method (see, e.g., Jones et al., 2015 Sci
Transl Med 7:283ra53). The positions of the sequence alterations
have not been affected by the different genome builds. Candidate
mutations, consisting of point mutations, small insertions, and
deletions, were identified using VariantDx (see, e.g., Jones et
al., 2015 Sci Transl Med 7:283ra53) (Personal Genome Diagnostics,
Baltimore, Md.) across the targeted regions of interest.
[0070] To analyze the fragment lengths of cfDNA molecules, each
read pair from a cfDNA molecule was required to have a Phred
quality score .gtoreq.30. All duplicate ctDNA fragments, defined as
having the same start, end, and index barcode were removed. For
each mutation, only fragments for which one or both of the read
pairs contained the mutated (or wild-type) base at the given
position were included. This analysis was done using the R packages
Rsamtools and GenomicAlignments.
[0071] For each genomic locus where a somatic mutation was
identified, the lengths of fragments containing the mutant allele
were compared to the lengths of fragments of the wild-type allele.
If more than 100 mutant fragments were identified, Welch's
two-sample t-test was used to compare the mean fragment lengths.
For loci with fewer than 100 mutant fragments, a bootstrap
procedure was implemented. Specifically, replacement N fragments
containing the wild-type allele, where N denotes the number of
fragments with the mutation, were sampled. For each bootstrap
replicate of wild type fragments their median length was computed.
The p-value was estimated as the fraction of bootstrap replicates
with a median wild-type fragment length as or more extreme than the
observed median mutant fragment length.
Analyses of Whole Genome Sequencing Data from cfDNA
[0072] Primary processing of whole genome NGS data for cfDNA
samples was performed using Illumina CASAVA (Consensus Assessment
of Sequence and Variation) software (version 1.8.2), including
demultiplexing and masking of dual-index adapter sequences.
Sequence reads were aligned against the human reference genome
(version hg19) using ELAND.
[0073] Read pairs with a MAPQ score below 30 for either read and
PCR duplicates were removed. hg19 autosomes were tiled into 26,236
adjacent, non-overlapping 100 kb bins. Regions of low mappability,
indicated by the 10% of bins with the lowest coverage, were removed
(see, e.g., Fortin et al., 2015 Genome Biol 16:180), as were reads
falling in the Duke blacklisted regions (see, e.g.,
hgdownload.cse.ucsc.edu/goldenpath/hg19/encodeDCC/wgEncodeMapability/).
Using this approach, 361 Mb (13%) of the hg19 reference genome was
excluded, including centromeric and telomeric regions. Short
fragments were defined as having a length between 100 and 150 bp
and long fragments were defined has having a length between 151 and
220 bp.
[0074] To account for biases in coverage attributable to GC content
of the genome, the locally weighted smoother loess with span 3/4
was applied to the scatterplot of average fragment GC versus
coverage calculated for each 100 kb bin. This loess regression was
performed separately for short and long fragments to account for
possible differences in GC effects on coverage in plasma by
fragment length (see, e.g., Benjamini et al., 2012 Nucleic Acids
Res 40:e72). The predictions for short and long coverage explained
by GC from the loess model were subtracted, obtaining residuals for
short and long that were uncorrelated with GC. The residuals were
returned to the original scale by adding back the genome-wide
median short and long estimates of coverage. This procedure was
repeated for each sample to account for possible differences in GC
effects on coverage between samples. To further reduce the feature
space and noise, the total GC-adjusted coverage in 5 Mb bins was
calculated.
[0075] To compare the variability of fragment lengths from healthy
subjects to fragments in patients with cancer, the standard
deviation of the short to long fragmentation profiles for each
individual was calculated. The standard deviations in the two
groups were compared by a Wilcoxon rank sum test.
Analyses of Chromosome Arm Copy Number Changes
[0076] To develop arm-level statistics for copy number changes, an
approach for aneuploidy detection in plasma as described elsewhere
(see, e.g., Leary et al., 2012 Sci Transl Med 4:162ra154) was
adopted. This approach divides the genome into non-overlapping 50
KB bins for which GC-corrected log 2 read depth was obtained after
correction by loess with span 3/4. This loess-based correction is
comparable to the approach outlined above, but is evaluated on a
log 2 scale to increase robustness to outliers in the smaller bins
and does not stratify by fragment length. To obtain an arm-specific
Z-score for copy number changes, the mean GC-adjusted read depth
for each arm (GR) was centered and scaled by the average and
standard deviation, respectively, of GR scores obtained from an
independent set of 50 healthy samples.
Analyses of Mitochondrial-Aligned Reads from cfDNA
[0077] Whole genome sequence reads that initially mapped to the
mitochondrial genome were extracted from bam files and realigned to
the hg19 reference genome in end-to-end mode with Bowtie2 as
described elsewhere (see, e.g., Langmead et al., 2012 Nat Methods
9:357-359). The resulting aligned reads were filtered such that
both mates aligned to the mitochondrial genome with MAPQ >=30.
The number of fragments mapping to the mitochondrial genome was
counted and converted to a percentage of the total number of
fragments in the original bam files.
Prediction Model for Cancer Classification
[0078] To distinguish healthy from cancer patients using
fragmentation profiles, a stochastic gradient boosting model was
used (gbm; see, e.g., Friedman et al., 2001 Ann Stat 29:1189-1232;
and Friedman et al., 2002 Comput Stat Data An 38:367-378).
GC-corrected total and short fragment coverage for all 504 bins
were centered and scaled for each sample to have mean 0 and unit
standard deviation. Additional features included Z-scores for each
of the 39 autosomal arms and mitochondrial representation (log
10-transformed proportion of reads mapped to the mitochondria). To
estimate the prediction error of this approach, 10-fold
cross-validation was used as described elsewhere (see, e.g., Efron
et al., 1997 J Am Stat Assoc 92, 548-560). Feature selection,
performed only on the training data in each cross-validation run,
removed bins that were highly correlated (correlation >0.9) or
had near zero variance. Stochastic gradient boosted machine
learning was implemented using the R package gbm package with
parameters n.trees=150, interaction.depth=3, shrinkage=0.1, and
n.minobsinside=10. To average over the prediction error from the
randomization of patients to folds, the 10-fold cross validation
procedure was repeated 10 times. Confidence intervals for
sensitivity fixed at 98% and 95% specificity were obtained from
2000 bootstrap replicates.
Prediction Model for Tumor Tissue of Origin Classification
[0079] For samples correctly classified as cancer patients at 90%
specificity (n=174), a separate stochastic gradient boosting model
was trained to classify the tissue of origin. To account for the
small number of lung samples used for prediction, 18 cfDNA baseline
samples from late stage lung cancer patients were included from the
monitoring analyses. Performance characteristics of the model were
evaluated by 10-fold cross-validation repeated 10 times. This gbm
model was trained using the same features as in the cancer
classification model. As previously described, features that
displayed correlation above 0.9 to each other or had near zero
variance were removed within each training dataset during
cross-validation. The tissue class probabilities were averaged
across the 10 replicates for each patient and the class with the
highest probability was taken as the predicted tissue.
Analyses of Nucleosomal DNA from Human Lymphocytes and cfDNA
[0080] From the nuclease treated lymphocytes, fragment sizes were
analyzed in 5 Mb bins as described for whole genome cfDNA analyses.
A genome-wide map of nucleosome positions was constructed from the
nuclease treated lymphocyte cell-lines. This approach identified
local biases in the coverage of circulating fragments, indicating a
region protected from degradation. A "Window positioning score"
(WPS) was used to score each base pair in the genome (see, e.g.,
Snyder et al., 2016 Cell 164:57). Using a sliding window of 60 bp
centered around each base, the WPS was calculated as the number of
fragments completely spanning the window minus the number of
fragments with only one end in the window. Since fragments arising
from nucleosomes have a median length of 167 bp, a high WPS
indicated a possible nucleosomic position. WPS scores were centered
at zero using a running median and smoothed using a
Kolmogorov-Zurbenko filter (see, e.g., Zurbenko, The spectral
analysis of time series. North-Holland series in statistics and
probability; Elsevier, New York, N Y, 1986). For spans of positive
WPS between 50 and 450 bp, a nucleosome peak was defined as the set
of base pairs with a WPS above the median in that window. The
calculation of nucleosome positions for cfDNA from 30 healthy
individuals with sequence coverage of 9.times. was determined in
the same manner as for lymphocyte DNA. To ensure that nucleosomes
in healthy cfDNA were representative, a consensus track of
nucleosomes was defined consisting only of nucleosomes identified
in two or more individuals. Median distances between adjacent
nucleosomes were calculated from the consensus track.
Monte Carlo Simulation of Detection Sensitivity
[0081] A Monte Carlo simulation was used to estimate the
probability of detecting a molecule with a tumor-derived
alteration. Briefly, 1 million molecules were generated from a
multinomial distribution. For a simulation with m alterations,
wild-type molecules were simulated with probability p and each of
the m tumor alterations were simulated with probability (1-p)/m.
Next, g*m molecules were sampled randomly with replacement, where g
denotes the number of genome equivalents in 1 ml of plasma. If a
tumor alteration was sampled s or more times, the sample was
classified as cancer-derived. The simulation was repeated 1000
times, estimating the probability that the in silico sample would
be correctly classified as cancer by the mean of the cancer
indicator. Setting g=2000 and s=5, the number of tumor alterations
was varied by powers of 2 from 1 to 256 and the fraction of
tumor-derived molecules from 0.0001% to 1%.
Statistical Analyses
[0082] All statistical analyses were performed using R version
3.4.3. The R packages caret (version 6.0-79) and gbm (version
2.1-4) were used to implement the classification of healthy versus
cancer and tissue of origin. Confidence intervals from the model
output were obtained with the pROC (version 1.13) R package (see,
e.g., Robin et al., 2011 BMC bioinformatics 12:77). Assuming the
prevalence of undiagnosed cancer cases in this population is high
(1 or 2 cases per 100 healthy), a genomic assay with a specificity
of 0.95 and sensitivity of 0.8 would have useful operating
characteristics (positive predictive value of 0.25 and negative
predictive value near 1). Power calculations suggest that an
analysis of more than 200 cancer patients and an approximately
equal number of healthy controls, enable an estimation of the
sensitivity with a margin of error of 0.06 at the desired
specificity of 0.95 or greater.
Data and Code Availability
[0083] Sequence data utilized in this study have been deposited at
the European Genome-phenome Archive under study accession nos.
EGAS00001003611 and EGAS00001002577. Code for analyses is available
at github.com/Cancer-Genomics/delfi_scripts.
Results
[0084] DELFI allows simultaneous analysis of a large number of
abnormalities in cfDNA through genome-wide analysis of
fragmentation patterns. The method is based on low coverage whole
genome sequencing and analysis of isolated cfDNA. Mapped sequences
are analyzed in non-overlapping windows covering the genome.
Conceptually, windows may range in size from thousands to millions
of bases, resulting in hundreds to thousands of windows in the
genome. 5 Mb windows were used for evaluating cfDNA fragmentation
patterns as these would provide over 20,000 reads per window even
at a limited amount of 1-2.times. genome coverage. Within each
window, the coverage and size distribution of cfDNA fragments was
examined. This approach was used to evaluate the variation of
genome-wide fragmentation profiles in healthy and cancer
populations (Table 1; Appendix A). The genome-wide pattern from an
individual can be compared to reference populations to determine if
the pattern is likely healthy or cancer-derived. As genome-wide
profiles reveal positional differences associated with specific
tissues that may be missed in overall fragment size distributions,
these patterns may also indicate the tissue source of cfDNA.
[0085] The fragmentation size of cfDNA was focused on as it was
found that cancer-derived cfDNA molecules may be more variable in
size than cfDNA derived from non-cancer cells. cfDNA fragments from
targeted regions that were captured and sequenced at high coverage
(43,706 total coverage, 8,044 distinct coverage) from patients with
breast, colorectal, lung or ovarian cancer (Table 1 (Appendix A),
Table 2 (Appendix B), and Table 3 (Appendix C)) were initially
examined. Analyses of loci containing 165 tumor-specific
alterations from 81 patients (range of 1-7 alterations per patient)
revealed an average absolute difference of 6.5 bp (95% CI, 5.4-7.6
bp) between lengths of median mutant and wild-type cfDNA fragments
(FIG. 3, Table 3 (Appendix C)). The median size of mutant cfDNA
fragments ranged from 30 bases smaller at chromosome 3 position
41,266,124 to 47 bases larger at chromosome 11 position 108,117,753
than the wild-type sequences at these regions (Table 3; Appendix
C). GC content was similar for mutated and non-mutated fragments
(FIG. 4a), and there was no correlation between GC content and
fragment length (FIG. 4b). Similar analyses of 44 germline
alterations from 38 patients identified median cfDNA size
differences of less than 1 bp between fragment lengths of different
alleles (FIG. 5, Table 3 (Appendix C)). Additionally, 41
alterations related to clonal hematopoiesis were identified through
a previous sequence comparison of DNA from plasma, buffy coat, and
tumors of the same individuals. Unlike tumor-derived fragments,
there were no significant differences between fragments with
hematopoietic alterations and wild type fragments (FIG. 6, Table 3
(Appendix C)). Overall, cancer-derived cfDNA fragment lengths were
significantly more variable compared to non-cancer cfDNA fragments
at certain genomic regions (p<0.001, variance ratio test). It
was hypothesized that these differences may be due to changes in
higher-order chromatin structure as well as other genomic and
epigenomic abnormalities in cancer and that cfDNA fragmentation in
a position-specific manner could therefore serve as a unique
biomarker for cancer detection.
[0086] As targeted sequencing only analyzes a limited number of
loci, larger-scale genome-wide analyses to detect additional
abnormalities in cfDNA fragmentation were investigated. cfDNA was
isolated from .about.4 ml of plasma from 8 lung cancer patients
with stage I-III disease, as well as from 30 healthy individuals
(Table 1 (Appendix A), Table 4 (Appendix D), and Table 5 (Appendix
E)). A high efficiency approach was used to convert cfDNA to next
generation sequencing libraries and performed whole genome
sequencing at .about.9.times. coverage (Table 4; Appendix D).
Overall cfDNA fragment lengths of healthy individuals were larger,
with a median fragment size of 167.3 bp, while patients with cancer
had median fragment sizes of 163.8 (p<0.01, Welch's t-test)
(Table 5; Appendix E). To examine differences in fragment size and
coverage in a position dependent manner across the genome,
sequenced fragments were mapped to their genomic origin and
fragment lengths were evaluated in 504 windows that were 5 Mb in
size, covering .about.2.6 Gb of the genome. For each window, the
fraction of small cfDNA fragments (100 to 150 bp in length) to
larger cfDNA fragments (151 to 220 bp) as well as overall coverage
were determined and used to obtain genome-wide fragmentation
profiles for each sample.
[0087] Healthy individuals had very similar fragmentation profiles
throughout the genome (FIG. 7 and FIG. 8). To examine the origins
of fragmentation patterns normally observed in cfDNA, nuclei were
isolated from elutriated lymphocytes of two healthy individuals and
treated with DNA nucleases to obtain nucleosomal DNA fragments.
Analyses of cfDNA patterns in observed healthy individuals revealed
a high correlation to lymphocyte nucleosomal DNA fragmentation
profiles (FIGS. 7b and 7d) and nucleosome distances (FIGS. 7c and
7f). Median distances between nucleosomes in lymphocytes were
correlated to open (A) and closed (B) compartments of
lymphoblastoid cells as revealed using the Hi-C method (see, e.g.,
Lieberman-Aiden et al., 2009 Science 326:289-293; and Fortin et
al., 2015 Genome Biol 16:180) for examining the three-dimensional
architecture of genomes (FIG. 7c). These analyses suggest that the
fragmentation patterns of normal cfDNA are the result of
nucleosomal DNA patterns that largely reflect the chromatin
structure of normal blood cells.
[0088] In contrast to healthy cfDNA, patients with cancer had
multiple distinct genomic differences with increases and decreases
in fragment sizes at different regions (FIGS. 7a and 7b). Similar
to our observations from targeted analyses, there was also greater
variation in fragment lengths genome-wide for patients with cancer
compared to healthy individuals.
[0089] To determine whether cfDNA fragment length patterns could be
used to distinguish patients with cancer from healthy individuals,
genome-wide correlation analyses were performed of the fraction of
short to long cfDNA fragments for each sample compared to the
median fragment length profile calculated from healthy individuals
(FIGS. 7a, 7b, and 7e). While the profiles of cfDNA fragments were
remarkably consistent among healthy individuals (median correlation
of 0.99), the median correlation of genome-wide fragment ratios
among cancer patients was 0.84 (0.15 lower, 95% CI 0.07-0.50,
p<0.001, Wilcoxon rank sum test; Table 5 (Appendix E)). Similar
differences were observed when comparing fragmentation profiles of
cancer patients to fragmentation profiles or nucleosome distances
in healthy lymphocytes (FIGS. 7c, 7d, and 7f). To account for
potential biases in the fragmentation profiles attributable to GC
content, a locally weighted smoother was applied independently to
each sample and found that differences in fragmentation profiles
between healthy individuals and cancer patients remained after this
adjustment (median correlation of cancer patients to healthy=0.83)
(Table 5; Appendix E).
[0090] Subsampling analyses of whole genome sequence data was
performed at 9.times. coverage from cfDNA of patients with cancer
at .about.2.times., .about.1.times., .about.0.5.times.,
.about.0.2.times., and .about.0.1.times. genome coverage, and it
was determined that altered fragmentation profiles were readily
identified even at 0.5.times. genome coverage (FIG. 9). Based on
these observations, whole genome sequencing was performed with
coverage of 1-2.times. to evaluate whether fragmentation profiles
may change during the course of targeted therapy in a manner
similar to monitoring of sequence alterations. cfDNA from 19
non-small cell lung cancer patients including 5 with partial
radiographic response, 8 with stable disease, 4 with progressive
disease, and 2 with unmeasurable disease, during the course of
anti-EGFR or anti-ERBB2 therapy was evaluated (Table 6; Appendix
F). As shown in FIG. 10, the degree of abnormality in the
fragmentation profiles during therapy closely matched levels of
EGFR or ERBB2 mutant allele fractions as determined using targeted
sequencing (Spearman correlation of mutant allele fractions to
fragmentation profiles=0.74). This correlation is remarkable as
genome-wide and mutation-based methods are orthogonal and examine
different cfDNA alterations that may be suppressed in these
patients due to prior therapy. Notably all cases that had
progression free survival of six or more months displayed a drop of
or had extremely low levels of ctDNA after initiation of therapy as
determined by fragmentation profiles, while cases with poor
clinical outcome had increases in ctDNA. These results demonstrate
the feasibility of fragmentation analyses for detecting the
presence of tumor-derived cfDNA, and suggests that such analyses
may also be useful for quantitative monitoring of cancer patients
during treatment.
[0091] The fragmentation profiles were examined in the context of
known copy number changes in a patient where parallel analyses of
tumor tissue were obtained. These analyses demonstrated that
altered fragmentation profiles were present in regions of the
genome that were copy neutral and that these may be further
affected in regions with copy number changes (FIG. 11a and FIG.
12a). Position dependent differences in fragmentation patterns
could be used to distinguish cancer-derived cfDNA from healthy
cfDNA in these regions (FIG. 12a, b), while overall cfDNA fragment
size measurements would have missed such differences (FIG.
12a).
[0092] These analyses were extended to an independent cohort of
cancer patients and healthy individuals. Whole genome sequencing of
cfDNA at 1-2.times. coverage from a total of 208 patients with
cancer, including breast (n=54), colorectal (n=27), lung (n=12),
ovarian (n=28), pancreatic (n=34), gastric (n=27), or bile duct
cancers (n=26), as well as 215 individuals without cancer was
performed (Table 1 (Appendix A) and Table 4 (Appendix D)). All
cancer patients were treatment naive and the majority had
resectable disease (n=183). After GC adjustment of short and long
cfDNA fragment coverage (FIG. 13a), coverage and size
characteristics of fragments in windows throughout the genome were
examined (FIG. 11b, Table 4 (Appendix D) and Table 7 (Appendix G)).
Genome-wide correlations of coverage to GC content were limited and
no differences in these correlations between cancer patients and
healthy individuals were observed (FIG. 13b). Healthy individuals
had highly concordant fragmentation profiles, while patients with
cancer had high variability with decreased correlation to the
median healthy profile (Table 7; Appendix G). An analysis of the
most commonly altered fragmentation windows in the genome among
cancer patients revealed a median of 60 affected windows across the
cancer types analyzed, highlighting the multitude of position
dependent alterations in fragmentation of cfDNA in individuals with
cancer (FIG. 11c).
[0093] To determine if position dependent fragmentation changes can
be used to detect individuals with cancer, a gradient tree boosting
machine learning model was implemented to examine whether cfDNA can
be categorized as having characteristics of a cancer patient or
healthy individual and estimated performance characteristics of
this approach by ten-fold cross validation repeated ten times
(FIGS. 14 and 15). The machine learning model included GC-adjusted
short and long fragment coverage characteristics in windows
throughout the genome. A machine learning classifier for copy
number changes from chromosomal arm dependent features rather than
a single score was also developed (FIG. 16a and Table 8 (Appendix
H)) and mitochondrial copy number changes were also included (FIG.
16b) as these could also help distinguish cancer from healthy
individuals. Using this implementation of DELFI, a score was
obtained that could be used to classify patients as healthy or
having cancer. 152 of the 208 cancer patients were detected (73%
sensitivity, 95% CI 67%-79%) while four of the 215 healthy
individuals were misclassified (98% specificity) (Table 9). At a
threshold of 95% specificity, 80% of patients with cancer were
detected (95% CI, 74%-85%), including 79% of resectable (stage
I-III) patients (145 of 183) and 82% of metastatic (stage IV)
patients (18 out of 22) (Table 9). Receiver operator characteristic
analyses for detection of patients with cancer had an AUC of 0.94
(95% CI 0.92-0.96), ranged among cancer types from 0.86 for
pancreatic cancer to .gtoreq.0.99 for lung and ovarian cancers
(FIGS. 17a and 17b), and had AUCs .gtoreq.0.92 across all stages
(FIG. 18). The DELFI classifier score did not differ with age among
either cancer patients or healthy individuals (Table 1; Appendix
A).
TABLE-US-00001 TABLE 9 DELFI performance for cancer detection. 95%
specificity 98% specificity Individuals Individuals Individuals
analyzed detected Sensitivity 95% Cl detected Sensitivity 95% Cl
Healthy 215 10 -- -- 4 -- -- Cancer 208 166 80% 74%-85% 152 73%
67%-79% Type Breast 54 38 70% 56%-82% 31 57% 43%-71% Bile duct 26
23 88% 70%-98% 21 81% 61%-93% Colorectal 27 22 81% 62%-94% 19 70%
50%-86% Gastric 27 22 81% 62%-94% 22 81% 62%-94% Lung 12 12 100%
74%-100% 12 100% 74%-100% Ovarian 28 25 89% 72%-98% 25 89% 72%-98%
Pancreatic 34 24 71% 53%-85% 22 65% 46%-80% Stage I 41 30 73%
53%-86% 28 68% 52%-82% II 109 85 78% 69%-85% 78 72% 62%-80% III 33
30 91% 76%-98% 26 79% 61%-91% IV 22 18 82% 60%-95% 17 77% 55%-92%
0, X 3 3 100% 29%-100% 3 100% 29%-100%
[0094] To assess the contribution of fragment size and coverage,
chromosome arm copy number, or mitochondrial mapping to the
predictive accuracy of the model, the repeated 10-fold
cross-validation procedure was implemented to assess performance
characteristics of these features in isolation. It was observed
that fragment coverage features alone (AUC=0.94) were nearly
identical to the classifier that combined all features (AUC=0.94)
(FIG. 17a). In contrast, analyses of chromosomal copy number
changes had lower performance (AUC=0.88) but were still more
predictive than copy number changes based on individual scores
(AUC=0.78) or mitochondrial mapping (AUC=0.72) (FIG. 17a). These
results suggest that fragment coverage is the major contributor to
our classifier. Including all features in the prediction model may
contribute in a complementary fashion for detection of patients
with cancer as they can be obtained from the same genome sequence
data.
[0095] As fragmentation profiles reveal regional differences in
fragmentation that may differ between tissues, a similar machine
learning approach was used to examine whether cfDNA patterns could
identify the tissue of origin of these tumors. It was found that
this approach had a 61% accuracy (95% CI 53%-67%), including 76%
for breast, 44% for bile duct, 71% for colorectal, 67% for gastric,
53% for lung, 48% for ovarian, and 50% for pancreatic cancers (FIG.
19, Table 10). The accuracy increased to 75% (95% CI 69%-81%) when
considering assigning patients with abnormal cfDNA to one of two
sites of origin (Table 10). For all tumor types, the classification
of the tissue of origin by DELFI was significantly higher than
determined by random assignment (p<0.01, binomial test, Table
10).
TABLE-US-00002 TABLE 10 DELFI tissue of origin prediction Cancer
Patients Top Prediction Top Two Predictions Random Assignment Type
Detected* Patients Accuracy (95% Cl) Patients Accuracy (95% Cl)
Patients Accuracy Breast 42 32 76% (61%-88%) 38 91% (77%-97%) 9 22%
Bile Duct 23 10 44% (23%-66%) 15 65% (43%-84%) 3 12% Colorectal 24
17 71% (49%-87%) 19 79% (58%-93%) 3 12% Gastric 24 16 67% (45%-84%)
19 79% (58%-93%) 3 12% Lung 30 16 53% (34%-72%) 23 77% (58%-90%) 2
6% Ovarian 27 13 48% (29%-68%) 16 59% (38%-78%) 4 14% Pancreatic 24
12 50% (29%-71%) 16 67% (45%-84%) 3 12% Total 194 116 61% (53%-67%)
146 75% (69%-81%) 26 13% *Patients detected are based on DELFI
detection at 90% specificity. Lung cohort includes additional lung
cancer patients with prior therapy.
[0096] As cancer-specific sequence alterations can be used to
identify patients with cancer, it was evaluated whether combining
DELFI with this approach could increase the sensitivity of cancer
detection (FIG. 20). An analysis of cfDNA from a subset of the
treatment naive cancer patients using both DELFI and targeted
sequencing revealed that 82% (103 of 126) of patients had
fragmentation profile alterations, while 66% (83 of 126) had
sequence alterations. Over 89% of cases with mutant allele
fractions >1% were detected by DELFI while for cases with mutant
allele fractions <1% the fraction detected by DELFI was 80%,
including for cases that were undetectable using targeted
sequencing (Table 7; Appendix G). When these approaches were used
together, the combined sensitivity of detection increased to 91%
(115 of 126 patients) with a specificity of 98% (FIG. 20).
[0097] Overall, genome-wide cfDNA fragmentation profiles are
different between cancer patients and healthy individuals. The
variability in fragment lengths and coverage in a position
dependent manner throughout the genome may explain the apparently
contradictory observations of previous analyses of cfDNA at
specific loci or of overall fragment sizes. In patients with
cancer, heterogeneous fragmentation patterns in cfDNA appear to be
a result of mixtures of nucleosomal DNA from both blood and
neoplastic cells. These studies provide a method for simultaneous
analysis of tens to potentially hundreds of tumor-specific
abnormalities from minute amounts of cfDNA, overcoming a limitation
that has precluded the possibility of more sensitive analyses of
cfDNA. DELFI analyses detected a higher fraction of cancer patients
than previous cfDNA analysis methods that have focused on sequence
or overall fragmentation sizes (see, e.g., Phallen et al., 2017 Sci
Transl Med 9:eaan2415; Cohen et al., 2018 Science 359:926; Newman
et al., 2014 Nat Med 20:548; Bettegowda et al., 2014 Sci Transl Med
6:224ra24; Newman et al., 2016 Nat Biotechnol 34:547). As
demonstrated in this Example, combining DELFI with analyses of
other cfDNA alterations may further increase the sensitivity of
detection. As fragmentation profiles appear related to nucleosomal
DNA patterns, DELFI may be used for determining the primary source
of tumor-derived cfDNA. The identification of the source of
circulating tumor DNA in over half of patients analyzed may be
further improved by including clinical characteristics, other
biomarkers, including methylation changes, and additional
diagnostic approaches (Ruibal Morell, 1992 The International
journal of biological markers 7:160; Galli et al., 2013 Clinical
chemistry and laboratory medicine 51:1369; Sikaris, 2011 Heart,
lung &circulation 20:634; Cohen et al., 2018 Science 359:926).
Finally, this approach requires only a small amount of whole genome
sequencing, without the need for deep sequencing typical of
approaches that focus on specific alterations. The performance
characteristics and limited amount of sequencing needed for DELFI
suggests that our approach could be broadly applied for screening
and management of patients with cancer.
[0098] These results demonstrate that genome-wide cfDNA
fragmentation profiles are different between cancer patients and
healthy individuals. As such, cfDNA fragmentation profiles can have
important implications for future research and applications of
non-invasive approaches for detection of human cancer.
OTHER EMBODIMENTS
[0099] It is to be understood that while the invention has been
described in conjunction with the detailed description thereof, the
foregoing description is intended to illustrate and not limit the
scope of the invention, which is defined by the scope of the
appended claims. Other aspects, advantages, and modifications are
within the scope of the following claims.
TABLE-US-00003 APPENDIX A Table 1. Summary or patients and samples
analyzed Whole Age Degree Location of Volume cfDNA Genome Targeted
at Site of Histopa- of Metastases of Ex- cfDNA Fragment Fragment
Targeted Patient Sample Diag- TNM Primary thological Differ- at
Plasma tracted Input Profile Profile Mutation Patient Type Type
Timepoint nosis Gender Stage Staging Tumor Diagnosis entiation
Diagnosis (ml) (ng/ml) (ng/ml) Analysis Analysis Analysis CGCRC291
Colorectal cfDNA Preoperative 69 F IV T3N2M1 Coecum Adencarcinoma
Moderate Synchronous 7.9 7.80 7.80 Y Y Y Cancer treatment naive
Liver CGCRC292 Colorectal cfDNA Preoperative 51 M IV T3N2M1 Sigmod
Adencarcinoma Moderate Synchronous 7.9 6.73 6.73 Y Y Y Cancer
treatment naive Colon Liver, Lung CGCRC293 Colorectal cfDNA
Preoperative 55 M IV T3N2M1 Rectum Adencarcinoma Moderate
Synchronous 7.2 3.83 3.83 Y Y Y Cancer treatment naive Liver
CGCRC294 Colorectal cfDNA Preoperative 67 F II T3N0M0 Sigmod
Adencarcinoma Moderate None 8.4 18.87 18.87 Y Y Y Cancer treatment
naive Colon CGCRC296 Colorectal cfDNA Preoperative 76 F II T4N0M0
Coecum Adencarcinoma Poor None 4.3 31.24 31.24 Y Y Y Cancer
treatment naive CGCRC299 Colorectal cfDNA Preoperative 71 M I
T1N0M0 Rectum Adencarcinoma Moderate None 8.8 10.18 10.18 Y Y Y
Cancer treatment naive CGCRC300 Colorectal cfDNA Preoperative 65 M
I T2N0M0 Rectum Adencarcinoma Moderate None 4.3 10.48 10.48 Y Y Y
Cancer treatment naive CGCRC301 Colorectal cfDNA Preoperative 76 F
I T2N0M0 Rectum Adencarcinoma Moderate None 4.1 6.51 6.51 Y Y Y
Cancer treatment naive CGCRC302 Colorectal cfDNA Preoperative 73 M
II T3N0M0 Traverse Adencarcinoma Moderate None 4.3 52.13 52.13 Y Y
Y Cancer treatment naive Colon CGCRC304 Colorectal cfDNA
Preoperative 86 F II T3N0M0 Rectum Adencarcinoma Moderate None 4.1
30.19 30.19 Y Y Y Cancer treatment naive CGCRC305 Colorectal cfDNA
Preoperative 83 F II T3N0M0 Traverse Adencarcinoma Moderate None
8.6 9.10 9.10 Y Y Y Cancer treatment naive Colon CGCRC306
Colorectal cfDNA Preoperative 80 F II T4N0M0 Ascending
Adencarcinoma Moderate None 4.5 24.31 24.31 Y Y Y Cancer treatment
naive Colon CGCRC307 Colorectal cfDNA Preoperative 78 F II T3N0M0
Ascending Adencarcinoma Moderate None 8.5 14.26 14.26 Y Y Y Cancer
treatment naive Colon CGCRC308 Colorectal cfDNA Preoperative 72 F
III T4N2M0 Ascending Adencarcinoma Moderate None 4.3 46.37 46.37 Y
Y Y Cancer treatment naive Colon CGCRC311 Colorectal cfDNA
Preoperative 59 M I T2N0M0 Sigmod Adencarcinoma Moderate None 8.5
3.91 3.91 Y Y Y Cancer treatment naive Colon CGCRC315 Colorectal
cfDNA Preoperative 74 M III T3N1M0 Sigmod Adencarcinoma Moderate
None 8.6 9.67 9.67 Y Y Y Cancer treatment naive Colon CGCRC316
Colorectal cfDNA Preoperative 80 M III T3N2M0 Traverse
Adencarcinoma Moderate None 4.9 52.16 52.16 Y Y Y Cancer treatment
naive Colon CGCRC317 Colorectal cfDNA Preoperative 74 M III T3N2M0
Descending Adencarcinoma Moderate None 8.8 16.08 16.08 Y Y Y Cancer
treatment naive Colon CGCRC318 Colorectal cfDNA Preoperative 81 M I
T2N0M0 Coecum Adencarcinoma Moderate None 9.8 18.24 18.24 Y Y Y
Cancer treatment naive CGCRC319 Colorectal cfDNA Preoperative 80 F
III T2N1M0 Descending Adencarcinoma Moderate None 4.2 53.84 53.84 Y
N Y Cancer treatment naive Colon CGCRC320 Colorectal cfDNA
Preoperative 73 F I T2N0M0 Ascending Adencarcinoma Moderate None
4.5 30.37 30.37 Y Y Y Cancer treatment naive Colon CGCRC321
Colorectal cfDNA Preoperative 68 M I T2N0M0 Rectum Adencarcinoma
Moderate None 9.3 4.25 4.25 Y Y Y Cancer treatment naive CGCRC333
Colorectal cfDNA Preoperative NA F IV NA Colon/ Adencarcinoma NA
Liver 4.0 113.88 113.88 Y Y Y Cancer treatment naive Rectum
CGCRC336 Colorectal cfDNA Preoperative NA M IV NA Colon/
Adencarcinoma NA Liver 4.4 211.74 211.74 Y Y Y Cancer treatment
naive Rectum CGCRC338 Colorectal cfDNA Preoperative NA F IV NA
Colon/ Adencarcinoma NA Liver 2.3 109.76 109.76 Y Y Y Cancer
treatment naive Rectum CGCRC341 Colorectal cfDNA Preoperative NA F
IV NA Colon/ Adencarcinoma NA Liver 4.6 156.62 156.62 Y N Y Cancer
treatment naive Rectum CGCRC342 Colorectal cfDNA Preoperative NA M
IV NA Colon/ Adencarcinoma NA Liver 3.9 56.09 56.09 Y N Y Cancer
treatment naive Rectum CGLU316 Lung cfDNA Pre-treatment, 50 F IV
T3N2M0 Left Upper Adeno, Poor Lung 5.0 2.38 2.38 Y N Y Cancer Day
53 Lobe of Lung Squamous, Small Cell Carcinoma CGLU316 Lung cfDNA
Pre-treatment, 50 F IV T3N2M0 Left Upper Adeno, Poor Lung 5.0 2.11
2.11 Y N Y Cancer Day -4 Lobe of Lung Squamous, Small Cell
Carcinoma CGLU316 Lung cfDNA Post-treatment, 50 F IV T3N2M0 Left
Upper Adeno, Poor Lung 5.0 0.87 1.07 Y N Y Cancer Day 18 Lobe of
Lung Squamous, Small Cell Carcinoma CGLU316 Lung cfDNA
Post-treatment, 50 F IV T3N2M0 Left Upper Adeno, Poor Lung 2.0 8.74
8.75 Y N Y Cancer Day 87 Lobe of Lung Squamous, Small Cell
Carcinoma CGLU344 Lung cfDNA Pre-treatment, 65 F IV T2N2M1 Right
Upper Adencarcinoma NA Pleura, 5.0 34.77 25.00 Y N Y Cancer Day -21
Lobe of Lung Liver, Pentoneum CGLU344 Lung cfDNA Pre-treatment, 65
F IV T2N2M1 Right Upper Adencarcinoma NA Pleura, 5.0 15.63 15.64 Y
N Y Cancer Day 0 Lobe of Lung Liver, Pentoneum CGLU344 Lung cfDNA
Post-treatment, 65 F IV T2N2M1 Right Upper Adencarcinoma NA Pleura,
5.0 9.22 9.22 Y N Y Cancer Day 0.1875 Lobe of Lung Liver, Pentoneum
CGLU344 Lung cfDNA Post-treatment, 65 F IV T2N2M1 Right Upper
Adencarcinoma NA Pleura, 5.0 5.31 5.32 Y N Y Cancer Day 59 Lobe of
Lung Liver, Pentoneum CGLU369 Lung cfDNA Pre-treatment, 48 F IV
T2NxM1 Right Upper Adencarcinoma NA Brain 2.0 11.28 11.28 Y N Y
Cancer Day -2 Lobe of Lung CGLU369 Lung cfDNA Post-treatment, 48 F
IV T2NxM1 Right Upper Adencarcinoma NA Brain 5.0 10.09 10.09 Y N Y
Cancer Day 12 Lobe of Lung CGLU369 Lung cfDNA Post-treatment, 48 F
IV T2NxM1 Right Upper Adencarcinoma NA Brain 5.0 6.69 6.70 Y N Y
Cancer Day 88 Lobe of Lung CGLU369 Lung cfDNA Post-treatment, 48 F
IV T2NxM1 Right Upper Adencarcinoma NA Brain 5.0 8.41 8.42 Y N Y
Cancer Day 110 Lobe of Lung CGLU373 Lung cfDNA Pre-treatment, 56 F
IV T3N1M0 Right Upper Adencarcinoma Moderate None 5.0 6.35 6.35 Y N
Y Cancer Day -2 Lobe of Lung CGLU373 Lung cfDNA Post-treatment, 56
F IV T3N1M0 Right Upper Adencarcinoma Moderate None 5.0 6.28 6.28 Y
N Y Cancer Day 0.125 Lobe of Lung CGLU373 Lung cfDNA
Post-treatment, 56 F IV T3N1M0 Right Upper Adencarcinoma Moderate
None 5.0 3.82 3.82 Y N Y Cancer Day 7 Lobe of Lung CGLU373 Lung
cfDNA Post-treatment, 56 F IV T3N1M0 Right Upper Adencarcinoma
Moderate None 3.5 5.55 5.55 Y N Y Cancer Day 47 Lobe of Lung
CGPLBR100 Breast cfDNA Preoperative 44 F III T2N2M0 Left Breast
Infiltrating NA None 4.0 4.25 4.25 Y N Y Cancer treatment naive
Ductal Carcinoma CGPLBR101 Breast cfDNA Preoperative 46 F II T2N1M0
Left Breast Infiltrating Moderate None 4.0 37.88 37.88 Y N Y Cancer
treatment naive Lobular Carcinoma CGPLBR102 Breast cfDNA
Preoperative 47 F II T2N1M0 Right Breast Infiltrating Moderate None
3.6 13.67 13.67 Y N Y Cancer treatment naive Ductal Carcinoma
CGPLBR103 Breast cfDNA Preoperative 48 F II T2N1M0 Left Breast
Infiltrating Moderate None 3.6 7.11 7.11 Y N Y Cancer treatment
naive Ductal Carcinoma CGPLBR104 Breast cfDNA Preoperative 68 F II
T2N0M0 Right Breast Infiltrating Moderate None 4.7 19.89 19.89 Y N
Y Cancer treatment naive Lobular Carcinoma CGPLBR12 Breast cfDNA
Preoperative NA F III NA Breast Ductal NA NA 4.3 4.21 4.21 Y N N
Cancer treatment naive Carcinoma insitu with Microinvasion CGPLBR18
Breast cfDNA Preoperative NA F III NA Breast Infiltrating NA NA 4.1
40.39 30.49 Y N N Cancer treatment naive Lobular Carcinoma CGPLBR23
Breast cfDNA Preoperative 53 F II NA Breast Infiltrating NA None
4.7 20.09 20.09 Y N N Cancer treatment naive Ductal Carcinoma
CGPLBR24 Breast cfDNA Preoperative 53 F II NA Breast Infiltrating
NA None 3.6 58.33 34.72 Y N N Cancer treatment naive Ductal
Carcinoma CGPLBR28 Breast cfDNA Preoperative 59 F III NA Breast
Infiltrating NA None 4.2 12.86 12.86 Y N N Cancer treatment naive
Ductal Carcinoma CGPLBR30 Breast cfDNA Preoperative 61 F II NA
Breast Infiltrating NA None 4.1 59.73 30.49 Y N N Cancer treatment
naive Ductal Carcinoma CGPLBR31 Breast cfDNA Preoperative 54 F II
NA Breast Infiltrating NA None 3.4 23.94 23.94 Y N N Cancer
treatment naive Ductal Carcinoma CGPLBR32 Breast cfDNA Preoperative
NA F II NA Breast Infiltrating NA None 4.4 71.23 28.41 Y N N Cancer
treatment naive Ductal Carcinoma CGPLBR33 Breast cfDNA Preoperative
47 F II NA Breast Infiltrating NA None 4.4 11.00 11.00 Y N N Cancer
treatment naive Lobular Carcinoma CGPLBR34 Breast cfDNA
Preoperative 60 F II NA Breast Infiltrating NA None 4.4 23.61 23.61
Y N N Cancer treatment naive Lobular Carcinoma CGPLBR35 Breast
cfDNA Preoperative 43 F II NA Breast Ductal NA None 4.5 22.58 22.58
Y N N Cancer treatment naive Carcinoma insitu with Microinvasion
CGPLBR36 Breast cfDNA Preoperative 36 F II NA Breast Infiltrating
NA None 4.4 17.73 17.73 Y N N Cancer treatment naive Ductal
Carcinoma CGPLBR37 Breast cfDNA Preoperative 58 F II NA Breast
Infiltrating NA None 4.4 9.39 9.39 Y N N Cancer treatment naive
Ductal Carcinoma CGPLBR38 Breast cfDNA Preoperative 54 F I T1N0M0
Left Breast Infiltrating Moderate None 4.0 5.77 5.77 Y Y Y Cancer
treatment naive Ductal Carcinoma CGPLBR40 Breast cfDNA Preoperative
66 F III T2N2M0 Left Breast Infiltrating Poor None 4.6 15.69 15.69
Y Y Y Cancer treatment naive Ductal Carcinoma CGPLBR41 Breast cfDNA
Preoperative 51 F III T3N1M0 Left Breast Infiltrating Moderate None
4.5 11.56 11.56 Y N Y Cancer treatment naive Ductal Carcinoma
CGPLBR45 Breast cfDNA Preoperative 57 F II NA Breast Infiltrating
NA None 4.5 20.36 20.36 Y N N Cancer treatment naive Ductal
Carcinoma CGPLBR46 Breast cfDNA Preoperative 54 F III NA Breast
Infiltrating NA None 3.5 20.17 20.17 Y N N Cancer treatment naive
Ductal Carcinoma CGPLBR47 Breast cfDNA Preoperative 54 F I NA
Breast Infiltrating NA None 4.5 13.89 13.89 Y N N Cancer treatment
naive Ductal
Carcinoma CGPLBR48 Breast cfDNA Preoperative 47 F II T2N1M0 Left
Breast Infiltrating Poor None 3.9 7.07 7.07 Y Y Y Cancer treatment
naive Ductal Carcinoma CGPLBR49 Breast cfDNA Preoperative 37 F II
T2N1M0 Left Breast Infiltrating Poor None 4.0 5.74 5.74 Y N Y
Cancer treatment naive Ductal Carcinoma CGPLBR50 Breast cfDNA
Preoperative 51 F I NA Breast Infiltrating NA None 4.5 45.58 27.78
Y N N Cancer treatment naive Ductal Carcinoma CGPLBR51 Breast cfDNA
Preoperative 53 F II NA Breast Infiltrating NA None 4.0 8.83 8.83 Y
N N Cancer treatment naive Ductal Carcinoma CGPLBR52 Breast cfDNA
Preoperative 68 F III NA Breast Infiltrating NA None 4.5 80.71
27.78 Y N N Cancer treatment naive Ductal Carcinoma CGPLBR55 Breast
cfDNA Preoperative 53 F III T3N1M0 Right Breast Infiltrating Poor
None 4.3 4.57 4.57 Y Y Y Cancer treatment naive Ductal Carcinoma
CGPLBR56 Breast cfDNA Preoperative 56 F II NA Breast Infiltrating
NA None 4.5 22.16 22.16 Y N N Cancer treatment naive Ductal
Carcinoma CGPLBR57 Breast cfDNA Preoperative 54 F III T2N2M0 Left
Breast Infiltrating NA None 4.3 4.02 4.02 Y N Y Cancer treatment
naive Ductal Carcinoma CGPLBR59 Breast cfDNA Preoperative 42 F I
T1N0M0 Left Breast Infiltrating Moderate None 4.1 8.24 8.24 Y N Y
Cancer treatment naive Ductal Carcinoma CGPLBR60 Breast cfDNA
Preoperative 61 F II NA Left Breast Infiltrating NA None 4.5 11.09
11.09 Y N N Cancer treatment naive Ductal Carcinoma CGPLBR61 Breast
cfDNA Preoperative 67 F II T2N1M0 Left Breast Infiltrating Moderate
None 4.1 13.25 13.25 Y N Y Cancer treatment naive Ductal Carcinoma
CGPLBR63 Breast cfDNA Preoperative 48 F II T2N1M0 Left Breast
Infiltrating Moderate None 4.0 6.19 6.19 Y Y Y Cancer treatment
naive Ductal Carcinoma CGPLBR65 Breast cfDNA Preoperative 50 F II
NA Left Breast Infiltrating NA None 3.5 41.75 35.71 Y N N Cancer
treatment naive Ductal Carcinoma CGPLBR68 Breast cfDNA Preoperative
64 F III T4N1M0 Breast Infiltrating Poor None 3.4 10.41 10.41 Y N Y
Cancer treatment naive Ductal Carcinoma CGPLBR69 Breast cfDNA
Preoperative 43 F II T2N0M0 Breast Infiltrating Moderate None 4.4
4.07 4.07 Y Y Y Cancer treatment naive Ductal Carcinoma CGPLBR70
Breast cfDNA Preoperative 60 F II T2N1M0 Breast Infiltrating
Moderate None 3.4 11.94 11.94 Y Y Y Cancer treatment naive Ductal
Carcinoma CGPLBR71 Breast cfDNA Preoperative 65 F II T2N0M0 Breast
Infiltrating Poor None 3.1 7.64 7.64 Y Y Y Cancer treatment naive
Ductal Carcinoma CGPLBR72 Breast cfDNA Preoperative 67 F II T2N0M0
Breast Infiltrating Well None 3.9 4.43 4.43 Y Y Y Cancer treatment
naive Ductal Carcinoma CGPLBR73 Breast cfDNA Preoperative 60 F II
T2N1M0 Breast Infiltrating Moderate None 3.3 14.69 14.69 Y Y Y
Cancer treatment naive Ductal Carcinoma CGPLBR76 Breast cfDNA
Preoperative 53 F II T2N0M0 Right Breast Infiltrating Well None 4.9
8.71 8.71 Y Y Y Cancer treatment naive Ductal Carcinoma CGPLBR81
Breast cfDNA Preoperative 54 F II NA Breast Infiltrating NA None
2.5 83.14 50.00 Y N N Cancer treatment naive Ductal Carcinoma
CGPLBR82 Breast cfDNA Preoperative 70 F I T1N0M0 Right Breast
Infiltrating Moderate None 4.8 23.39 23.39 Y N Y Cancer treatment
naive Lobular Carcinoma CGPLBR83 Breast cfDNA Preoperative 53 F II
T2N1M0 Right Breast Infiltrating Moderate None 3.7 100.17 100.17 Y
Y Y Cancer treatment naive Ductal Carcinoma CGPLBR84 Breast cfDNA
Preoperative NA F III NA Breast Infiltrating NA NA 3.6 16.95 16.95
Y N N Cancer treatment naive Ductal Carcinoma CGPLBR87 Breast cfDNA
Preoperative 80 F II T2N1M0 Right Breast Papilary Well None 3.6
277.39 69.44 Y Y Y Cancer treatment naive Carcinoma CGPLBR88 Breast
cfDNA Preoperative 48 F II T1N1M0 Left Breast Infiltrating Poor
None 3.6 49.75 49.75 Y Y Y Cancer treatment naive Ductal Carcinoma
CGPLBR90 Breast cfDNA Preoperative 51 F II NA Right Breast
Infiltrating NA None 3.0 14.24 14.24 Y N N Cancer treatment naive
Ductal Carcinoma CGPLBR91 Breast cfDNA Preoperative 62 F III T2N2M0
Breast Infiltrating Poor None 3.2 22.41 22.41 Y N Y Cancer
treatment naive Lobular Carcinoma CGPLBR92 Breast cfDNA
Preoperative 58 F II T2N1M0 Breast Infiltrating Poor None 3.1 81.00
81.00 Y Y Y Cancer treatment naive Meduilary Carcinoma CGPLBR93
Breast cfDNA Preoperative 59 F II T1N0M0 Breast Infiltrating
Moderate None 3.3 27.94 27.94 Y N Y Cancer treatment naive Ductal
Carcinoma CGPLH189 Healthy cfDNA Preoperative 74 M NA NA NA NA NA
NA 5.0 5.84 5.84 Y N N treatment naive CGPLH190 Healthy cfDNA
Preoperative 67 M NA NA NA NA NA NA 4.7 18.07 18.07 Y N N treatment
naive CGPLH192 Healthy cfDNA Preoperative 74 M NA NA NA NA NA NA
4.7 12.19 12.19 Y N N treatment naive CGPLH193 Healthy cfDNA
Preoperative 72 F NA NA NA NA NA NA 5.0 5.47 5.47 Y N N treatment
naive CGPLH194 Healthy cfDNA Preoperative 75 F NA NA NA NA NA NA
5.0 9.98 9.98 Y N N treatment naive CGPLH196 Healthy cfDNA
Preoperative 64 M NA NA NA NA NA NA 5.0 11.69 11.69 Y N N treatment
naive CGPLH197 Healthy cfDNA Preoperative 74 M NA NA NA NA NA NA
5.0 5.69 5.69 Y N N treatment naive CGPLH198 Healthy cfDNA
Preoperative 66 M NA NA NA NA NA NA 5.0 4.36 4.36 Y N N treatment
naive CGPLH199 Healthy cfDNA Preoperative 75 F NA NA NA NA NA NA
5.0 9.77 9.77 Y N N treatment naive CGPLH200 Healthy cfDNA
Preoperative 51 M NA NA NA NA NA NA 5.0 5.60 5.60 Y N N treatment
naive CGPLH201 Healthy cfDNA Preoperative 68 F NA NA NA NA NA NA
5.0 8.82 8.82 Y N N treatment naive CGPLH202 Healthy cfDNA
Preoperative 73 M NA NA NA NA NA NA 5.0 5.54 5.54 Y N N treatment
naive CGPLH203 Healthy cfDNA Preoperative 59 M NA NA NA NA NA NA
5.0 9.03 9.03 Y N N treatment naive CGPLH205 Healthy cfDNA
Preoperative 68 F NA NA NA NA NA NA 5.0 4.74 4.74 Y N N treatment
naive CGPLH208 Healthy cfDNA Preoperative 75 F NA NA NA NA NA NA
5.0 4.67 4.67 Y N N treatment naive CGPLH209 Healthy cfDNA
Preoperative 74 M NA NA NA NA NA NA 5.0 5.15 5.15 Y N N treatment
naive CGPLH210 Healthy cfDNA Preoperative 75 M NA NA NA NA NA NA
5.0 5.41 5.41 Y N N treatment naive CGPLH211 Healthy cfDNA
Preoperative 75 F NA NA NA NA NA NA 5.0 6.24 6.24 Y N N treatment
naive CGPLH300 Hettithy cfDNA Preoperative 72 F NA NA NA NA NA NA
4.4 6.75 6.75 Y N N treatment naive CGPLH307 Healthy cfDNA
Preoperative 53 M NA NA NA NA NA NA 4.5 3.50 3.50 Y N N treatment
naive CGPLH308 Healthy cfDNA Preoperative 60 M NA NA NA NA NA NA
4.5 6.01 6.01 Y N N treatment naive CGPLH309 Healthy cfDNA
Preoperative 61 F NA NA NA NA NA NA 4.5 5.21 5.21 Y N N treatment
naive CGPLH310 Healthy cfDNA Preoperative 55 F NA NA NA NA NA NA
4.5 15.25 15.25 Y N N treatment naive CGPLH311 Healthy cfDNA
Preoperative 50 M NA NA NA NA NA NA 4.5 4.47 4.47 Y N N treatment
naive CGPLH314 Healthy cfDNA Preoperative 59 M NA NA NA NA NA NA
4.5 9.62 9.62 Y N N treatment naive CGPLH314 Healthy cfDNA,
Preoperative 59 M NA NA NA NA NA NA 4.4 16.24 16.24 Y N N technical
treatment naive replicate CGPLH315 Healthy cfDNA Preoperative 59 F
NA NA NA NA NA NA 4.2 11.55 11.55 Y N N treatment naive CGPLH316
Healthy cfDNA Preoperative 64 M NA NA NA NA NA NA 4.5 28.92 27.79 Y
N N treatment naive CGPLH317 Healthy cfDNA Preoperative 53 F NA NA
NA NA NA NA 4.5 7.62 7.62 Y N N treatment naive CGPLH319 Healthy
cfDNA Preoperative 60 F NA NA NA NA NA NA 4.2 4.41 4.41 Y N N
treatment naive CGPLH320 Healthy cfDNA Preoperative 75 F NA NA NA
NA NA NA 4.5 6.93 6.93 Y N N treatment naive CGPLH322 Healthy cfDNA
Preoperative 53 F NA NA NA NA NA NA 4.2 8.17 8.17 Y N N treatment
naive CGPLH324 Healthy cfDNA Preoperative 59 F NA NA NA NA NA NA
5.0 6.63 6.63 Y N N treatment naive CGPLH325 Healthy cfDNA
Preoperative 54 M NA NA NA NA NA NA 4.6 4.15 4.15 Y N N treatment
naive CGPLH326 Healthy cfDNA Preoperative 67 F NA NA NA NA NA NA
4.5 6.06 6.06 Y N N treatment naive CGPLH327 Healthy cfDNA
Preoperative 50 M NA NA NA NA NA NA 4.8 1.24 1.24 Y N N treatment
naive CGPLH328 Healthy cfDNA, Preoperative 68 F NA NA NA NA NA NA
4.4 3.42 3.42 Y N N technical treatment naive replicate CGPLH328
Healthy cfDNA Preoperative 68 F NA NA NA NA NA NA 4.9 5.47 5.47 Y N
N treatment naive CGPLH329 Healthy cfDNA Preoperative 59 M NA NA NA
NA NA NA 4.5 5.27 5.27 Y N N treatment naive CGPLH330 Healthy cfDNA
Preoperative 75 M NA NA NA NA NA NA 4.3 10.21 10.21 Y N N treatment
naive CGPLH331 Healthy cfDNA Preoperative 55 M NA NA NA NA NA NA
4.6 2.63 2.63 Y N N treatment naive CGPLH331 Healthy cfDNA,
Preoperative 55 M NA NA NA NA NA NA 4.3 4.15 4.15 Y N N technical
treatment naive replicate CGPLH333 Healthy cfDNA Preoperative 60 M
NA NA NA NA NA NA 4.7 4.06 4.06 Y N N
treatment naive CGPLH335 Healthy cfDNA Preoperative 74 M NA NA NA
NA NA NA 4.4 9.39 9.39 Y N N treatment naive CGPLH336 Healthy cfDNA
Preoperative 53 F NA NA NA NA NA NA 4.6 6.64 6.64 Y N N treatment
naive CGPLH337 Healthy cfDNA Preoperative 53 F NA NA NA NA NA NA
4.2 4.48 4.48 Y N N treatment naive CGPLH338 Healthy cfDNA
Preoperative 75 M NA NA NA NA NA NA 4.5 59.44 59.44 Y N N treatment
naive CGPLH339 Healthy cfDNA Preoperative 70 M NA NA NA NA NA NA
4.5 12.27 12.27 Y N N treatment naive CGPLH340 Healthy cfDNA
Preoperative 62 M NA NA NA NA NA NA 4.5 4.86 4.86 Y N N treatment
naive CGPLH341 Healthy cfDNA Preoperative 61 F NA NA NA NA NA NA
4.1 7.62 7.62 Y N N treatment naive CGPLH342 Healthy cfDNA
Preoperative 49 F NA NA NA NA NA NA 4.2 18.29 18.29 Y N N treatment
naive CGPLH343 Healthy cfDNA Preoperative 58 M NA NA NA NA NA NA
4.5 3.49 3.49 Y N N treatment naive CGPLH344 Healthy cfDNA
Preoperative 50 M NA NA NA NA NA NA 4.2 8.41 8.41 Y N N treatment
naive CGPLH345 Healthy cfDNA Preoperative 55 F NA NA NA NA NA NA
4.5 9.73 9.73 Y N N treatment naive CGPLH346 Healthy cfDNA
Preoperative 50 F NA NA NA NA NA NA 4.5 7.86 7.86 Y N N treatment
naive CGPLH35 Healthy cfDNA Preoperative 48 F NA NA NA NA NA NA 4.0
13.15 13.15 Y N Y treatment naive CGPLH350 Healthy cfDNA
Preoperative 65 M NA NA NA NA NA NA 3.5 6.09 6.09 Y N N treatment
naive CGPLH351 Healthy cfDNA Preoperative 71 M NA NA NA NA NA NA
4.0 15.91 15.91 Y N N treatment naive CGPLH352 Healthy cfDNA
Preoperative 50 F NA NA NA NA NA NA 4.2 6.47 6.47 Y N N treatment
naive CGPLH353 Healthy cfDNA Preoperative 50 F NA NA NA NA NA NA
4.2 4.47 4.47 Y N N treatment naive CGPLH354 Healthy cfDNA
Preoperative 50 F NA NA NA NA NA NA 4.2 17.49 17.49 Y N N treatment
naive CGPLH355 Healthy cfDNA Preoperative 70 M NA NA NA NA NA NA
4.2 11.58 11.58 Y N N treatment naive CGPLH356 Healthy cfDNA
Preoperative 50 F NA NA NA NA NA NA 4.5 3.84 3.84 Y N N treatment
naive CGPLH357 Healthy cfDNA Preoperative 52 F NA NA NA NA NA NA
4.2 11.79 11.79 Y N N treatment naive CGPLH358 Healthy cfDNA
Preoperative 55 M NA NA NA NA NA NA 4.2 21.08 21.08 Y N N treatment
naive CGPLH36 Healthy cfDNA Preoperative 36 F NA NA NA NA NA NA 4.0
13.00 13.00 Y N Y treatment naive CGPLH360 Healthy cfDNA
Preoperative 60 M NA NA NA NA NA NA 4.2 3.48 3.48 Y N N treatment
naive CGPLH361 Healthy cfDNA Preoperative 50 M NA NA NA NA NA NA
4.3 6.98 6.98 Y N N treatment naive CGPLH362 Healthy cfDNA
Preoperative 72 F NA NA NA NA NA NA 4.4 8.49 8.49 Y N N treatment
naive CGPLH363 Healthy cfDNA Preoperative 68 F NA NA NA NA NA NA
4.5 4.44 4.44 Y N N treatment naive CGPLH364 Healthy cfDNA
Preoperative 50 F NA NA NA NA NA NA 4.5 17.31 17.31 Y N N treatment
naive CGPLH365 Healthy cfDNA Preoperative 68 F NA NA NA NA NA NA
4.5 0.55 0.55 Y N N treatment naive CGPLH366 Healthy cfDNA
Preoperative 61 M NA NA NA NA NA NA 4.5 4.88 4.88 Y N N treatment
naive CGPLH367 Healthy cfDNA Preoperative 50 F NA NA NA NA NA NA
4.4 6.48 6.48 Y N N treatment naive CGPLH368 Healthy cfDNA
Preoperative 50 M NA NA NA NA NA NA 4.3 2.53 2.53 Y N N treatment
naive CGPLH369 Healthy cfDNA Preoperative 55 F NA NA NA NA NA NA
4.3 10.18 10.18 Y N N treatment naive CGPLH369 Healthy cfDNA,
Preoperative 55 F NA NA NA NA NA NA 4.4 10.71 10.71 Y N N technical
treatment naive replicate CGPLH37 Healthy cfDNA Preoperative 39 F
NA NA NA NA NA NA 4.0 9.73 9.73 Y N Y treatment naive CGPLH370
Healthy cfDNA Preoperative 50 F NA NA NA NA NA NA 4.5 7.22 7.22 Y N
N treatment naive CGPLH371 Healthy cfDNA Preoperative 57 F NA NA NA
NA NA NA 4.6 5.62 5.62 Y N N treatment naive CGPLH380 Healthy cfDNA
Preoperative 53 F NA NA NA NA NA NA 4.2 6.61 6.61 Y N N treatment
naive CGPLH381 Healthy cfDNA Preoperative 56 F NA NA NA NA NA NA
4.2 27.38 27.38 Y N N treatment naive CGPLH382 Healthy cfDNA
Preoperative 53 F NA NA NA NA NA NA 4.5 11.58 11.58 Y N N treatment
naive CGPLH383 Healthy cfDNA Preoperative 62 F NA NA NA NA NA NA
4.5 25.50 25.50 Y N N treatment naive CGPLH384 Healthy cfDNA
Preoperative 50 M NA NA NA NA NA NA 4.5 15.66 15.66 Y N N treatment
naive CGPLH385 Healthy cfDNA Preoperative 69 M NA NA NA NA NA NA
4.5 19.35 19.35 Y N N treatment naive CGPLH386 Healthy cfDNA
Preoperative 62 M NA NA NA NA NA NA 4.5 6.46 6.46 Y N N treatment
naive CGPLH386 Healthy cfDNA, Preoperative 62 M NA NA NA NA NA NA
4.6 6.54 6.54 Y N N technical treatment naive replicate CGPLH387
Healthy cfDNA Preoperative 71 F NA NA NA NA NA NA 4.5 6.19 6.19 Y N
N treatment naive CGPLH388 Healthy cfDNA Preoperative 57 F NA NA NA
NA NA NA 4.5 6.62 6.62 Y N N treatment naive CGPLH389 Healthy cfDNA
Preoperative 73 F NA NA NA NA NA NA 4.6 14.78 14.78 Y N N treatment
naive CGPLH390 Healthy cfDNA Preoperative 50 F NA NA NA NA NA NA
4.5 12.14 12.14 Y N N treatment naive CGPLH391 Healthy cfDNA
Preoperative 58 M NA NA NA NA NA NA 4.5 8.88 8.88 Y N N treatment
naive CGPLH391 Healthy cfDNA, Preoperative 58 M NA NA NA NA NA NA
4.5 8.37 8.37 Y N N technical treatment naive replicate CGPLH392
Healthy cfDNA Preoperative 57 F NA NA NA NA NA NA 4.5 8.39 8.39 Y N
N treatment naive CGPLH393 Healthy cfDNA Preoperative 54 M NA NA NA
NA NA NA 4.5 5.27 5.27 Y N N treatment naive CGPLH394 Healthy cfDNA
Preoperative 55 F NA NA NA NA NA NA 4.4 3.79 3.79 Y N N treatment
naive CGPLH395 Healthy cfDNA Preoperative 56 F NA NA NA NA NA NA
4.4 9.56 9.56 Y N N treatment naive CGPLH395 Healthy cfDNA,
Preoperative 56 F NA NA NA NA NA NA 4.4 5.40 5.40 Y N N technical
treatment naive replicate CGPLH396 Healthy cfDNA Preoperative 50 M
NA NA NA NA NA NA 4.4 20.31 20.31 Y N N treatment naive CGPLH398
Healthy cfDNA Preoperative 68 M NA NA NA NA NA NA 4.3 13.01 13.01 Y
N N treatment naive CGPLH399 Healthy cfDNA Preoperative 62 F NA NA
NA NA NA NA 4.4 4.79 4.79 Y N N treatment naive CGPLH400 Healthy
cfDNA Preoperative 64 M NA NA NA NA NA NA 4.4 7.70 7.70 Y N N
treatment naive CGPLH400 Healthy cfDNA, Preoperative 64 M NA NA NA
NA NA NA 4.4 6.26 6.26 Y N N technical treatment naive replicate
CGPLH401 Healthy cfDNA Preoperative 50 M NA NA NA NA NA NA 4.3
13.01 13.01 Y N N treatment naive CGPLH401 Healthy cfDNA,
Preoperative 50 M NA NA NA NA NA NA 4.4 11.13 11.13 Y N N technical
treatment naive replicate CGPLH402 Healthy cfDNA Preoperative 57 F
NA NA NA NA NA NA 4.5 2.89 2.89 Y N N treatment naive CGPLH403
Healthy cfDNA Preoperative 64 M NA NA NA NA NA NA 4.3 4.41 4.41 Y N
N treatment naive CGPLH404 Healthy cfDNA Preoperative 50 M NA NA NA
NA NA NA 4.2 6.38 6.38 Y N N treatment naive CGPLH405 Healthy cfDNA
Preoperative 50 F NA NA NA NA NA NA 4.4 7.28 7.28 Y N N treatment
naive CGPLH406 Healthy cfDNA Preoperative 57 M NA NA NA NA NA NA
4.2 5.40 5.40 Y N N treatment naive CGPLH407 Healthy cfDNA
Preoperative 75 F NA NA NA NA NA NA 4.0 13.30 13.30 Y N N treatment
naive CGPLH408 Healthy cfDNA Preoperative 50 F NA NA NA NA NA NA
4.2 5.18 5.18 Y N N treatment naive CGPLH409 Healthy cfDNA
Preoperative 53 M NA NA NA NA NA NA 3.7 3.98 3.98 Y N N treatment
naive CGPLH410 Healthy cfDNA Preoperative 52 M NA NA NA NA NA NA
4.1 6.91 6.91 Y N N treatment naive CGPLH411 Healthy cfDNA
Preoperative 50 F NA NA NA NA NA NA 4.1 3.30 3.30 Y N N treatment
naive CGPLH412 Healthy cfDNA Preoperative 53 F NA NA NA NA NA NA
4.1 5.55 5.55 Y N N treatment naive CGPLH413 Healthy cfDNA
Preoperative 54 F NA NA NA NA NA NA 4.5 8.18 8.18 Y N N treatment
naive CGPLH414 Healthy cfDNA Preoperative 56 M NA NA NA NA NA NA
3.8 5.85 5.85 Y N N treatment naive CGPLH415 Healthy cfDNA
Preoperative 59 M NA NA NA NA NA NA 4.7 10.20 10.20 Y N N treatment
naive CGPLH416 Healthy cfDNA Preoperative 58 F NA NA NA NA NA NA
4.5 11.73 11.73 Y N N treatment naive CGPLH417 Healthy cfDNA
Preoperative 70 M NA NA NA NA NA NA 4.2 10.98 10.98 Y N N treatment
naive CGPLH418 Healthy cfDNA Preoperative 70 F NA NA NA NA NA NA
4.5 10.96 10.96 Y N N treatment naive CGPLH419 Healthy cfDNA
Preoperative 65 F NA NA NA NA NA NA 4.5 10.17 10.17 Y N N treatment
naive CGPLH42 Healthy cfDNA Preoperative 54 F NA NA NA NA NA NA 4.0
14.30 14.30
Y N Y treatment naive CGPLH420 Healthy cfDNA Preoperative 51 M NA
NA NA NA NA NA 4.2 12.32 12.32 Y N N treatment naive CGPLH422
Healthy cfDNA Preoperative 68 F NA NA NA NA NA NA 4.6 5.42 5.42 Y N
N treatment naive CGPLH423 Healthy cfDNA Preoperative 54 M NA NA NA
NA NA NA 4.2 2.85 2.85 Y N N treatment naive CGPLH424 Healthy cfDNA
Preoperative 53 F NA NA NA NA NA NA 4.7 1.66 1.66 Y N N treatment
naive CGPLH425 Healthy cfDNA Preoperative 53 F NA NA NA NA NA NA
4.4 5.98 5.98 Y N N treatment naive CGPLH426 Healthy cfDNA
Preoperative 68 M NA NA NA NA NA NA 4.4 2.84 2.84 Y N N treatment
naive CGPLH427 Healthy cfDNA Preoperative 68 M NA NA NA NA NA NA
4.4 10.86 10.86 Y N N treatment naive CGPLH428 Healthy cfDNA
Preoperative 50 F NA NA NA NA NA NA 4.5 6.27 6.27 Y N N treatment
naive CGPLH429 Healthy cfDNA Preoperative 63 F NA NA NA NA NA NA
4.5 3.89 3.89 Y N N treatment naive CGPLH43 Healthy cfDNA
Preoperative 49 F NA NA NA NA NA NA 4.0 8.50 8.50 Y N Y treatment
naive CGPLH430 Healthy cfDNA Preoperative 69 F NA NA NA NA NA NA
4.2 10.33 10.33 Y N N treatment naive CGPLH431 Healthy cfDNA
Preoperative 59 F NA NA NA NA NA NA 4.8 12.81 12.81 Y N N treatment
naive CGPLH432 Healthy cfDNA Preoperative 59 F NA NA NA NA NA NA
4.8 2.42 2.42 Y N N treatment naive CGPLH434 Healthy cfDNA
Preoperative 59 M NA NA NA NA NA NA 4.6 8.83 8.83 Y N N treatment
naive CGPLH435 Healthy cfDNA Preoperative 50 M NA NA NA NA NA NA
4.5 8.95 8.95 Y N N treatment naive CGPLH436 Healthy cfDNA
Preoperative 50 F NA NA NA NA NA NA 4.5 4.29 4.29 Y N N treatment
naive CGPLH437 Healthy cfDNA Preoperative 56 M NA NA NA NA NA NA
4.6 18.07 18.07 Y N N treatment naive CGPLH438 Healthy cfDNA
Preoperative 69 M NA NA NA NA NA NA 4.8 16.62 16.62 Y N N treatment
naive CGPLH439 Healthy cfDNA Preoperative 50 F NA NA NA NA NA NA
4.7 4.38 4.38 Y N N treatment naive CGPLH440 Healthy cfDNA
Preoperative 72 M NA NA NA NA NA NA 4.7 4.32 4.32 Y N N treatment
naive CGPLH441 Healthy cfDNA Preoperative 50 F NA NA NA NA NA NA
4.7 7.80 7.80 Y N N treatment naive CGPLH442 Healthy cfDNA
Preoperative 59 F NA NA NA NA NA NA 4.5 6.15 6.15 Y N N treatment
naive CGPLH443 Healthy cfDNA Preoperative 52 F NA NA NA NA NA NA
4.4 3.44 3.44 Y N N treatment naive CGPLH444 Healthy cfDNA
Preoperative 60 F NA NA NA NA NA NA 4.4 4.12 4.12 Y N N treatment
naive CGPLH445 Healthy cfDNA Preoperative 53 F NA NA NA NA NA NA
4.4 4.36 4.36 Y N N treatment naive CGPLH446 Healthy cfDNA
Preoperative 51 F NA NA NA NA NA NA 4.4 2.92 2.92 Y N N treatment
naive CGPLH447 Healthy cfDNA Preoperative 50 F NA NA NA NA NA NA
4.6 3.87 3.87 Y N N treatment naive CGPLH448 Healthy cfDNA
Preoperative 51 F NA NA NA NA NA NA 4.4 5.29 5.29 Y N N treatment
naive CGPLH449 Healthy cfDNA Preoperative 51 F NA NA NA NA NA NA
4.5 3.77 3.77 Y N N treatment naive CGPLH45 Healthy cfDNA
Preoperative 58 F NA NA NA NA NA NA 4.0 10.85 10.85 Y N Y treatment
naive CGPLH450 Healthy cfDNA Preoperative 50 F NA NA NA NA NA NA
4.5 5.62 5.62 Y N N treatment naive CGPLH451 Healthy cfDNA
Preoperative 54 F NA NA NA NA NA NA 4.6 7.24 7.24 Y N N treatment
naive CGPLH452 Healthy cfDNA Preoperative 69 M NA NA NA NA NA NA
4.4 2.54 2.54 Y N N treatment naive CGPLH453 Healthy cfDNA
Preoperative 53 F NA NA NA NA NA NA 4.6 9.11 9.11 Y N N treatment
naive CGPLH455 Healthy cfDNA Preoperative 55 F NA NA NA NA NA NA
4.4 2.64 2.64 Y N N treatment naive CGPLH455 Healthy cfDNA,
Preoperative 55 F NA NA NA NA NA NA 4.5 2.42 2.42 Y N N technical
treatment naive replicate CGPLH456 Healthy cfDNA Preoperative 54 F
NA NA NA NA NA NA 4.5 3.11 3.11 Y N N treatment naive CGPLH457
Healthy cfDNA Preoperative 54 F NA NA NA NA NA NA 4.4 5.92 5.92 Y N
N treatment naive CGPLH458 Healthy cfDNA Preoperative 52 F NA NA NA
NA NA NA 4.5 16.04 16.04 Y N N treatment naive CGPLH459 Healthy
cfDNA Preoperative 50 F NA NA NA NA NA NA 4.4 6.52 6.52 Y N N
treatment naive CGPLH46 Healthy cfDNA Preoperative 35 F NA NA NA NA
NA NA 4.0 8.25 8.25 Y N Y treatment naive CGPLH460 Healthy cfDNA
Preoperative 50 F NA NA NA NA NA NA 4.6 5.24 5.24 Y N N treatment
naive CGPLH463 Healthy cfDNA Preoperative 53 F NA NA NA NA NA NA
4.5 22.77 22.77 Y N N treatment naive CGPLH464 Healthy cfDNA
Preoperative 50 F NA NA NA NA NA NA 4.4 2.90 2.90 Y N N treatment
naive CGPLH465 Healthy cfDNA Preoperative 50 F NA NA NA NA NA NA
4.5 4.76 4.76 Y N N treatment naive CGPLH466 Healthy cfDNA
Preoperative 50 F NA NA NA NA NA NA 4.6 5.68 5.68 Y N N treatment
naive CGPLH466 Healthy cfDNA, Preoperative 50 F NA NA NA NA NA NA
4.5 6.75 6.75 Y N N technical treatment naive replicate CGPLH467
Healthy cfDNA Preoperative 50 F NA NA NA NA NA NA 4.5 4.59 4.59 Y N
N treatment naive CGPLH468 Healthy cfDNA Preoperative 53 M NA NA NA
NA NA NA 4.5 11.19 11.19 Y N N treatment naive CGPLH469 Healthy
cfDNA Preoperative 50 F NA NA NA NA NA NA 4.5 3.25 3.25 Y N N
treatment naive CGPLH47 Healthy cfDNA Preoperative 50 F NA NA NA NA
NA NA 4.0 7.43 7.43 Y N Y treatment naive CGPLH470 Healthy cfDNA
Preoperative 68 F NA NA NA NA NA NA 4.5 13.64 13.64 Y N N treatment
naive CGPLH471 Healthy cfDNA Preoperative 70 F NA NA NA NA NA NA
4.3 13.00 13.00 Y N N treatment naive CGPLH472 Healthy cfDNA
Preoperative 69 F NA NA NA NA NA NA 4.2 10.17 10.17 Y N N treatment
naive CGPLH473 Healthy cfDNA Preoperative 62 M NA NA NA NA NA NA
4.3 2.98 2.98 Y N N treatment naive CGPLH474 Healthy cfDNA
Preoperative 63 M NA NA NA NA NA NA 4.3 29.15 29.15 Y N N treatment
naive CGPLH475 Healthy cfDNA Preoperative 67 F NA NA NA NA NA NA
4.0 7.26 7.26 Y N N treatment naive CGPLH476 Healthy cfDNA
Preoperative 65 F NA NA NA NA NA NA 4.3 6.16 6.16 Y N N treatment
naive CGPLH477 Healthy cfDNA Preoperative 61 F NA NA NA NA NA NA
4.3 15.21 15.21 Y N N treatment naive CGPLH478 Healthy cfDNA
Preoperative 51 F NA NA NA NA NA NA 4.4 7.29 7.29 Y N N treatment
naive CGPLH479 Healthy cfDNA Preoperative 52 M NA NA NA NA NA NA
4.5 8.73 8.73 Y N N treatment naive CGPLH48 Healthy cfDNA
Preoperative 38 F NA NA NA NA NA NA 4.0 6.38 6.38 Y N Y treatment
naive CGPLH480 Healthy cfDNA Preoperative 50 F NA NA NA NA NA NA
4.4 10.62 10.62 Y N N treatment naive CGPLH481 Healthy cfDNA
Preoperative 53 F NA NA NA NA NA NA 4.3 6.75 6.75 Y N N treatment
naive CGPLH482 Healthy cfDNA Preoperative 50 M NA NA NA NA NA NA
4.3 23.58 23.58 Y N N treatment naive CGPLH483 Healthy cfDNA
Preoperative 66 M NA NA NA NA NA NA 4.4 14.44 14.44 Y N N treatment
naive CGPLH484 Healthy cfDNA Preoperative 72 M NA NA NA NA NA NA
4.2 14.32 14.32 Y N N treatment naive CGPLH485 Healthy cfDNA
Preoperative 50 F NA NA NA NA NA NA 4.3 9.64 9.64 Y N N treatment
naive CGPLH486 Healthy cfDNA Preoperative 50 F NA NA NA NA NA NA
4.3 10.16 10.16 Y N N treatment naive CGPLH487 Healthy cfDNA
Preoperative 50 M NA NA NA NA NA NA 4.4 6.11 6.11 Y N N treatment
naive CGPLH488 Healthy cfDNA Preoperative 50 F NA NA NA NA NA NA
4.5 7.88 7.88 Y N N treatment naive CGPLH49 Healthy cfDNA
Preoperative 39 F NA NA NA NA NA NA 4.0 6.60 6.60 Y N Y treatment
naive CGPLH490 Healthy cfDNA Preoperative 50 F NA NA NA NA NA NA
4.5 4.18 4.18 Y N N treatment naive CGPLH491 Healthy cfDNA
Preoperative 50 F NA NA NA NA NA NA 4.5 13.16 13.16 Y N N treatment
naive CGPLH492 Healthy cfDNA Preoperative 51 F NA NA NA NA NA NA
4.5 3.83 3.83 Y N N treatment naive CGPLH493 Healthy cfDNA
Preoperative 64 M NA NA NA NA NA NA 4.5 25.06 25.06 Y N N treatment
naive CGPLH494 Healthy cfDNA Preoperative 53 F NA NA NA NA NA NA
4.4 5.24 5.24 Y N N treatment naive CGPLH495 Healthy cfDNA
Preoperative 50 F NA NA NA NA NA NA 4.4 5.03 5.03 Y N N treatment
naive CGPLH496 Healthy cfDNA Preoperative 74 M NA NA NA NA NA NA
4.5 34.01 27.78 Y N N treatment naive CGPLH497 Healthy cfDNA
Preoperative 68 F NA NA NA NA NA NA 4.5 8.24 8.24 Y N N treatment
naive CGPLH497 Healthy cfDNA, Preoperative 68 F NA NA NA NA NA NA
4.4 5.88 5.88 Y N N technical treatment naive replicate CGPLH498
Healthy cfDNA Preoperative 54 F NA NA NA NA NA NA 4.4 5.33 5.33 Y N
N treatment naive
CGPLH499 Healthy cfDNA Preoperative 52 F NA NA NA NA NA NA 4.5 7.85
7.85 Y N N treatment naive CGPLH50 Healthy cfDNA Preoperative 55 F
NA NA NA NA NA NA 4.0 7.05 7.05 Y N Y treatment naive CGPLH500
Healthy cfDNA Preoperative 51 F NA NA NA NA NA NA 4.5 3.49 3.49 Y N
N treatment naive CGPLH501 Healthy cfDNA Preoperative 50 F NA NA NA
NA NA NA 4.3 6.29 6.29 Y N N treatment naive CGPLH502 Healthy cfDNA
Preoperative 53 F NA NA NA NA NA NA 4.5 2.24 2.24 Y N N treatment
naive CGPLH503 Healthy cfDNA Preoperative 67 M NA NA NA NA NA NA
4.5 11.01 11.01 Y N N treatment naive CGPLH504 Healthy cfDNA
Preoperative 57 F NA NA NA NA NA NA 4.3 6.60 6.60 Y N N treatment
naive CGPLH504 Healthy cfDNA, Preoperative 57 F NA NA NA NA NA NA
4.2 10.02 10.02 Y N N technical treatment naive replicate CGPLH505
Healthy cfDNA Preoperative 50 F NA NA NA NA NA NA 4.1 5.23 5.23 Y N
N treatment naive CGPLH506 Healthy cfDNA Preoperative 51 F NA NA NA
NA NA NA 4.5 12.23 12.23 Y N N treatment naive CGPLH507 Healthy
cfDNA Preoperative 56 F NA NA NA NA NA NA 4.1 9.89 9.89 Y N N
treatment naive CGPLH508 Healthy cfDNA Preoperative 54 M NA NA NA
NA NA NA 4.5 8.66 8.66 Y N N treatment naive CGPLH508 Healthy
cfDNA, Preoperative 54 F NA NA NA NA NA NA 4.4 9.55 9.55 Y N N
technical treatment naive replicate CGPLH509 Healthy cfDNA
Preoperative 60 M NA NA NA NA NA NA 4.0 9.79 9.79 Y N N treatment
naive CGPLH51 Healthy cfDNA Preoperative 48 F NA NA NA NA NA NA 4.0
7.85 7.85 Y N Y treatment naive CGPLH510 Healthy cfDNA Preoperative
67 M NA NA NA NA NA NA 4.2 14.20 14.20 Y N N treatment naive
CGPLH511 Healthy cfDNA Preoperative 75 M NA NA NA NA NA NA 4.5
12.94 12.94 Y N N treatment naive CGPLH512 Healthy cfDNA
Preoperative 52 M NA NA NA NA NA NA 4.3 8.60 8.60 Y N N treatment
naive CGPLH513 Healthy cfDNA Preoperative 57 M NA NA NA NA NA NA
4.3 6.54 6.54 Y N N treatment naive CGPLH514 Healthy cfDNA
Preoperative 55 F NA NA NA NA NA NA 4.4 10.94 10.94 Y N N treatment
naive CGPLH515 Healthy cfDNA Preoperative 68 F NA NA NA NA NA NA
4.5 8.71 8.71 Y N N treatment naive CGPLH516 Healthy cfDNA
Preoperative 65 F NA NA NA NA NA NA 4.5 7.32 7.32 Y N N treatment
naive CGPLH517 Healthy cfDNA Preoperative 54 F NA NA NA NA NA NA
4.6 5.16 5.16 Y N N treatment naive CGPLH517 Healthy cfDNA,
Preoperative 54 F NA NA NA NA NA NA 4.5 9.74 9.74 Y N N technical
treatment naive replicate CGPLH518 Healthy cfDNA Preoperative 50 F
NA NA NA NA NA NA 4.4 5.92 5.92 Y N N treatment naive CGPLH519
Healthy cfDNA Preoperative 54 M NA NA NA NA NA NA 4.4 6.96 6.96 Y N
N treatment naive CGPLH52 Healthy cfDNA Preoperative 40 F NA NA NA
NA NA NA 4.0 9.90 9.90 Y N Y treatment naive CGPLH520 Healthy cfDNA
Preoperative 51 F NA NA NA NA NA NA 4.3 8.27 8.27 Y N N treatment
naive CGPLH54 Healthy cfDNA Preoperative 47 F NA NA NA NA NA NA 4.0
14.18 14.18 Y N Y treatment naive CGPLH55 Healthy cfDNA
Preoperative 46 F NA NA NA NA NA NA 4.0 7.35 7.35 Y N Y treatment
naive CGPLH56 Healthy cfDNA Preoperative 42 F NA NA NA NA NA NA 4.0
5.20 5.20 Y N Y treatment naive CGPLH57 Healthy cfDNA Preoperative
39 F NA NA NA NA NA NA 4.0 7.15 7.15 Y N Y treatment naive CGPLH59
Healthy cfDNA Preoperative 34 F NA NA NA NA NA NA 4.0 6.03 6.03 Y N
Y treatment naive CGPLH625 Healthy cfDNA Preoperative 53 F NA NA NA
NA NA NA 4.5 2.64 2.64 Y N N treatment naive CGPLH625 Healthy cfDNA
Preoperative 53 F NA NA NA NA NA NA 4.5 1.69 1.69 Y N N treatment
naive CGPLH626 Healthy cfDNA, Preoperative 50 F NA NA NA NA NA NA
4.0 11.12 11.12 Y N N technical treatment naive replicate CGPLH63
Healthy cfDNA Preoperative 47 F NA NA NA NA NA NA 4.0 10.10 10.10 Y
N Y treatment naive CGPLH639 Healthy cfDNA Preoperative 50 F NA NA
NA NA NA NA 4.5 2.00 2.00 Y N N treatment naive CGPLH64 Healthy
cfDNA Preoperative 55 F NA NA NA NA NA NA 4.0 8.03 8.03 Y N Y
treatment naive CGPLH640 Healthy cfDNA Preoperative 50 F NA NA NA
NA NA NA 4.5 9.36 9.36 Y N N treatment naive CGPLH642 Healthy cfDNA
Preoperative 54 F NA NA NA NA NA NA 4.5 4.99 4.99 Y N N treatment
naive CGPLH643 Healthy cfDNA Preoperative 55 F NA NA NA NA NA NA
4.4 7.12 7.12 Y N N treatment naive CGPLH644 Healthy cfDNA
Preoperative 50 F NA NA NA NA NA NA 4.4 5.06 5.06 Y N N treatment
naive CGPLH646 Healthy cfDNA Preoperative 50 F NA NA NA NA NA NA
4.4 6.75 6.75 Y N N treatment naive CGPLH75 Healthy cfDNA
Preoperative 46 F NA NA NA NA NA NA 4.0 3.87 3.87 Y N Y treatment
naive CGPLH76 Healthy cfDNA Preoperative 53 F NA NA NA NA NA NA 4.0
4.03 4.03 Y N Y treatment naive CGPLH77 Healthy cfDNA Preoperative
46 F NA NA NA NA NA NA 4.0 5.89 5.89 Y N Y treatment naive CGPLH78
Healthy cfDNA Preoperative 34 F NA NA NA NA NA NA 4.0 2.51 2.51 Y N
Y treatment naive CGPLH79 Healthy cfDNA Preoperative 37 F NA NA NA
NA NA NA 4.0 3.68 3.68 Y N Y treatment naive CGPLH80 Healthy cfDNA
Preoperative 37 F NA NA NA NA NA NA 4.0 1.94 1.94 Y N Y treatment
naive CGPLH81 Healthy cfDNA Preoperative 54 F NA NA NA NA NA NA 4.0
5.16 5.16 Y N Y treatment naive CGPLH82 Healthy cfDNA Preoperative
38 F NA NA NA NA NA NA 4.0 3.30 3.30 Y N Y treatment naive CGPLH83
Healthy cfDNA Preoperative 60 F NA NA NA NA NA NA 4.0 5.04 5.04 Y N
Y treatment naive CGPLH84 Healthy cfDNA Preoperative 45 F NA NA NA
NA NA NA 4.0 3.33 3.33 Y N Y treatment naive CGPLLU13 Lung cfDNA
Pre-treatment, 72 F IV T1BN2bM1a Right Adenocarcinoma NA Bone 5.0
7.67 7.67 Y N Y Cancer Day 2 Lung CGPLLU13 Lung cfDNA
Post-treatment, 72 F IV T1BN2bM1a Right Adenocarcinoma NA Bone 4.5
8.39 8.39 Y N Y Cancer Day 5 Lung CGPLLU13 Lung cfDNA
Post-treatment, 72 F IV T1BN2bM1a Right Adenocarcinoma NA Bone 3.2
8.66 8.66 Y N Y Cancer Day 28 Lung CGPLLU13 Lung cfDNA
Post-treatment, 72 F IV T1BN2bM1a Right Adenocarcinoma NA Bone 5.0
5.97 5.97 Y N Y Cancer Day 91 Lung CGPLLU14 Lung cfDNA
Pre-treatment, 55 F IV T1N1M0 Right Lower Adenocarcinoma Moderate
NA 2.0 2.55 2.55 Y N Y Cancer Day -38 Lobe of Lung CGPLLU14 Lung
cfDNA Pre-treatment, 55 F IV T1N1M0 Right Lower Adenocarcinoma
Moderate NA 2.0 2.55 2.55 Y N Y Cancer Day -16 Lobe of Lung
CGPLLU14 Lung cfDNA Pre-treatment, 55 F IV T1N1M0 Right Lower
Adenocarcinoma Moderate NA 2.0 2.55 2.55 Y N Y Cancer Day -8 Lobe
of Lung CGPLLU14 Lung cfDNA Pre-treatment, 55 F IV T1N1M0 Right
Lower Adenocarcinoma Moderate NA 2.0 2.55 2.55 Y N Y Cancer Day 0
Lobe of Lung CGPLLU14 Lung cfDNA Post-treatment, 55 F IV T1N1M0
Right Lower Adenocarcinoma Moderate NA 2.0 2.55 2.55 Y N Y Cancer
Day 0.33 Lobe of Lung CGPLLU14 Lung cfDNA Post-treatment, 55 F IV
T1N1M0 Right Lower Adenocarcinoma Moderate NA 2.0 2.55 2.55 Y N Y
Cancer Day 7 Lobe of Lung CGPLLU144 Lung cfDNA Preoperative 52 M II
T2aN1M0 Lung Adenocarcinoma Poor None 3.5 31.51 31.51 Y Y Y Cancer
treatment naive CGPLLU147 Lung cfDNA Preoperative 60 M III T3N2M0
Lung Adenosquamous Poor None 3.8 6.72 6.72 Y Y Y Cancer treatment
naive Carcinoma CGPLLU151 Lung cfDNA Preoperative 41 F II T3N2M0
Lung Adenocarcinoma Well None 4.0 83.04 83.04 Y N Y Cancer
treatment naive CGPLLU162 Lung cfDNA Preoperative 38 M II T1N1M0
Right Adenocarcinoma Moderate None 3.1 40.32 40.32 Y Y Y Cancer
treatment naive Lung CGPLLU163 Lung cfDNA Preoperative 66 M II
T1N1M0 Left Adenocarcinoma Poor None 5.0 54.03 54.03 Y Y Y Cancer
treatment naive Lung CGPLLU165 Lung cfDNA Preoperative 68 F II
T1N1M0 Right Adenocarcinoma Well None 4.5 20.13 20.13 Y Y Y Cancer
treatment naive Lung CGPLLU168 Lung cfDNA Preoperative 70 F I
T2aN0M0 Lung Adenocarcinoma Poor None 4.3 19.38 19.38 Y Y Y Cancer
treatment naive CGPLLU169 Lung cfDNA Preoperative 64 M I T1bN0M0
Lung Squamous Cel Moderate None 4.2 13.70 13.70 Y N Y Cancer
treatment naive Carcinoma CGPLLU175 Lung cfDNA Preoperative 47 M I
T2N0M0 Lung Squamous Cel Moderate None 4.4 16.84 16.84 Y Y Y Cancer
treatment naive Carcinoma CGPLLU176 Lung cfDNA Preoperative 58 M I
T2N0M0 Lung Adenosquamous Moderate None 3.2 7.86 7.86 Y Y Y Cancer
treatment naive Carcinoma CGPLLU177 Lung cfDNA Preoperative 45 M II
T3N0M0 Right Adenocarcinoma NA None 3.9 19.07 19.07 Y Y Y Cancer
treatment naive Lung CGPLLU180 Lung cfDNA Preoperative 57 M I
T2N0M0 Right Large Cel Poor None 3.2 19.31 19.31 Y Y Y Cancer
treatment naive Lung Carcinoma CGPLLU198 Lung cfDNA Preoperative 49
F I T2N0M0 Left Adenocarcinoma Moderate None 4.2 14.09 14.09 Y Y Y
Cancer treatment naive Lung CGPLLU202 Lung cfDNA Preoperative 68 M
I T2aN0M0 Right Adenocarcinoma NA None 4.4 24.72 24.72 Y Y Y Cancer
treatment naive Lung CGPLLU203 Lung cfDNA Preoperative 68 M II
T3N0M0 Right Squamous Cel Well None 4.2 26.24 26.24 Y N Y Cancer
treatment naive Lung Carcinoma CGPLLU205 Lung cfDNA Preoperative 65
M II T3N0M0 Left Adenocarcinoma Poor None 4.0 18.56 18.56 Y Y Y
Cancer treatment naive Lung CGPLLU206 Lung cfDNA Preoperative 55 M
III T3N1M0 Right Squamous Cel Poor None 3.5 18.24 18.24 Y Y Y
Cancer treatment naive Lung Carcinoma CGPLLU207 Lung cfDNA
Preoperative 60 F II T2N1M0 Lung Adenocarcinoma Well None 4.0 17.29
17.29 Y Y Y Cancer treatment naive CGPLLU208 Lung cfDNA
Preoperative 56 F II T2N1M0 Lung Adenocarcinoma
Moderate None 3.0 24.34 24.34 Y Y Y Cancer treatment naive
CGPLLU209 Lung cfDNA Preoperative 65 M II T2aN0M0 Lung Large Cel
Poor None 5.5 53.95 53.95 Y Y Y Cancer treatment naive Carcinoma
CGPLLU244 Lung cfDNA Pre-treatment, 66 F IV NA Right Upper
Adenocarcinoma Moderate/ Liver, Rib, 4.5 17.84 17.84 Y N Y Cancer
Day -7 Lobe of Lung Poor Brain, Pleura CGPLLU244 Lung cfDNA
Pre-treatment, 66 F IV NA Right Upper Adenocarcinoma Moderate/
Liver, Rib, 4.5 17.84 17.84 Y N Y Cancer Day -1 Lobe of Lung Poor
Brain, Pleura CGPLLU244 Lung cfDNA Post-treatment, 66 F IV NA Right
Upper Adenocarcinoma Moderate/ Liver, Rib, 4.5 17.84 17.84 Y N Y
Cancer Day 6 Lobe of Lung Poor Brain, Pleura CGPLLU244 Lung cfDNA
Post-treatment, 66 F IV NA Right Upper Adenocarcinoma Moderate/
Liver, Rib, 4.5 17.84 17.84 Y N Y Cancer Day 62 Lobe of Lung Poor
Brain, Pleura CGPLLU245 Lung cfDNA Pre-treatment, 49 M IV T2aN2M1B
Left Upper Adenocarcinoma NA Brain 4.7 19.42 19.42 Y N Y Cancer Day
32 Lobe of Lung CGPLLU245 Lung cfDNA Pre-treatment, 49 M IV
T2aN2M1B Left Upper Adenocarcinoma NA Brain 4.7 19.42 19.42 Y N Y
Cancer Day 0 Lobe of Lung CGPLLU245 Lung cfDNA Post-treatment, 49 M
IV T2aN2M1B Left Upper Adenocarcinoma NA Brain 4.7 19.42 19.42 Y N
Y Cancer Day 7 Lobe of Lung CGPLLU245 Lung cfDNA Post-treatment, 49
M IV T2aN2M1B Left Upper Adenocarcinoma NA Brain 4.7 19.42 19.42 Y
N Y Cancer Day 21 Lobe of Lung CGPLLU246 Lung cfDNA Pre-treatment,
65 F IV NA Right Lower Adenocarcinoma Poor Peura 5.5 18.51 18.51 Y
N Y Cancer Day -21 Lobe of Lung CGPLLU246 Lung cfDNA Pre-treatment,
65 F IV NA Right Lower Adenocarcinoma Poor Peura 5.5 18.51 18.51 Y
N Y Cancer Day 0 Lobe of Lung CGPLLU246 Lung cfDNA Post-treatment,
65 F IV NA Right Lower Adenocarcinoma Poor Peura 5.5 18.51 18.51 Y
N Y Cancer Day 9 Lobe of Lung CGPLLU246 Lung cfDNA Post-treatment,
65 F IV NA Right Lower Adenocarcinoma Poor Peura 5.5 18.51 18.51 Y
N Y Cancer Day 42 Lobe of Lung CGPLLU264 Lung cfDNA Pre-treatment,
84 M IV T4N2BM1 Left Adenocarcinoma NA Lung 4.0 22.97 22.97 Y N Y
Cancer Day -1 Middle Lung CGPLLU264 Lung cfDNA Post-treatment, 84 M
IV T4N2BM1 Left Adenocarcinoma NA Lung 4.5 10.53 10.53 Y N Y Cancer
Day 8 Middle Lung CGPLLU264 Lung cfDNA Post-treatment, 84 M IV
T4N2BM1 Left Adenocarcinoma NA Lung 3.0 7.15 7.15 Y N Y Cancer Day
27 Middle Lung CGPLLU264 Lung cfDNA Post-treatment, 84 M IV T4N2BM1
Left Adenocarcinoma NA Lung 4.0 9.60 9.60 Y N Y Cancer Day 69
Middle Lung CGPLLU265 Lung cfDNA Pre-treatment, 71 F IV T1N0Mx Left
Lower Adenocarcinoma NA None 4.2 7.16 7.16 Y N Y Cancer Day 0 Lobe
of Lung CGPLLU265 Lung cfDNA Post-treatment, 71 F IV T1N0Mx Left
Lower Adenocarcinoma NA None 4.0 8.11 8.11 Y N Y Cancer Day 3 Lobe
of Lung CGPLLU265 Lung cfDNA Post-treatment, 71 F IV T1N0Mx Left
Lower Adenocarcinoma NA None 4.2 7.53 7.53 Y N Y Cancer Day 7 Lobe
of Lung CGPLLU265 Lung cfDNA Post-treatment, 71 F IV T1N0Mx Left
Lower Adenocarcinoma NA None 5.0 16.17 16.17 Y N Y Cancer Day 84
Lobe of Lung CGPLLU266 Lung cfDNA Pre-treatment, 78 M IV T2aN1 Left
Lower Adenocarcinoma Moderate None 5.0 5.32 5.32 Y N Y Cancer Day 0
Lobe of Lung CGPLLU266 Lung cfDNA Post-treatment, 78 M IV T2aN1
Left Lower Adenocarcinoma Moderate None 3.5 6.31 6.31 Y N Y Cancer
Day 16 Lobe of Lung CGPLLU266 Lung cfDNA Post-treatment, 78 M IV
T2aN1 Left Lower Adenocarcinoma Moderate None 5.0 7.64 7.64 Y N Y
Cancer Day 83 Lobe of Lung CGPLLU266 Lung cfDNA Post-treatment, 78
M IV T2aN1 Left Lower Adenocarcinoma Moderate None 5.0 14.39 14.39
Y N Y Cancer Day 328 Lobe of Lung CGPLLU267 Lung cfDNA
Pre-treatment, 55 F IV T3NxM1a Right Upper Squamous Cel Poor Lung
4.5 2.87 2.87 Y N Y Cancer Day -1 Lobe of Lung Carcinoma CGPLLU267
Lung cfDNA Post-treatment, 55 F IV T3NxM1a Right Upper Squamous Cel
Poor Lung 4.5 3.34 3.34 Y N Y Cancer Day 34 Lobe of Lung Carcinoma
CGPLLU267 Lung cfDNA Post-treatment, 55 F IV T3NxM1a Right Upper
Squamous Cel Poor Lung 3.5 3.00 3.00 Y N Y Cancer Day 90 Lobe of
Lung Carcinoma CGPLLU269 Lung cfDNA Pre-treatment, 52 F IV T1CNxM1C
Right Adenocarcinoma NA Brain, Liver, 5.0 11.40 11.40 Y N Y Cancer
Day 0 Paratracheal Bone, Peura Lesion CGPLLU269 Lung cfDNA
Post-treatment, 52 F IV T1CNxM1C Right Adenocarcinoma NA Brain,
Liver, 5.0 8.35 8.35 Y N Y Cancer Day 9 Paratracheal Bone, Peura
Lesion CGPLLU269 Lung cfDNA Post-treatment, 52 F IV T1CNxM1C Right
Adenocarcinoma NA Brain, Liver, 3.5 17.79 17.79 Y N Y Cancer Day 28
Paratracheal Bone, Peura Lesion CGPLLU271 Lung cfDNA
Post-treatment, 73 M IV T1aNxM1 Left Upper Adenocarcinoma Moderate
Peura 4.0 4.70 4.70 Y N Y Cancer Day 259 Lobe of Lung CGPLLU271
Lung cfDNA Pre-treatment, 73 M IV T1aNxM1 Left Upper Adenocarcinoma
Moderate Peura 5.0 18.86 18.86 Y N Y Cancer Day 0 Lobe of Lung
CGPLLU271 Lung cfDNA Post-treatment, 73 M IV T1aNxM1 Left Upper
Adenocarcinoma Moderate Peura 4.5 13.84 13.84 Y N Y Cancer Day 8
Lobe of Lung CGPLLU271 Lung cfDNA Post-treatment, 73 M IV T1aNxM1
Left Upper Adenocarcinoma Moderate Peura 3.5 13.46 13.46 Y N Y
Cancer Day 20 Lobe of Lung CGPLLU271 Lung cfDNA Post-treatment, 73
M IV T1aNxM1 Left Upper Adenocarcinoma Moderate Peura 4.0 13.77
13.77 Y N Y Cancer Day 104 Lobe of Lung CGPLLU43 Lung cfDNA
Pre-treatment, 57 F IV T1BN0M0 Right Lower Adenocarcinoma Moderate
None 4.9 2.17 2.17 Y N Y Cancer Day -1 Lobe of Lung CGPLLU43 Lung
cfDNA Post-treatment, 57 F IV T1BN0M0 Right Lower Adenocarcinoma
Moderate None 3.7 3.26 3.26 Y N Y Cancer Day 6 Lobe of Lung
CGPLLU43 Lung cfDNA Post-treatment, 57 F IV T1BN0M0 Right Lower
Adenocarcinoma Moderate None 4.0 4.12 4.12 Y N Y Cancer Day 27 Lobe
of Lung CGPLLU43 Lung cfDNA Post-treatment, 57 F IV T1BN0M0 Right
Lower Adenocarcinoma Moderate None 3.7 8.20 8.20 Y N Y Cancer Day
83 Lobe of Lung CGPLLU86 Lung cfDNA Pre-treatment, 55 M IV NA Left
Upper Adenocarcinoma NA Lung 4.0 7.90 7.90 Y N Y Cancer Day 0 Lobe
of Lung CGPLLU86 Lung cfDNA Post-treatment, 55 M IV NA Left Upper
Adenocarcinoma NA Lung 4.0 7.90 7.90 Y N Y Cancer Day 0.5 Lobe of
Lung CGPLLU86 Lung cfDNA Post-treatment, 55 M IV NA Left Upper
Adenocarcinoma NA Lung 4.0 7.90 7.90 Y N Y Cancer Day 7 Lobe of
Lung CGPLLU86 Lung cfDNA Post-treatment, 55 M IV NA Left Upper
Adenocarcinoma NA Lung 4.0 7.90 7.90 Y N Y Cancer Day 17 Lobe of
Lung CGPLLU88 Lung cfDNA Pre-treatment, 59 M IV NA Right
Adenocarcinoma NA None 5.0 27.66 27.66 Y N Y Cancer Day 0 Middle
Lobe of Lung CGPLLU88 Lung cfDNA Post-treatment, 59 M IV NA Right
Adenocarcinoma NA None 5.0 6.49 6.49 Y N Y Cancer Day 7 Middle Lobe
of Lung CGPLLU88 Lung cfDNA Post-treatment, 59 M IV NA Right
Adenocarcinoma NA None 4.0 3.04 3.04 Y N Y Cancer Day 297 Middle
Lobe of Lung CGPLLU89 Lung cfDNA Pre-treatment, 54 F IV NA Right
Upper Adenocarcinoma NA Brain, 8.0 8.43 8.43 Y N Y Cancer Day 0
Lobe of Lung Bone, Lung CGPLLU89 Lung cfDNA Post-treatment, 54 F IV
NA Right Upper Adenocarcinoma NA Brain, 8.0 8.43 8.43 Y N Y Cancer
Day 7 Lobe of Lung Bone, Lung CGPLLU89 Lung cfDNA Post-treatment,
54 F IV NA Right Upper Adenocarcinoma NA Brain, 8.0 8.43 8.43 Y N Y
Cancer Day 22 Lobe of Lung Bone, Lung CGPLOV11 Ovarian cfDNA
Preoperative 51 F IV T3cN0M1 Right Endometrioid Moderate Omentum
3.4 17.35 17.35 Y Y Y Cancer treatment naive Ovary Adenocarcinoma
CGPLOV12 Ovarian cfDNA Preoperative 45 F I T1aN0MX Ovary
Endometrioid NA None 3.2 12.44 12.44 Y N Y Cancer treatment naive
Adenocarcinoma CGPLOV13 Ovarian cfDNA Preoperative 62 F IV T1bN0M1
Right Endometrioid Poor Omentum 3.8 27.00 27.00 Y Y Y Cancer
treatment naive Ovary Adenocarcinoma CGPLOV15 Ovarian cfDNA
Preoperative 54 F III T3N1M0 Ovary Adenocarcinoma Poor None 5.0
4.77 4.77 Y Y Y Cancer treatment naive CGPLOV16 Ovarian cfDNA
Preoperative 40 F III T3aN0M0 Ovary Serous Moderate None 4.5 27.28
27.28 Y N Y Cancer treatment naive Adenocarcinoma CGPLOV19 Ovarian
cfDNA Preoperative 52 F II T2aN0M0 Ovary Endometrioid Moderate None
5.0 23.46 23.46 Y Y Y Cancer treatment naive Adenocarcinoma
CGPLOV20 Ovarian cfDNA Preoperative 52 F II T2aN0M0 Left
Endometrioid Poor None 4.2 5.67 5.67 Y Y Y Cancer treatment naive
Ovary Adenocarcinoma CGPLOV21 Ovarian cfDNA Preoperative 51 F IV
TanyN1M1 Ovary Serous Poor Omentum, 4.3 56.32 56.32 Y Y Y Cancer
treatment naive Adenocarcinoma Appendix CGPLOV22 Ovarian cfDNA
Preoperative 64 F III T1cNXMX Left Serous Well None 4.6 17.42 17.42
Y Y Y Cancer treatment naive Ovary Adenocarcinoma CGPLOV23 Ovarian
cfDNA Preoperative 47 F I T1aN0M0 Ovary Serous Poor None 5.0 26.73
26.73 Y N Y Cancer treatment naive Adenocarcinoma CGPLOV24 Ovarian
cfDNA Preoperative 14 F I T1aN0M0 Ovary Germ Cell Poor None 4.2
10.71 10.71 Y N Y Cancer treatment naive Tumor CGPLOV25 Ovarian
cfDNA Preoperative 18 F I T1aN0M0 Ovary Germ Cell Poor None 4.8
6.78 6.78 Y N Y Cancer treatment naive Tumor CGPLOV26 Ovarian cfDNA
Preoperative 35 F I T1aN0M0 Ovary Germ Cell Poor None 4.5 27.90
27.90 Y N Y Cancer treatment naive Tumor CGPLOV28 Ovarian cfDNA
Preoperative 63 F I T1aN0M0 Right Serous NA None 3.2 10.74 10.74 Y
N Y Cancer treatment naive Ovary Carcinoma CGPLOV31 Ovarian cfDNA
Preoperative 45 F III T3aNxM0 Right Clear Cell NA None 4.0 14.45
14.45 Y N Y Cancer treatment naive Ovary adenocarcinoma CGPLOV32
Ovarian cfDNA Preoperative 53 F I T1aNxM0 Left Mucinous NA None 3.2
27.36 27.36 Y N Y Cancer treatment naive Ovary Cystadenoma CGPLOV37
Ovarian cfDNA Preoperative 40 F I T1cN0M0 Ovary Serous NA None 3.2
46.88 46.88 Y N Y Cancer treatment naive Carcinoma CGPLOV38 Ovarian
cfDNA Preoperative 46 F I T1cN0M0 Ovary Serous NA None 2.4 34.29
34.29 Y N Y Cancer treatment naive Carcinoma CGPLOV40 Ovarian cfDNA
Preoperative 53 F IV T3N0M1 Ovary Serous NA Omentum, 1.6 193.60
156.25 Y N Y Cancer treatment naive Carcinoma Uterus, Appendix
CGPLOV41 Ovarian cfDNA Preoperative 57 F IV T3N0M1 Ovary Serous NA
Omentum, 4.4 10.03 10.03 Y N Y Cancer treatment naive Carcinoma
Uterus, Cervix CGPLOV42 Ovarian cfDNA Preoperative 52 F I T3aN0M0
Ovary Serous NA None 4.2 49.51 49.51 Y N Y Cancer treatment naive
Carcinoma CGPLOV43 Ovarian cfDNA Preoperative 30 F I T1aN0M0 Ovary
Mucinous NA None 4.4 9.09 9.09 Y N Y Cancer treatment naive Cyst-
adenocarcinoma CGPLOV44 Ovarian cfDNA Preoperative 69 F I T1aN0M0
Ovary Mucinous NA None 4.5 8.79 8.79 Y N Y Cancer treatment naive
Adenocarcinoma CGPLOV46 Ovarian cfDNA Preoperative 58 F I T1bN0M0
Ovary Serous NA None 4.1 8.97 8.97 Y N Y Cancer treatment naive
Carcinoma CGPLOV47 Ovarian cfDNA Preoperative 41 F I T1aN0M0 Ovary
Serous NA None 4.5 19.35 19.35 Y N Y Cancer treatment naive
Adenocarcinoma CGPLOV48 Ovarian cfDNA Preoperative 52 F I T1bN0M0
Ovary Serous NA None 3.5 22.80 22.80 Y N Y Cancer treatment naive
Carcinoma CGPLOV49 Ovarian cfDNA Preoperative 68 F III T3bN0M0
Ovary Serous NA None 4.2 16.48 16.48 Y N Y Cancer treatment naive
Carcinoma CGPLOV50 Ovarian cfDNA Preoperative 30 F III T3cN0M0
Ovary Serous NA None 4.5 8.89 8.89 Y N Y Cancer treatment naive
Carcinoma CGPLPA112 Pancreatic cfDNA Preoperative 58 M II NA Intra
NA NA None 3.5 18.52 18.52 Y N N
Cancer treatment naive Pancreatic Bile Duct CGPLPA113 Duodenal
cfDNA Preoperative 71 M I NA Intra NA NA None 4.8 8.24 8.24 Y N N
Cancer treatment naive Pancreatic Bile Duct CGPLPA114 Bile Duct
cfDNA Preoperative NA F II NA Intra NA NA None 4.8 26.43 26.43 Y N
N Cancer treatment naive Pancreatic Bile Duct CGPLPA115 Bile Duct
cfDNA Preoperative NA M IV NA Intra NA NA NA 5.0 31.41 31.41 Y N N
Cancer treatment naive Hepatic Bile Duct CGPLPA117 Bile Duct cfDNA
Preoperative NA M II NA Intra NA NA NA 3.4 2.29 2.29 Y N N Cancer
treatment naive Pancreatic Bile Duct CGPLPA118 Bile Duct cfDNA
Preoperative 68 F I NA Bile Duct Intra- NA None 3.8 9.93 9.93 Y N Y
Cancer treatment naive Ampuliary Bile Duct CGPLPA122 Bile Duct
cfDNA Preoperative 62 F II NA Bile Duct Intra- NA None 3.8 66.54
32.89 Y N Y Cancer treatment naive Pancreatic Bile Duct CGPLPA124
Bile Duct cfDNA Preoperative 83 F II NA Bile Duct Intra- moderate
None 4.6 29.24 27.17 Y N Y Cancer treatment naive Ampuliary Bile
Duct CGPLPA125 Bile Duct cfDNA Preoperative 58 M II NA Bile Duct
Intra- poor None 2.7 8.31 8.31 Y N N Cancer treatment naive
Pancreatic Bile Duct CGPLPA126 Bile Duct cfDNA Preoperative 60 M II
NA Bile Duct Intra- NA None 4.2 80.56 29.07 Y N Y Cancer treatment
naive Pancreatic Bile Duct CGPLPA127 Bile Duct cfDNA Preoperative
71 F IV NA Bile Duct Extra- NA NA 3.0 20.60 20.60 Y N N Cancer
treatment naive Pancreatic Bile Duct CGPLPA128 Bile Duct cfDNA
Preoperative 67 M II NA Bile Duct Intra- NA None 3.9 5.91 5.91 Y N
Y Cancer treatment naive Pancreatic Bile Duct CGPLPA129 Bile Duct
cfDNA Preoperative 56 F II NA Bile Duct Intra- NA None 4.6 27.07
27.07 Y N Y Cancer treatment naive Pancreatic Bile Duct CGPLPA130
Bile Duct cfDNA Preoperative 82 F II NA Bile Duct Intra- well None
4.0 4.34 4.34 Y N Y Cancer treatment naive Ampuliary Bile Duct
CGPLPA131 Bile Duct cfDNA Preoperative 71 M II NA Bile Duct Intra-
NA None 3.9 68.95 32.05 Y N Y Cancer treatment naive Pancreatic
Bile Duct CGPLPA134 Bile Duct cfDNA Preoperative 68 M II NA Bile
Duct Intra- NA None 4.1 58.98 30.49 Y N Y Cancer treatment naive
Pancreatic Bile Duct CGPLPA135 Bile Duct cfDNA Preoperative 67 F I
NA Bile Duct Intra- NA NA 3.9 4.22 4.22 Y N N Cancer treatment
naive Pancreatic Bile Duct CGPLPA136 Bile Duct cfDNA Preoperative
69 F II NA Bile Duct Intra- NA None 4.1 20.23 20.23 Y N Y Cancer
treatment naive Pancreatic Bile Duct CGPLPA137 Bile Duct cfDNA
Preoperative NA M II NA Bile Duct NA NA NA 4.0 5.75 5.75 Y N N
Cancer treatment naive CGPLPA139 Bile Duct cfDNA Preoperative NA M
IV NA Bile Duct NA NA NA 4.0 14.89 14.89 Y N N Cancer treatment
naive CGPLPA14 Pancreatic cfDNA Preoperative 68 M II NA Pancreas
Ductal Poor None 4.0 1.30 1.30 Y N N Cancer treatment naive
Adenocarcinoma CGPLPA140 Bile Duct cfDNA Preoperative 52 M II NA
Extra- Intra- Poor None 4.7 29.34 26.60 Y N Y Cancer treatment
naive Hepatic Pancreatic Bile Duct Bile Duct CGPLPA141 Bile Duct
cfDNA Preoperative 68 F II NA Extra- Intra- Moderate None 2.8 53.67
44.64 Y N N Cancer treatment naive Hepatic Pancreatic Bile Duct
Bile Duct CGPLPA15 Pancreatic cfDNA Preoperative 70 F II NA
Pancreas Ductal Well Lymph 4.0 1.92 1.92 Y N N Cancer treatment
naive Adenocarcinoma Node CGPLPA155 Bile Duct cfDNA Preoperative NA
F II NA NA NA NA NA 4.0 25.72 25.72 Y N N Cancer treatment naive
CGPLPA156 Pancreatic cfDNA Preoperative 73 F II NA Pancreas Ductal
Poor Lymph 4.5 7.54 7.54 Y N N Cancer treatment naive
Adenocarcinoma Node CGPLPA165 Bile Duct cfDNA Preoperative 42 M I
NA Bile Duct Intra- well None 3.9 10.48 10.48 Y N N Cancer
treatment naive Pancreatic Bile Duct with Meduliary Features
CGPLPA168 Bile Duct cfDNA Preoperative 58 M II NA Bile Duct NA NA
NA 3.0 139.12 34.72 Y N N Cancer treatment naive CGPLPA17
Pancreatic cfDNA Preoperative 65 M II NA Pancreas Ductal Well Lymph
4.0 13.08 13.08 Y N N Cancer treatment naive Adenocarcinoma Node
CGPLPA184 Bile Duct cfDNA Preoperative 75 F II NA Bile Duct Intra-
NA None NA NA NA Y N N Cancer treatment naive Pancreatic Bile Duct
CGPLPA187 Bile Duct cfDNA Preoperative 67 F II NA Bile Duct Intra-
NA None NA NA NA Y N N Cancer treatment naive Pancreatic Bile Duct
CGPLPA23 Pancreatic cfDNA Preoperative 58 F II NA Pancreas Ductal
Moderate Lymph 4.0 16.62 16.62 Y N N Cancer treatment naive
Adenocarcinoma Node CGPLPA25 Pancreatic cfDNA Preoperative 69 F II
NA Pancreas Ductal Poor Lymph 4.0 8.71 8.71 Y N N Cancer treatment
naive Adenocarcinoma Node CGPLPA26 Pancreatic cfDNA Preoperative 64
M II NA Pancreas Ductal Well Lymph 4.0 6.97 6.97 Y N N Cancer
treatment naive Adenocarcinoma Node CGPLPA28 Pancreatic cfDNA
Preoperative 79 F II NA Pancreas Ductal Well Lymph 4.0 18.13 18.13
Y N N Cancer treatment naive Adenocarcinoma Node CGPLPA33
Pancreatic cfDNA Preoperative 67 F II NA Pancreas Ductal Well Lymph
4.0 1.80 1.80 Y N N Cancer treatment naive Adenocarcinoma Node
CGPLPA34 Pancreatic cfDNA Preoperative 73 M II NA Pancreas Ductal
Well Lymph 4.0 3.36 3.36 Y N N Cancer treatment naive
Adenocarcinoma Node CGPLPA37 Pancreatic cfDNA Preoperative 67 F II
NA Pancreas Ductal NA Lymph 4.0 21.83 21.83 Y N N Cancer treatment
naive Adenocarcinoma Node CGPLPA38 Pancreatic cfDNA Preoperative 65
M II NA Pancreas Ductal Moderate None 4.0 5.29 5.29 Y N N Cancer
treatment naive Adenocarcinoma CGPLPA39 Pancreatic cfDNA
Preoperative 67 F II NA Pancreas Ductal Well Lymph 4.0 11.73 11.73
Y N N Cancer treatment naive Adenocarcinoma Node CGPLPA40
Pancreatic cfDNA Preoperative 64 M II NA Pancreas Ductal Well Lymph
4.0 4.78 4.78 Y N N Cancer treatment naive Adenocarcinoma Node
CGPLPA42 Pancreatic cfDNA Preoperative 73 M II NA Pancreas Ductal
Moderate Lymph 4.0 3.41 3.41 Y N N Cancer treatment naive
Adenocarcinoma Node CGPLPA46 Pancreatic cfDNA Preoperative 59 F II
NA Pancreas Ductal Poor Lymph 4.0 0.74 0.74 Y N N Cancer treatment
naive Adenocarcinoma Node CGPLPA47 Pancreatic cfDNA Preoperative 67
M II NA Pancreas Ductal Well Lymph 4.0 6.01 6.01 Y N N Cancer
treatment naive Adenocarcinoma Node CGPLPA48 Pancreatic cfDNA
Preoperative 72 F II NA Pancreas Ductal Well None NA NA NA Y N N
Cancer treatment naive Adenocarcinoma CGPLPA52 Pancreatic cfDNA
Preoperative 63 M II NA Pancreas Ductal Moderate None 2.5 9.86 9.86
Y N N Cancer treatment naive Adenocarcinoma CGPLPA53 Pancreatic
cfDNA Preoperative 46 M I NA Pancreas Ductal Poor Lymph 3.0 14.48
14.48 Y N N Cancer treatment naive Adenocarcinoma Node CGPLPA58
Pancreatic cfDNA Preoperative 74 F II NA Pancreas Ductal NA None
3.0 6.87 6.87 Y N N Cancer treatment naive Adenocarcinoma CGPLPA59
Pancreatic cfDNA Preoperative 59 F II NA Pancreas Ductal Well Lymph
NA NA NA Y N N Cancer treatment naive Adenocarcinoma Node or
Adenoma CGPLPA67 Pancreatic cfDNA Preoperative 55 M III NA Pancreas
Ductal Well Lymph 3.2 9.72 9.72 Y N N Cancer treatment naive
Adenocarcinoma Node CGPLPA69 Pancreatic cfDNA Preoperative 70 M I
NA Pancreas Ductal Well None 2.0 1.72 1.72 Y N N Cancer treatment
naive Adenocarcinoma CGPLPA71 Pancreatic cfDNA Preoperative 64 M II
NA Pancreas Ductal Well Lymph 2.2 39.07 39.07 Y N N Cancer
treatment naive Adenocarcinoma Node CGPLPA74 Pancreatic cfDNA
Preoperative 71 F II NA Pancreas Ductal Moderate Lymph 2.5 4.99
4.99 Y N N Cancer treatment naive Adenocarcinoma Node CGPLPA76
Pancreatic cfDNA Preoperative 69 M II NA Pancreas Ductal Poor None
2.5 23.19 23.19 Y N N Cancer treatment naive Adenocarcinoma
CGPLPA85 Pancreatic cfDNA Preoperative 77 F II NA Pancreas Ductal
Poor Lymph 3.0 152.46 41.67 Y N N Cancer treatment naive
Adenocarcinoma Node CGPLPA86 Pancreatic cfDNA Preoperative 66 M II
NA Pancreas Ductal Moderate Lymph 2.5 11.92 11.92 Y N N Cancer
treatment naive Adenocarcinoma Node CGPLPA92 Pancreatic cfDNA
Preoperative 72 M II NA Pancreas Ductal NA Lymph 2.0 5.34 5.34 Y N
N Cancer treatment naive Adenocarcinoma Node CGPLPA93 Pancreatic
cfDNA Preoperative 48 M II NA Pancreas Ductal Poor None 3.0 96.28
41.67 Y N N Cancer treatment naive Adenocarcinoma CGPLPA94
Pancreatic cfDNA Preoperative 72 F II NA Pancreas Ductal NA Lymph
3.0 29.66 29.66 Y N N Cancer treatment naive Adenocarcinoma Node
CGPLPA95 Pancreatic cfDNA Preoperative 64 F II NA Pancreas Ductal
Well Lymph NA NA NA Y N N Cancer treatment naive Adenocarcinoma
Node CGST102 Gastric cfDNA Preoperative 76 F II T3N0M0 Stomach
Tubular Moderate None 4.1 8.03 8.03 Y N Y Cancer treatment naive
Adenocarcinoma CGST11 Gastric cfDNA Preoperative 49 M IV TXNXM1
Stomach Mixed Moderate None 3.8 3.57 3.57 Y N N Cancer treatment
naive Carcinoma CGST110 Gastric cfDNA Preoperative 77 M III
T4AN3aM0 Stomach Tubular Moderate None 3.8 5.00 5.00 Y N Y Cancer
treatment naive Adenocarcinoma CGST114 Gastric cfDNA Preoperative
65 M III T4N1M0 Stomach Tubular Poor None 4.4 10.35 10.35 Y N Y
Cancer treatment naive Adenocarcinoma CGST13 Gastric cfDNA
Preoperative 72 F II T1AN2M0 Stomach Signet Ring Poor None 4.4
24.33 24.33 Y N Y Cancer treatment naive Cell Carcinoma CGST131
Gastric cfDNA Preoperative 63 M III T2N3aM0 Stomach Signet ring
Poor None 4.0 4.28 4.28 Y N N Cancer treatment naive cell Carcinoma
CGST141 Gastric cfDNA Preoperative 33 F III T3N2M0 Stomach Signet
Ring Poor None 4.4 10.84 10.84 Y N Y Cancer treatment naive Cell
Carcinoma CGST16 Gastric cfDNA Preoperative 78 M III T4AN3aM0
Stomach Tubular Poor None 4.0 40.69 40.69 Y N Y Cancer treatment
naive Adenocarcinoma CGST18 Gastric cfDNA Preoperative 50 M II
T3N0M0 Stomach Mucinous Well None 4.3 9.78 9.78 Y N Y Cancer
treatment naive Adenocarcinoma CGST21 Gastric cfDNA Preoperative 39
M II T2N1(mi)M0 Stomach Papillary Moderate None 4.0 0.83 0.83 Y N N
Cancer treatment naive Adenocarcinoma CGST26 Gastric cfDNA
Preoperative 51 M IV TXNXM1 Stomach Signet ring Poor None 3.5 5.56
5.56 Y N N Cancer treatment naive cell Carcinoma CGST28 Gastric
cfDNA Preoperative 55 M X TXNXMX Stomach Undifferentiated Poor None
4.0 5.86 5.86 Y N Y Cancer treatment naive Carcinoma CGST30 Gastric
cfDNA Preoperative 64 F III T3N2M0 Stomach Signet Ring Poor None
3.0 4.22 4.22 Y N Y Cancer treatment naive Cell Carcinoma CGST32
Gastric cfDNA Preoperative 67 M II T3N1M0 Stomach Tubular Moderate
None 4.0 11.49 11.49 Y N Y Cancer treatment naive Adenocarcinoma
CGST33 Gastric cfDNA Preoperative 61 M I T2N0M0 Stomach Tubular
Moderate None 3.5 5.71 5.71 Y N Y Cancer treatment naive
Adenocarcinoma CGST38 Gastric cfDNA Preoperative 71 F 0 T0N0M0
Stomach Mucinous NA None 4.0 NA NA Y N N
Cancer treatment naive Adenocarcinoma CGST39 Gastric cfDNA
Preoperative 51 M IV TXNXM1 Stomach Signet Ring Poor None 3.5 20.69
20.69 Y N Y Cancer treatment naive Cell Carcinoma CGST41 Gastric
cfDNA Preoperative 66 F IV TXNXM1 Stomach Signet Ring Poor None 3.5
7.83 7.83 Y N Y Cancer treatment naive Cell Carcinoma CGST45
Gastric cfDNA Preoperative 41 F II T3N0M0 Stomach Signet Ring Poor
None 3.8 7.14 7.14 Y N Y Cancer treatment naive Cell Carcinoma
CGST47 Gastric cfDNA Preoperative 74 F I T1AN0M0 Stomach Tubular
Moderate None 4.0 4.55 4.55 Y N Y Cancer treatment naive
Adenocarcinoma CGST48 Gastric cfDNA Preoperative 62 M IV TXNXM1
Stomach Tubular Poor None 4.5 8.79 8.79 Y N Y Cancer treatment
naive Adenocarcinoma CGST53 Gastric cfDNA Preoperative 70 M 0
T0N0M0 Stomach NA NA None 3.8 15.82 15.82 Y N N Cancer treatment
naive CGST58 Gastric cfDNA Preoperative 58 M III T4AN3bM0 Stomach
Signet Ring Poor None 3.8 19.81 19.81 Y N Y Cancer treatment naive
Cell Carcinoma CGST67 Gastric cfDNA Preoperative 69 M I T1RN0M0
Stomach Tubular Moderate None 3.0 23.01 23.01 Y N N Cancer
treatment naive adenocarcinoma CGST77 Gastric cfDNA Preoperative 70
M IV TXNXM1 Stomach Tubular Moderate None 4.5 15.09 15.09 Y N N
Cancer treatment naive adenocarcinoma CGST80 Gastric cfDNA
Preoperative 58 M III T3N3aM0 Stomach Mucinous Poor None 4.5 8.56
8.56 Y N Y Cancer treatment naive Adenocarcinoma CGST81 Gastric
cfDNA Preoperative 64 F I T2N0M1 Stomach Signet Ring Poor None 3.5
37.32 37.32 Y N Y Cancer treatment naive Cell Carcinoma CGH14
Healthy Human NA NA M NA NA NA NA NA NA NA NA NA Y N N Adult
elutriated lymphoc CGH15 Healthy Human NA NA F NA NA NA NA NA NA NA
NA NA Y N N Adult elutriated lymphoc *NA denotes data not available
or not applicable for healthy individuals.
TABLE-US-00004 APPENDIX B Table 2 Summary of targeted cfDNA
analyses Fragment Profile Mutation Bases in Bases Mapped to Bases
Mapped to Percent Mapped to Total Distinct Patient Patient Type
Timepoint Analysis Analysis Read Length Target Region Genome Target
Regions Target Regions Coverage Coverage CGCRC291 Colorectal Cancer
Preoperative, Treatment naive Y Y 100 80930 7501485600 3771359756
50% 44345 10359 CGCRC292 Colorectal Cancer Preoperative, Treatment
naive Y Y 100 80930 6736035200 3098886973 46% 36448 8603 CGCRC293
Colorectal Cancer Preoperative, Treatment naive Y Y 100 80930
6300244000 2818734206 45% 33117 5953 CGCRC294 Colorectal Cancer
Preoperative, Treatment naive Y Y 100 80930 7766872600 3911796709
50% 46016 12071 CGCRC295 Colorectal Cancer Preoperative, Treatment
naive Y N 100 80930 8240660200 3478059753 42% 40787 5826 CGCRC296
Colorectal Cancer Preoperative, Treatment naive Y Y 100 80930
5718556500 2898549356 51% 33912 10180 CGCRC291 Colorectal Cancer
Preoperative, Treatment naive Y N 100 80930 7550826100 3717222432
49% 43545 5870 CGCRC298 Colorectal Cancer Preoperative, Treatment
naive Y N 100 80930 12501036400 6096393764 49% 71196 9617 CGCRC299
Colorectal Cancer Preoperative, Treatment naive Y Y 100 80930
7812602900 4121569690 53% 48098 10338 CGCRC300 Colorectal Cancer
Preoperative, Treatment naive Y Y 100 80930 8648090300 3962285136
46% 46364 5756 CGCRC301 Colorectal Cancer Preoperative, Treatment
naive Y Y 100 80930 7538758100 3695480348 49% 43024 6618 CGCRC302
Colorectal Cancer Preoperative, Treatment naive Y Y 100 80930
8573658300 4349420574 51% 51006 13799 CGCRC303 Colorectal Cancer
Preoperative, Treatment naive Y Y 100 80930 5224046400 2505714343
48% 29365 8372 CGCRC304 Colorectal Cancer Preoperative, Treatment
naive Y Y 100 80930 5762112600 2942170530 51% 34462 10208 CGCRC305
Colorectal Cancer Preoperative, Treatment naive Y Y 100 80930
7213384100 3726953480 52% 43516 8589 CGCRC306 Colorectal Cancer
Preoperative, Treatment naive Y Y 100 80930 7075579700 3552441899
50% 41507 7372 CGCRC307 Colorectal Cancer Preoperative, Treatment
naive Y Y 100 80930 7572687100 3492191519 46% 40793 9680 CGCRC308
Colorectal Cancer Preoperative, Treatment naive Y Y 100 80930
7945738000 3895908986 49% 45224 11809 CGCRC309 Colorectal Cancer
Preoperative, Treatment naive Y Y 100 80930 8487455800 3921079811
46% 45736 10739 CGCRC310 Colorectal Cancer Preoperative, Treatment
naive Y Y 100 80930 9003580500 4678812441 52% 54713 11139 CGCRC311
Colorectal Cancer Preoperative, Treatment naive Y Y 100 80930
6528162700 3276653864 50% 38324 6044 CGCRC312 Colorectal Cancer
Preoperative, Treatment naive Y N 100 80930 7683294300 3316719187
43% 38652 4622 CGCRC313 Colorectal Cancer Preoperative, Treatment
naive Y N 100 80930 5874099200 2896148722 49% 33821 6506 CGCRC314
Colorectal Cancer Preoperative, Treatment naive Y N 100 80930
6883148500 3382767492 49% 39414 6664 CGCRC315 Colorectal Cancer
Preoperative, Treatment naive Y Y 100 80930 7497252500 3775556051
50% 44034 8666 CGCRC316 Colorectal Cancer Preoperative, Treatment
naive Y Y 100 80930 10684720400 5533857153 52% 64693 14289 CGCRC317
Colorectal Cancer Preoperative, Treatment naive Y Y 100 80930
7086877600 3669434216 52% 43538 10944 CGCRC318 Colorectal Cancer
Preoperative, Treatment naive Y Y 100 80930 6880041100 3326357413
48% 39077 11571 CGCRC319 Colorectal Cancer Preoperative, Treatment
naive N Y 100 80930 7485342900 3982677483 53% 47327 10502 CGCRC320
Colorectal Cancer Preoperative, Treatment naive Y Y 100 80930
7058703200 3450648135 49% 40888 10198 CGCRC321 Colorectal Cancer
Preoperative, Treatment naive Y Y 100 80930 7203625900 3633396892
50% 43065 6499 CGCRC332 Colorectal Cancer Preoperative, Treatment
naive Y N 100 80930 7202969100 3758323705 52% 44580 3243 CGCRC333
Colorectal Cancer Preoperative, Treatment naive Y Y 100 80930
8767144700 4199126827 48% 49781 8336 CGCRC334 Colorectal Cancer
Preoperative, Treatment naive Y N 100 80930 7771869100 3944518280
51% 46518 5014 CGCRC335 Colorectal Cancer Preoperative, Treatment
naive Y N 100 80930 7972524600 4064901201 51% 48308 6151 CGCRC336
Colorectal Cancer Preoperative, Treatment naive Y Y 100 80930
8597346400 4333410573 50% 51390 7551 CGCRC337 Colorectal Cancer
Preoperative, Treatment naive Y N 100 80930 7399611700 3800666199
51% 45083 8092 CGCRC338 Colorectal Cancer Preoperative, Treatment
naive Y Y 100 80930 8029493700 4179383804 52% 49380 5831 CGCRC339
Colorectal Cancer Preoperative, Treatment naive Y N 100 80930
7938963500 4095555110 52% 48397 3808 CGCRC340 Colorectal Cancer
Preoperative, Treatment naive Y N 100 80930 7214889500 3706643098
51% 43805 3014 CGCRC341 Colorectal Cancer Preoperative, Treatment
naive N Y 100 80930 8803159200 3668208527 42% 43106 11957 CGCRC342
Colorectal Cancer Preoperative, Treatment naive N Y 100 80930
8478811500 3425540889 40% 40328 9592 CGCRC344 Colorectal Cancer
Preoperative, Treatment naive N Y 100 80930 6942167800 3098232737
45% 36823 2300 CGCRC345 Colorectal Cancer Preoperative, Treatment
naive N Y 100 80930 8182868200 2383173431 29% 28233 7973 CGCRC346
Colorectal Cancer Preoperative, Treatment naive N Y 100 80930
7448272300 3925056341 53% 46679 5582 CGCRC347 Colorectal Cancer
Preoperative, Treatment naive N Y 100 80930 5804744500 2986809912
51% 35490 4141 CGCRC349 Colorectal Cancer Preoperative, Treatment
naive N Y 100 80930 6943451600 3533145275 51% 41908 5762 CGCRC350
Colorectal Cancer Preoperative, Treatment naive N Y 100 80930
7434818400 3848923016 52% 45678 4652 CGCRC351 Colorectal Cancer
Preoperative, Treatment naive N Y 100 80930 7306546400 3636910409
50% 43162 5205 CGCRC352 Colorectal Cancer Preoperative, Treatment
naive N Y 100 80930 7864655000 3336939252 42% 39587 4502 CGCRC353
Colorectal Cancer Preoperative, Treatment naive N Y 100 80930
7501674800 3642919375 49% 43379 4666 CGCRC354 Colorectal Cancer
Preoperative, Treatment naive N Y 100 80930 7938270200 2379068977
30% 28256 4858 CGCRC356 Colorectal Cancer Preoperative, Treatment
naive N Y 100 80930 6013175900 3046754994 51% 36127 3425 CGCRC357
Colorectal Cancer Preoperative, Treatment naive N Y 100 80930
6013454600 3022035300 50% 35813 4259 CGCRC358 Colorectal Cancer
Preoperative, Treatment naive N Y 100 80930 7227212400 3188723303
44% 37992 5286 CGCRC359 Colorectal Cancer Preoperative, Treatment
naive N Y 100 80930 7818567700 425110101 5% 5040 2566 CGCRC367
Colorectal Cancer Preoperative, Treatment naive N Y 100 80930
6582043200 3363063597 51% 39844 5839 CGCRC368 Colorectal Cancer
Preoperative, Treatment naive N Y 100 80930 8042242400 4101646000
51% 48636 11471 CGCRC370 Colorectal Cancer Preoperative, Treatment
naive N Y 100 80930 6940330100 3198954121 46% 38153 4826 CGCRC373
Colorectal Cancer Preoperative, Treatment naive N Y 100 80930
6587201700 3120088035 47% 37234 5190 CGCRC376 Colorectal Cancer
Preoperative, Treatment naive N Y 100 80930 6727983100 3162416807
47% 37735 3445 CGCRC377 Colorectal Cancer Preoperative, Treatment
naive N Y 100 80930 6716339200 3131415570 47% 37160 4524 CGCRC378
Colorectal Cancer Preoperative, Treatment naive N Y 100 80930
6523969900 2411096720 37% 28728 3239 CGCRC379 Colorectal Cancer
Preoperative, Treatment naive N Y 100 80930 6996252100 3371081103
48% 39999 2891 CGCRC380 Colorectal Cancer Preoperative, Treatment
naive N Y 100 80930 7097496300 2710244446 38% 32020 3251 CGCRC381
Colorectal Cancer Preoperative, Treatment naive N Y 100 80930
6961936100 3287050681 47% 38749 9357 CGCRC382 Colorectal Cancer
Preoperative, Treatment naive N Y 100 80930 6959048700 2552325859
37% 30040 5148 CGCRC384 Colorectal Cancer Preoperative, Treatment
naive N Y 100 80930 7012798900 3293884583 47% 39158 3653 CGCRC385
Colorectal Cancer Preoperative, Treatment naive N Y 100 80930
7542017900 3356570505 45% 39884 3686 CGCRC386 Colorectal Cancer
Preoperative, Treatment naive N Y 100 80930 6876059600 3064412286
45% 36431 2787 CGCRC387 Colorectal Cancer Preoperative, Treatment
naive N Y 100 80930 7399564700 3047254560 41% 36141 6675 CGCRC386
Colorectal Cancer Preoperative, Treatment naive N Y 100 80930
6592692900 3137284885 48% 37285 5114 CGCRC389 Colorectal Cancer
Preoperative, Treatment naive N Y 100 80930 6651206300 3102100941
47% 36764 6123 CGCRC390 Colorectal Cancer Preoperative, Treatment
naive N Y 100 80930 7260616800 3376667585 47% 40048 4368 CGCRC391
Colorectal Cancer Preoperative, Treatment naive N Y 100 80930
6883624500 3202877881 47% 37978 5029 CGLU316 Lung Cancer
Pre-treatment Day -53 Y N 100 80930 7864415100 1991331171 25% 23601
3565 CGLU316 Lung Cancer Pre-treatment, Day -53 Y N 100 80930
7502591600 3730963390 50% 44262 3966 CGLU316 Lung Cancer
Pro-treatment, Day -53 Y N 100 80930 6582515900 3187059470 48%
37813 3539 CGLU316 Lung Cancer Pre-treatment, Day -53 Y N 100 60930
6587281800 1947630979 30% 23094 4439 CGLU344 Lung Cancer
Pretreatment, Day -21 Y N 100 80930 6151628500 2748983603 45% 32462
8063 CGLU344 Lung Cancer Pre-treatment, Day -21 Y N 100 80930
7842910900 1147703178 15% 13565 4303 CGLU344 Lung Cancer
Pretreatment, Day -21 Y N 100 80930 5838083100 2291108925 39% 27067
4287 CGLU344 Lung Cancer Pre-treatment, Day -21 Y N 100 80930
7685989200 3722274529 48% 43945 3471 CGLU369 Lung Cancer
Pre-treatment, Day -2 Y N 100 80930 7080245300 1271457982 18% 15109
2354 CGLU369 Lung Cancer Pre-treatment, Day -2 Y N 100 00930
7078131900 1482448715 21% 17583 4275 CGLU369 Lung Cancer
Pre-treatment, Day -2 Y N 100 60930 6904701700 2124660124 31% 25230
5278 CGLU369 Lung Cancer Pre-treatment, Day -2 Y N 100 80930
7003452200 3162195578 45% 37509 6062 CGLU373 Lung Cancer
Pro-treatment, Day -2 Y N 100 00930 6346267200 3053520676 48% 36137
6251 CGLU373 Lung Cancer Pre-treatment, Day -2 Y N 100 80930
6517189900 3192984468 49% 38066 8040 CGLU373 Lung Cancer
Pre-treatment, Day -2 Y N 100 60930 7767146300 3572598842 46% 42378
5306 CGLU373 Lung Cancer Pre-treatment, Day -2 Y N 100 80930
7190999100 3273648804 46% 38784 4454 CGPLBR100 Breast Cancer
Preoperative, Treatment naive N Y 100 00930 7299964400 3750278051
51% 44794 3249 CGPLBR101 Breast Cancer Preoperative, Treatment
naive N Y 100 80930 7420822800 3810365416 51% 45565 9784 CGPLBR102
Breast Cancer Preoperative, Treatment naive N Y 100 80930
6679304900 3269688319 49% 38679 7613 CGPLBR103 Breast Cancer
Preoperative, Treatment naive N Y 100 60930 7040304400 3495542468
50% 41786 6748 CGPLBR104 Breast Cancer Preoperative, Treatment
naive N Y 100 80930 7188389200 3716096781 52% 44316 9448 CGPLBR38
Breast Cancer Preoperative, Treatment naive Y Y 100 80930
7810293900 4057576306 52% 48098 9868 CGPLBR39 Breast Cancer
Preoperative, Treatment naive N Y 100 80930 7745701500 3805623239
49% 45084 11065 CGPLBR40 Breast Cancer Preoperative, Treatment
naive Y Y 100 80930 7558990500 3652442341 48% 43333 12948 CGPLBR41
Breast Cancer Preoperative, Treatment naive N Y 100 80930
7900994600 3836800101 49% 45535 10847 CGPLBR44 Breast Cancer
Preoperative, Treatment naive Y N 100 80930 7017744200 3269110569
47% 38672 8344 CGPLBR48 Breast Cancer Preoperative, Treatment naive
Y Y 100 80930 5629044200 2611554623 46% 30860 8652 CGPLBR49 Breast
Cancer Preoperative, Treatment naive N Y 100 80930 5784711600
2673457893 46% 31274 10429 CGPLBR55 Breast Cancer Preoperative,
Treatment naive Y Y 100 80930 8309154900 4306956261 52% 51143 8328
CGPLBR57 Breast Cancer Preoperative, Treatment naive N Y 100 80930
8636181000 4391502618 51% 52108 5857 CGPLBR59 Breast Cancer
Preoperative, Treatment naive N Y 100 80930 8799457700 4152328555
47% 49281 5855 CGPLBR61 Breast Cancer Preoperative, Treatment naive
N Y 100 80930 8163706700 3952010628 48% 46755 8522 CGPLBR63 Breast
Cancer Preoperative, Treatment naive Y Y 100 80930 7020533100
3542447304 50% 41956 4773 CGPLBR67 Breast Cancer Preoperative,
Treatment naive Y N 100 80930 8264353900 3686093696 45% 43516 7752
CGPLBR68 Breast Cancer Preoperative, Treatment naive N Y 100 80930
7629312300 4078969547 53% 48389 7402 CGPLBR69 Breast Cancer
Preoperative, Treatment naive Y Y 100 80930 7571501500 3857354512
51% 45322 7047 CGPLBR70 Breast Cancer Preoperative, Treatment naive
Y Y 100 80930 7251760700 3641333708 50% 43203 8884 CGPLBR71 Breast
Cancer Preoperative, Treatment naive Y Y 100 80930 8515402600
4496696391 53% 53340 6805 CGPLBR72 Breast Cancer Preoperative,
Treatment naive Y Y 100 80930 8556946900 4389761697 51% 52081 5632
CGPLBR73 Breast Cancer Preoperative, Treatment naive Y Y 100 80930
7959392300 4006933338 50% 47555 8791 CGPLBR74 Breast Cancer
Preoperative, Treatment naive Y N 100 80930 8524536400 4063900599
48% 48252 7013 CGPLBR75 Breast Cancer Preoperative, Treatment naive
Y Y 100 80930 8260379100 3960599885 48% 46955 6319 CGPLBR76 Breast
Cancer Preoperative, Treatment naive Y Y 100 80930 7774235200
3893622420 50% 46192 9628 CGPLBR77 Breast Cancer Preoperative,
Treatment naive Y N 100 80930 7572797600 3255963429 43% 38568 8263
CGPLBR80 Breast Cancer Preoperative, Treatment naive Y N 100 80930
6845325800 3147476693 46% 37201 5595 CGPLBR82 Breast Cancer
Preoperative, Treatment naive N Y 100 80930 8236705200 4170465005
51% 49361 12319
CGPLBR83 Breast Cancer Preoperative, Treatment naive Y Y 100 80930
7434568100 3676855019 49% 43628 5458 CGPLBR86 Breast Cancer
Preoperative, Treatment naive Y Y 100 80930 7616282500 3644791327
48% 43490 7048 CGPLBR87 Breast Cancer Preoperative, Treatment naive
Y Y 100 80930 6194021300 3004882010 49% 35765 5306 CGPLBR88 Breast
Cancer Preoperative, Treatment naive Y Y 100 80930 6071567200
2847926237 47% 33945 10319 CGPLBR91 Breast Cancer Preoperative,
Treatment naive N Y 100 80930 7192457700 3480203404 48% 41570 9912
CGPLBR92 Breast Cancer Preoperative, Treatment naive Y Y 100 80930
7678981800 3600279233 47% 42975 13580 CGPLBR93 Breast Cancer
Preoperative, Treatment naive N Y 100 80930 7605717800 3998713397
53% 47866 10329 CGPLBR96 Breast Cancer Preoperative, Treatment
naive Y N 100 80930 6297446700 2463064737 39% 29341 7937 CGPLBR97
Breast Cancer Preoperative, Treatment naive Y N 100 80930
7114921600 3557069027 50% 42488 10712 CGPLH35 Healthy Preoperative,
Treatment naive N Y 100 80930 6919126300 2312758764 33% 25570 1989
CGPLH36 Healthy Preoperative, Treatment naive N Y 100 80930
6089923400 2038548115 33% 22719 1478 CGPLH37 Healthy Preoperative,
Treatment naive N Y 100 80930 5557270200 1935301929 35% 21673 2312
CGPLH42 Healthy Preoperative, Treatment naive N Y 100 80930
5792045400 2388036949 41% 27197 2523 CGPLH43 Healthy Preoperative,
Treatment naive N Y 100 80930 5568321700 2017813329 36% 23228 1650
CGPLH45 Healthy Preoperative, Treatment naive N Y 100 80930
8485593200 2770176078 33% 32829 3114 CGPLH46 Healthy Preoperative,
Treatment naive N Y 100 80930 5083171100 1899395790 37% 21821 1678
CGPLH47 Healthy Preoperative, Treatment naive N Y 100 80930
6016388500 2062392156 34% 23459 1431 CGPLH48 Healthy Preoperative,
Treatment naive N Y 100 80930 4958945900 1809825992 36% 20702 1698
CGPLH49 Healthy Preoperative, Treatment naive N Y 100 80930
7953812200 2511365904 32% 27006 1440 CGPLH50 Healthy Preoperative,
Treatment naive N Y 100 80930 6989407600 2561288100 37% 29177 2591
CGPLH51 Healthy Preoperative, Treatment naive N Y 100 80930
7862073200 2525091396 32% 29999 1293 CGPLH52 Healthy Preoperative,
Treatment naive N Y 100 80930 6939636800 2397922699 35% 27029 2501
CGPLH54 Healthy Preoperative, Treatment naive N Y 100 80930
10611934700 2290823134 22% 27175 3306 CGPLH55 Healthy Preoperative,
Treatment naive N Y 100 80930 9912569200 2521962244 25% 27082 3161
CGRLH56 Healthy Preoperative, Treatment naive N Y 100 80930
5777591900 2023874863 35% 22916 1301 CGPLH57 Healthy Preoperative,
Treatment naive N Y 100 80930 9234904800 1493926244 16% 15843 1655
CGPLH59 Healthy Preoperative, Treatment naive N Y 100 80930
9726052100 2987875484 31% 35427 2143 CGPLH63 Healthy Preoperative,
Treatment naive N Y 100 80930 8696405000 2521574759 29% 26689 1851
CGPLH64 Healthy Preoperative, Treatment naive N Y 100 80930
5438852600 996198502 18% 11477 1443 CGPLH75 Healthy Preoperative,
Treatment naive Y N 100 80930 3446444000 1505718480 44% 17805 3016
CGPLH76 Healthy Preoperative, Treatment naive N Y 100 80930
7499116400 3685762725 49% 43682 4643 CGPLH77 Healthy Preoperative,
Treatment naive Y N 100 80930 6512408400 2537359345 39% 30280 3131
CGPLH78 Healthy Preoperative, Treatment naive N Y 100 80930
7642949300 3946069680 52% 46316 5358 CGPLH79 Healthy Preoperative,
Treatment naive N Y 100 80930 7785475700 3910639227 50% 45280 6714
CGPLH80 Healthy Preoperative, Treatment naive N Y 100 80930
7918361500 3558236955 45% 42171 5062 CGPLH81 Healthy Preoperative,
Treatment naive Y N 100 80930 6646268900 3112369850 47% 37119 3678
CGPLH82 Healthy Preoperative, Treatment naive N Y 100 80930
7744065000 3941700596 51% 46820 5723 CGPLH83 Healthy Preoperative,
Treatment naive Y N 100 80930 6957686000 1447603106 21% 17280 2875
CGPLH84 Healthy Preoperative, Treatment naive Y N 100 80930
8326493200 3969908122 48% 47464 3647 CGPLH86 Healthy Preoperative,
Treatment naive N Y 100 80930 8664194700 4470145091 52% 53398 5094
CGPLH90 Healthy Preoperative, Treatment naive N Y 100 80930
7516078800 3841504088 51% 45907 4414 CGPLLU13 Lung Cancer
Pre-treatment, Day -2 Y N 100 80930 5659546100 1721618955 30% 20587
6025 CGPLLU13 Lung Cancer Pre-treatment, Day -2 Y N 100 80930
6199049700 2563659840 41% 30728 6514 CGPLLU13 Lung Cancer
Pre-treatment, Day -2 Y N 100 80930 5864396500 1194237002 20% 14331
3952 CGPLLU13 Lung Cancer Pre-treatment, Day -2 Y N 100 80930
5080197700 1373550586 27% 16480 5389 CGPLLU14 Lung Cancer
Pre-treatment, Day -38 N Y 100 80930 8668655700 398731089 46% 48628
3148 CGPLLU14 Lung Cancer Pre-treatment, Day -16 N Y 100 80930
8271043600 4105092738 50% 50152 4497 CGPLLU14 Lung Cancer
Pre-treatment, Day -3 N Y 100 80930 7149809200 3405754720 48% 40382
6170 CGPLLU14 Lung Cancer Pre-treatment, Day 0 N Y 100 80930
6556332200 3289504484 50% 39004 4081 CGPLLU14 Lung Cancer
Post-treatment, Day 0.33 N Y 100 80930 7410378300 3464236558 47%
41108 4259 CGPLLU14 Lung Cancer Post-treatment, Day 7 N Y 100 80930
7530190700 3752054349 50% 45839 2469 CGPLLU144 Lung Cancer
Preoperative, Treatment naive Y Y 100 80930 8716827400 4216576624
48% 49370 10771 CGPLLU146 Lung Cancer Preoperative, Treatment naive
Y N 100 80930 8506844200 4195033049 49% 49084 6968 CGPLLU147 Lung
Cancer Preoperative, Treatment naive Y N 100 80930 7416300600
3530746046 48% 41302 4691 CGPLLU161 Lung Cancer Preoperative,
Treatment naive N Y 100 80930 7789148700 3280139772 42% 38568 12229
CGPLLU162 Lung Cancer Preoperative, Treatment naive Y Y 100 80930
7625462000 3470147667 46% 40918 10099 CGPLLU163 Lung Cancer
Preoperative, Treatment naive Y Y 100 80930 8019293200 3946533983
49% 46471 12108 CGPLLU164 Lung Cancer Preoperative, Treatment naive
Y N 100 80930 8110030900 3592748235 44% 42161 6947 CGPLLU165 Lung
Cancer Preoperative, Treatment naive Y N 100 80930 8389514600
4147501817 49% 48770 8996 CGPLLU168 Lung Cancer Preoperative,
Treatment naive Y Y 100 80930 7600630000 3868237773 50% 45625 9711
CGPLLU169 Lung Cancer Preoperative, Treatment naive N Y 100 80930
9378353000 4800407624 51% 56547 10261 CGPLLU174 Lung Cancer
Preoperative, Treatment naive Y N 100 80930 7481844600 3067532518
41% 36321 6137 CGPLLU175 Lung Cancer Preoperative, Treatment naive
Y N 100 80930 8532324200 4002541569 47% 47084 7862 CGPLLU176 Lung
Cancer Preoperative, Treatment naive Y Y 100 80930 8143905000
4054098929 50% 47708 5588 CGPLLU177 Lung Cancer Preoperative,
Treatment naive Y Y 100 80930 8421611300 4197108809 50% 49476 8780
CGPLLU178 Lung Cancer Preoperative, Treatment naive Y N 100 80930
8483124700 4169577489 49% 48580 6445 CGPLLU179 Lung Cancer
Preoperative, Treatment naive Y N 100 80930 7774358700 3304915738
43% 38768 6862 CGPLLU180 Lung Cancer Preoperative, Treatment naive
Y N 100 80930 8192813800 3937552475 48% 46498 6568 CGPLLU197 Lung
Cancer Preoperative, Treatment naive Y N 100 80930 7906779200
3082397881 39% 36381 5388 CGPLLU198 Lung Cancer Preoperative,
Treatment naive Y N 100 80930 7175247200 3545719100 49% 42008 6817
CGPLLU202 Lung Cancer Preoperative, Treatment naive Y N 100 80930
6840112800 3427820669 50% 40670 7951 CGPLLU203 Lung Cancer
Preoperative, Treatment naive N Y 100 80930 7458749900 3762726574
50% 44500 9917 CGPLLU204 Lung Cancer Preoperative, Treatment naive
Y N 100 80930 7445026400 3703545153 50% 44317 6856 CGPLLU205 Lung
Cancer Preoperative, Treatment naive Y Y 100 80930 9205429100
4350573991 47% 51627 9810 CGPLLU206 Lung Cancer Preoperative,
Treatment naive Y N 100 80930 7397914600 3635210205 49% 43016 7124
CGPLLU207 Lung Cancer Preoperative, Treatment naive Y Y 100 80930
7133043900 3736258011 52% 44291 8499 CGPLLU208 Lung Cancer
Preoperative, Treatment naive Y Y 100 80930 7346976400 3855814032
52% 45782 8940 CGPLLU209 Lung Cancer Preoperative, Treatment naive
Y N 100 80930 6723337800 3362944595 50% 39531 11946 CGPLLU244 Lung
Cancer Pre-treatment Day -7 N Y 100 80930 8305560600 4182616104 50%
50851 7569 CGPLLU244 Lung Cancer Pre-treatment, Day -1 N Y 100
80930 7739951100 3788487116 49% 45925 8552 CGPLLU244 Lung Cancer
Post-treatment, Day 6 N Y 100 80930 8061928000 4225322272 52% 51279
8646 CGPLLU244 Lung Cancer Post-treatment, Day 62 N Y 100 80930
8894936700 4437962639 50% 53862 7361 CGPLLU245 Lung Cancer
Pre-treatment, Day -32 N Y 100 80930 7679235200 3935822054 51%
47768 7266 CGPLLU245 Lung Cancer Pre-treatment Day 0 N Y 100 80930
8985252500 4824268339 54% 58338 10394 CGPLLU245 Lung Cancer
Post-treatment, Day 7 N Y 100 80930 8518229300 4480236927 53% 54083
10125 CGPLLU245 Lung Cancer Post-treatment, Day 21 N Y 100 80930
9031131000 4824738475 53% 58313 10598 CGPLLU246 Lung Cancer
Pre-treatment. Day -21 N Y 100 80930 8520360800 3509660305 41%
42349 8086 CGPLLU246 Lung Cancer Pre-treatment, Day 0 N Y 100 80930
5451467800 2828351657 52% 34243 8256 CGPLLU246 Lung Cancer
Post-treatment, Day 9 N Y 100 80930 8137616600 4135036174 51% 50121
6466 CGPLLU246 Lung Cancer Post-treatment, Day 42 N Y 100 80930
8385724600 4413323333 53% 53495 7303 CGPLLU264 Lung Cancer
Pre-treatment, Day -1 Y N 100 80930 6254777700 3016326208 48% 36164
12138 CGPLLU264 Lung Cancer Pre-treatment, Day -1 Y N 100 80930
6185331000 3087883231 50% 37003 8388 CGPLLU264 Lung Cancer
Pre-treatment, Day -1 Y N 100 80930 6274540300 2861143666 46% 34308
6817 CGPLLU264 Lung Cancer Pre-treatment, Day -1 Y N 100 80930
5701274000 1241270938 22% 14886 4273 CGPLLU265 Lung Cancer
Pre-treatment, Day 0 Y N 100 80930 6091276800 2922585558 48% 35004
7742 CGPLLU265 Lung Cancer Pre-treatment, Day 0 Y N 100 80930
6430107900 2945953499 46% 35219 8574 CGPLLU265 Lung Cancer
Pre-treatment, Day 0 Y N 100 80930 5869510300 2792208995 48% 33423
8423 CGPLLU265 Lung Cancer Pre-treatment, Day 0 Y N 100 80930
5884330900 2588386038 44% 30977 9803 CGPLLU266 Lung Cancer
Pre-treatment, Day 0 Y N 100 80930 5807524900 2347651479 40% 28146
5793 CGPLLU266 Lung Cancer Pre-treatment, Day 0 Y N 100 80930
6064269800 2086938782 34% 24994 6221 CGPLLU266 Lung Cancer
Pre-treatment, Day 0 Y N 100 80930 6785913900 3458588505 51% 41432
7785 CGPLLU266 Lung Cancer Pre-treatment, Day 0 Y N 100 80930
6513702000 2096370387 32% 25142 6598 CGPLLU267 Lung Cancer
Pre-treatment, Day -1 Y N 100 80930 6610761200 2576886619 39% 31095
4485 CGPLLU267 Lung Cancer Pre-treatment, Day -1 Y N 100 80930
6156402000 2586081726 42% 30714 5309 CGPLLU267 Lung Cancer
Pre-treatment, Day -1 Y N 100 80930 6180799700 2013434756 33% 23902
3885 CGPLLU269 Lung Cancer Pre-treatment, Day 0 Y N 100 80930
6221168600 1499602843 24% 17799 6098 CGPLLU269 Lung Cancer
Pre-treatment, Day 0 Y N 100 80930 5353961600 1698331125 32% 20094
5252 CGPLLU269 Lung Cancer Pre-treatment, Day 0 Y N 100 80930
5831612800 1521114956 26% 18067 6210 CGPLLU271 Lung Cancer
Post-treatment, Day 259 Y N 100 80930 6229704000 1481468974 24%
17608 4633 CGPLLU271 Lung Cancer Post-treatment, Day 259 Y N 100
80930 6134366400 1351029627 22% 16170 7024 CGPLLU271 Lung Cancer
Post-treatment, Day 259 Y N 100 80930 6491884900 1622578435 25%
19433 5792 CGPLLU271 Lung Cancer Post-treatment, Day 259 Y N 100
80930 5742881200 2349421128 41% 28171 5723 CGPLLU271 Lung Cancer
Post-treatment, Day 259 Y N 100 80930 5503999300 1695782705 31%
20320 5907 CGPLLU43 Lung Cancer Pre-treatment, Day -1 Y N 100 80930
6575907000 3002048491 46% 35997 5445 CGPLLU43 Lung Cancer
Pre-treatment, Day -1 Y N 100 80930 6204350900 3016077187 49% 36162
5704 CGPLLU43 Lung Cancer Pre-treatment, Day -1 Y N 100 80930
5997724300 2989608757 50% 35873 6228 CGPLLU43 Lung Cancer
Pre-treatment, Day -1 Y N 100 80930 6026261500 2881177658 48% 34568
7221 CGPLLU86 Lung Cancer Pre-treatment, Day 0 N Y 100 80930
8222093400 3523035056 43% 41165 3614 CGPLLU86 Lung Cancer
Post-treatment, Day 0.5 N Y 100 80930 8305719500 4271264008 51%
49508 6681 CGPLLU86 Lung Cancer Post-treatment, Day 7 N Y 100 80930
6787785300 3443658418 51% 40192 3643 CGPLLU86 Lung Cancer
Post-treatment, Day 17 N Y 100 80930 6213229400 3120325926 50%
36413 3560 CGPLLU88 Lung Cancer Pre-treatment, Day 0 Y N 100 80930
7252433900 3621678746 50% 42719 8599 CGPLLU88 Lung Cancer
Pre-treatment, Day 0 Y N 100 80930 7679995800 4004738253 52% 46951
6387 CGPLLU88 Lung Cancer Pre-treatment, Day 0 Y N 100 80930
6509178000 3316053733 51% 39274 2651 CGPLLU89 Lung Cancer
Pre-treatment, Day 0 N Y 100 80930 7662496600 3781536306 49% 44097
7909 CGPLLU89 Lung Cancer Post-treatment, Day 7 N Y 100 80930
7005599600
3339612564 48% 38977 5034 CGPLLU89 Lung Cancer Post-treatment, Day
22 N Y 100 80930 8325998600 3094796789 37% 36061 2822 CGPLOV10
Ovarian Cancer Preoperative, Treatment naive Y Y 100 80930
7073534200 3402306123 48% 39820 4059 CGPLOV11 Ovarian Cancer
Preoperative, Treatment naive Y Y 100 80930 6924062200 3324593050
48% 38796 7185 CGPLOV12 Ovarian Cancer Preoperative, Treatment
naive N Y 100 80930 6552080100 3181854993 49% 37340 6114 CGPLOV13
Ovarian Cancer Preoperative, Treatment naive Y Y 100 80930
6796755500 3264897084 48% 38340 7931 CGPLOV14 Ovarian Cancer
Preoperative, Treatment naive Y Y 100 80930 7856573900 3408425065
43% 39997 7712 CGPLOV15 Ovarian Cancer Preoperative, Treatment
naive Y Y 100 80930 7239201500 3322285607 46% 38953 6644 CGPLOV16
Ovarian Cancer Preoperative, Treatment naive N Y 100 80930
8570755900 4344288233 51% 51009 11947 CGPLOV17 Ovarian Cancer
Preoperative, Treatment naive Y N 100 80930 6910310400 2805243492
41% 32828 4307 CGPLOV18 Ovarian Cancer Preoperative, Treatment
naive N N 100 80930 8173037600 4064432407 50% 47714 5182 CGPLOV19
Ovarian Cancer Preoperative, Treatment naive Y Y 100 80930
7732198900 3672564399 47% 43020 11127 CGPLOV20 Ovarian Cancer
Preoperative, Treatment naive Y Y 100 80930 7559602000 3678700179
49% 43230 4872 CGPLOV21 Ovarian Cancer Preoperative, Treatment
naive Y Y 100 80930 8949032900 4616255499 52% 54012 12777 CGPLOV22
Ovarian Cancer Preoperative, Treatment naive Y Y 100 80930
8680136500 4049934586 47% 46912 9715 CGPLOV23 Ovarian Cancer
Preoperative, Treatment naive N Y 100 80930 6660696600 3422631774
51% 40810 9460 CGPLOV24 Ovarian Cancer Preoperative, Treatment
naive N Y 100 80930 8634287200 4272258165 49% 50736 8689 CGPLOV25
Ovarian Cancer Preoperative, Treatment naive N Y 100 80930
6978295000 3390206388 49% 40188 5856 CGPLOV26 Ovarian Cancer
Preoperative, Treatment naive N Y 100 80930 7041038300 3728879661
53% 44341 8950 CGPLOV28 Ovarian Cancer Preoperative, Treatment
naive N Y 100 80930 7429236900 3753051715 51% 45430 4155 CGPLOV31
Ovarian Cancer Preoperative, Treatment naive N Y 100 80930
8961384000 4621838729 51% 55429 5458 CGPLOV32 Ovarian Cancer
Preoperative, Treatment naive N Y 100 80930 9344536800 4737698323
51% 57234 6165 CGPLOV37 Ovarian Cancer Preoperative, Treatment
naive N Y 100 80930 8158083200 4184432898 51% 50648 6934 CGPLOV38
Ovarian Cancer Preoperative, Treatment naive N Y 100 80930
8654435400 4492987085 52% 53789 6124 CGPLOV40 Ovarian Cancer
Preoperative, Treatment naive N Y 100 80930 9868640700 4934400809
50% 59049 7721 CGPLOV41 Ovarian Cancer Preoperative, Treatment
naive N Y 100 80930 7689013600 3861448829 50% 46292 4469 CGPLOV42
Ovarian Cancer Preoperative, Treatment naive N Y 100 80930
9836516300 4864154366 49% 58302 7632 CGPLOV43 Ovarian Cancer
Preoperative, Treatment naive N Y 100 80930 8756507100 4515479918
52% 54661 4310 CGPLOV44 Ovarian Cancer Preoperative, Treatment
naive N Y 100 80930 7576310800 4120933922 54% 49903 4969 CGPLOV46
Ovarian Cancer Preoperative, Treatment naive N Y 100 80930
9346036300 5037820346 54% 61204 3927 CGPLOV47 Ovarian Cancer
Preoperative, Treatment naive N Y 100 80930 10880620200 5491357828
50% 66363 6895 CGPLOV48 Ovarian Cancer Preoperative, Treatment
naive N Y 100 80930 7658787800 3335991337 44% 40332 4066 CGPLOV49
Ovarian Cancer Preoperative, Treatment naive N Y 100 80930
10076208000 5519656698 55% 67117 5097 CGPLOV50 Ovarian Cancer
Preoperative, Treatment naive N Y 100 80930 8239290400 4472380276
54% 54150 3836 CGPLPA118 Bile Duct Cancer Preoperative, Treatment
naive N Y 100 80930 9094827600 4828332902 53% 57021 4002 CGPLPA122
Bile Duct Cancer Preoperative, Treatment naive N Y 100 80930
7303323100 3990160379 55% 47240 7875 CGPLPA124 Bile Duct Cancer
Preoperative, Treatment naive N Y 100 80930 7573482800 3965807442
52% 46388 8658 CGPLPA126 Bile Duct Cancer Preoperative, Treatment
naive N Y 100 80930 7904953600 4061463168 51% 47812 10498 CGPLPA128
Bile Duct Cancer Preoperative, Treatment naive N Y 100 80930
7249238300 2244188735 31% 26436 3413 CGPLPA129 Bile Duct Cancer
Preoperative, Treatment naive N Y 100 80930 7559858900 4003725804
53% 47182 5733 CGPLPA130 Bile Duct Cancer Preoperative, Treatment
naive N Y 100 80930 6973946500 1247144905 18% 14691 1723 CGPLPA131
Bile Duct Cancer Preoperative, Treatment naive N Y 100 80930
7226237900 3370664342 47% 39661 5054 CGPLPA134 Bile Duct Cancer
Preoperative, Treatment naive N Y 100 80930 7268866100 3754945844
52% 44306 7023 CGPLPA136 Bile Duct Cancer Preoperative, Treatment
naive N Y 100 80930 7476690700 4073978408 54% 48134 5244 CGPLPA140
Bile Duct Cancer Preoperative, Treatment naive N Y 100 80930
7364654600 3771765342 51% 44479 7080 CGST102 Gastric Cancer
Preoperative, Treatment naive N Y 100 80930 5715504500 2644902854
46% 31309 4503 CGST110 Gastric Cancer Preoperative, Treatment naive
N Y 100 80930 9179291500 4298269268 47% 51666 3873 CGST114 Gastric
Cancer Preoperative, Treatment naive N Y 100 80930 7151572200
3254967293 46% 38496 4839 CGST13 Gastric Cancer Preoperative,
Treatment naive N Y 100 80930 6449701500 3198545984 50% 38515 6731
CGST141 Gastric Cancer Preoperative, Treatment naive N Y 100 80930
6781001300 3440927391 51% 40762 5404 CGST16 Gastric Cancer
Preoperative, Treatment naive N Y 100 80930 6396470600 2931380289
46% 35354 8148 CGST18 Gastric Cancer Preoperative, Treatment naive
N Y 100 80930 6647324000 3138967777 47% 37401 4992 CGST28 Gastric
Cancer Preoperative, Treatment naive N Y 100 80930 6288486100
2884997993 46% 34538 2586 CGST30 Gastric Cancer Preoperative,
Treatment naive N Y 100 80930 6141213100 3109994564 51% 37194 2555
CGST32 Gastric Cancer Preoperative, Treatment naive N Y 100 80930
6969139300 3099120469 44% 36726 3935 CGST33 Gastric Cancer
Preoperative, Treatment naive N Y 100 80930 6560309400 3168371917
48% 37916 4597 CGST39 Gastric Cancer Preoperative, Treatment naive
N Y 100 80930 7043791400 2992501875 42% 35620 6737 CGST41 Gastric
Cancer Preoperative, Treatment naive N Y 100 80930 6975053100
3224065662 46% 38300 4016 CGST45 Gastric Cancer Preoperative,
Treatment naive N Y 100 80930 6130812200 2944524278 48% 35264 4745
CGST47 Gastric Cancer Preoperative, Treatment naive N Y 100 80930
5961400000 3083523351 52% 37008 3112 CGST48 Gastric Cancer
Preoperative, Treatment naive N Y 100 80930 6418652700 1497230327
23% 17782 2410 CGST58 Gastric Cancer Preoperative, Treatment naive
N Y 100 80930 5818344500 1274708429 22% 15281 2924 CGST80 Gastric
Cancer Preoperative, Treatment naive N Y 100 80930 6388064600
3298497188 52% 39692 5280 CGST81 Gastric Cancer Preoperative,
Treatment naive N Y 100 80930 8655691400 1519121452 18% 17988
6419
TABLE-US-00005 APPENDIX C Table 3. Targeted cfDNA fragment analyses
in cancer patients Stage at Amino Acid Patient Patient Type
Diagnosis Alteration Type Gene (Protein) CGCRC291 Colorectal Cancer
IV Tumor-derived STK11 39R > C CGCRC291 Colorectal Cancer IV
Tumor-derived TP53 272V > M CGCRC291 Colorectal Cancer IV
Tumor-derived TP53 167Q > X CGCRC291 Colorectal Cancer IV
Tumor-derived KRAS 12G > A CGCRC291 Colorectal Cancer IV
Tumor-derived APC 1260Q > X CGCRC291 Colorectal Cancer IV
Tumor-derived APC 1450R > X CGCRC291 Colorectal Cancer IV
Tumor-derived PIK3CA 542E > K CGCRC292 Colorectal Cancer IV
Tumor-derived KRAS 146A > V CGCRC292 Colorectal Cancer IV
Tumor-derived CTNNB1 41T > A CGCRC292 Colorectal Cancer IV
Germline EGFR 2284 - 4C > 3 CGCRC293 Colorectal Cancer IV
Tumor-derived TP53 176C > S CGCRC294 Colorectal Cancer II
Tumor-derived APC 213R > X CGCRC294 Colorectal Cancer II
Tumor-derived APC 1367Q > X CGCRC295 Colorectal Cancer IV
Tumor-derived PDBFRA 49 + 4C > T CGCRC295 Colorectal Cancer IV
Hematopoietic IDH1 104G > V CGCRC296 Colorectal Cancer II
Germline EGFR 922E > K CGCRC297 Colorectal Cancer III Germline
KIT 18L > F CGCRC298 Colorectal Cancer II Hematopoietic DNMT3A
882R > H CGCRC298 Colorectal Cancer II Hematopoietic DNMT3A 714S
> C CGCRC298 Colorectal Cancer II Tumor-derived PIK3CA 414G >
V CGCRC299 Colorectal Cancer I Hematopoietic DNMT3A 735Y > C
CGCRC299 Colorectal Cancer I Hematopoietic DNMT3A 710C > S
CGCRC300 Colorectal Cancer I Hematopoietic DNMT3A 720R > G
CGCRC301 Colorectal Cancer I Tumor-derived ATM 2397Q > X
CGCRC302 Colorectal Cancer II Tumor-derived TP53 141C > Y
CGCRC302 Colorectal Cancer II Tumor-derived BRAF 600V > E
CGCRC303 Colorectal Cancer III Tumor-derived TP53 173V > L
CGCRC303 Colorectal Cancer III Hematopoietic DNMT3A 755F > S
CGCRC303 Colorectal Cancer III Hematopoietic DNMT3A 2173 + 1G >
A CGCRC304 Colorectal Cancer II Tumor-derived EGFR 1131T > S
CGCRC304 Colorectal Cancer II Tumor-derived ATM 3077 + 1G > A
CGCRC304 Colorectal Cancer II Hematopoietic ATM 3008R > C
CGCRC305 Colorectal Cancer II Tumor-derived GNA11 213R > Q
CGCRC305 Colorectal Cancer II Tumor-derived TP53 273R > H
CGCRC306 Colorectal Cancer II Tumor-derived TP53 196R > X
CGCRC306 Colorectal Cancer II Tumor-derived CDKN2A 107R > C
CGCRC306 Colorectal Cancer II Tumor-derived KRAS 61Q > K
CGCRC306 Colorectal Cancer II Germline PDGFRA 200T > S CGCRC306
Colorectal Cancer II Tumor-derived EGFR 618H > R CGCRC306
Colorectal Cancer II Tumor-derived PIK3CA 545E > A CGCRC306
Colorectal Cancer II Germline ERBB4 1155R > X CGCRC307
Colorectal Cancer II Tumor-derived JAK2 805L > V CGCRC307
Colorectal Cancer II Tumor-derived SMARCB1 501 - 2A > G CGCRC307
Colorectal Cancer II Tumor-derived GNAS 201R > C CGCRC307
Colorectal Cancer II Tumor-derived BRAF 600V > E CGCRC307
Colorectal Cancer II Tumor-derived FBXW7 465R > C CGCRC307
Colorectal Cancer II Tumor-derived ERBB4 17A > V CGCRC308
Colorectal Cancer III Hematopoietic DNMT3A 882R > H CGCRC308
Colorectal Cancer III Germline EGFR 848P > L CGCRC308 Colorectal
Cancer III Tumor-derived APC 1480Q > X CGCRC309 Colorectal
Cancer III Tumor-derived AKT1 17E > K CGCRC309 Colorectal Cancer
III Tumor-derived BRAF 600V > E CGCRC310 Colorectal Cancer II
Tumor-derived KRAS 12G > V CGCRC310 Colorectal Cancer II
Tumor-derived APC 1513E > X CGCRC310 Colorectal Cancer II
Tumor-derived APC 1521E > X CGCRC311 Colorectal Cancer I
Hematopoietic DNMT3A 882R > H CGCRC312 Colorectal Cancer III
Tumor-derived APC 960S > X CGCRC312 Colorectal Cancer III
Tumor-derived NRAS 61Q > K CGCRC313 Colorectal Cancer III
Tumor-derived KRAS 12G > S CGCRC313 Colorectal Cancer III
Tumor-derived APC 876R > X CGCRC314 Colorectal Cancer I
Tumor-derived KRAS 12G > D CGCRC314 Colorectal Cancer I
Hematopoietic DNMT3A 738L > Q CGCRC314 Colorectal Cancer I
Tumor-derived APC 1379E > X CGCRC315 Colorectal Cancer III
Tumor-derived NRAS 12G > D CGCRC315 Colorectal Cancer III
Tumor-derived FBXW7 505R > C Alteration Mutant Mutation Hotspot
Detected Allele Patient Nucleotide Type Alteration in Tissue
Fraction CGCRC291 chr19_1207027-127027_C_T Substitution No No 0.14%
CGCRC291 chr17_7577124-7577124_C_T Substitution Yes No 0.10%
CGCRC291 chr17_7578431-7578431_G_A Substitution Yes Yes 22.85%
CGCRC291 chr12_25398284-25398284_C_G Substitution Yes Yes 14.65%
CGCRC291 chr5_112175069-112175069_C_T Substitution No Yes 11.23%
CGCRC291 chr5_11215639-11215639_C_T Substitution Yes Yes 11.05%
CGCRC291 chr3_178936082-178936082_G_A Substitution Yes Yes 18.11%
CGCRC292 chr12_25378561-25378561_G_A Substitution Yes No 1.41%
CGCRC292 chr3_41266124-41266124_A_G Substitution Yes Yes 0.13%
CGCRC292 chr7_55248982-55248982_C_G Substitution NA Yes 31.99%
CGCRC293 chr17_7578404-7578404_A_T Substitution No No 0.35%
CGCRC294 chr5_12116592-12116592_C_T Substitution Yes Yes 0.14%
CGCRC294 chr5_12175390-12175390_C_T Substitution Yes Yes 0.13%
CGCRC295 chr4_55124988-55124988_C_T Substitution No No 0.45%
CGCRC295 chr2_209113196-209113196_C_A Substitution No Yes 0.34%
CGCRC296 chr7_55266472-55266472_G_A Substitution NA Yes 30.48%
CGCRC297 chr4_55524233-55524233_C_T Substitution NA Yes 41.39%
CGCRC298 chr2_25457242-25457242_C_T Substitution Yes Yes 0.08%
CGCRC298 chr2_25463541-25463541_G_C Substitution No No 0.11%
CGCRC298 chr3_178927478-178927478_G_T Substitution No No 0.55%
CGCRC299 chr2_25463289-25463289_T_C Substitution No Yes 0.30%
CGCRC299 chr2_25463553-2546355_C_G Substitution No Yes 0.12%
CGCRC300 chr2_25463524-25463524_G_C Substitution No No 0.15%
CGCRC301 chr11_108199847-108199847_C_T Substitution No No 0.21%
CGCRC302 chr17_7578508-7578508_C_T Substitution Yes Yes 0.05%
CGCRC302 chr7_140453136-140453136_A_T Substitution Yes Yes 0.12%
CGCRC303 chr17_7578413-7578413_C_A Substitution Yes Yes 0.08%
CGCRC303 chr2_25463229-25463229_A_G Substitution No No 0.21%
CGCRC303 chr2_25463508-25463508_C_T Substitution No No 0.17%
CGCRC304 chr7_55273068-55273068_A_T Substitution No No 0.22%
CGCRC304 chr11_108142134-108142134_G_A Substitution No No 0.27%
CGCRC304 chr11_108236086-108236086_C_T Substitution No Yes 0.43%
CGCRC305 chr19_3118954-3118954_G_A Substitution No Yes 0.11%
CGCRC305 chr17_7577120-7577120_C_T Substitution Yes No 0.19%
CGCRC306 chr17_7578263-7578263_G_A Substitution Yes No 0.12%
CGCRC306 chr9_21971039-21971039_G_A Substitution No Yes 8.02%
CGCRC306 chr12_25380277-25380277_G_T Substitution Yes Yes 7.30%
CGCRC306 chr4_55130065-55130065_C_G Substitution NA Yes 34.78%
CGCRC306 chr7_55233103-55233103_A_G Substitution No Yes 8.32%
CGCRC306 chr3_178936092-178936092_A_C Substitution Yes No 0.96%
CGCRC306 chr2_2122596-2122596_G_A Substitution NA Yes 38.70%
CGCRC307 chr9_5080662-5080662_C_G Substitution No No 0.56% CGCRC307
chr22_24145480-24145480_A_G Substitution No Yes 0.34% CGCRC307
chr20_57484420-57484420_C_T Substitution Yes Yes# 0.24% CGCRC307
chr7_140453136-140453136_A_T Substitution Yes Yes 0.38% CGCRC307
chr4_153249385-153249385_G_A Substitution Yes Yes 0.31% CGCRC307
chr2_213403205-213403205_G_A Substitution No No 0.15% CGCRC308
chr2_25457242-25457242_C_T Substitution Yes No 0.06% CGCRC308
chr7_55259485-55259485_C_T Substitution NA Yes 27.69% CGCRC308
chr5_112175242-112175242_C_T Substitution No Yes 0.11% CGCRC309
chr14_105246551-105246551_C_T Substitution Yes Yes 2.70% CGCRC309
chr7_140453136-140453136_A_T Substitution Yes Yes 3.00% CGCRC310
chr12_25398284-25398284_C_A Substitution Yes Yes 0.13% CGCRC310
chr5_11215828-11215828_G_T Substitution No Yes 0.11% CGCRC310
chr5_11215852-11215852_G_T Substitution No Yes 0.15% CGCRC311
chr2_25457242-25457242_C_T Substitution Yes No 0.86% CGCRC312
chr5_112174170-112174170_C_G Substitution No Yes 0.59% CGCRC312
chr1_115256530-115256530_G_T Substitution Yes Yes 0.47% CGCRC313
chr12_25398285-25398285_C_T Substitution Yes Yes 0.17% CGCRC313
chr5_112173917-112173917_C_T Substitution Yes Yes 0.07% CGCRC314
chr12_25398284-25398284_C_T Substitution Yes Yes 0.30% CGCRC314
chr2_25463280-25463280_A_T Substitution No Yes 2.50% CGCRC314
chr5_112175426-112175426_G_T Substitution Yes Yes 0.38% CGCRC315
chr1_115258747-115258747_C_T Substitution Yes Yes 0.27% CGCRC315
chr4_153247289-53247289_G_A Substitution Yes Yes 0.25% Wild-type
Fragments 25th Minimum Percentile Mode Median cfDNA cfDNA cfDNA
cfDNA Fragment Fragment Fragment Fragment Distinct Size Size Size
Size Patient Coverage (bp) (bp) (bp) (bp) CGCRC291 11688 100 151
167 159 CGCRC291 11779 100 155 171 159 CGCRC291 11026 100 156 166
159 CGCRC291 7632 97 152 169 157 CGCRC291 7218 101 155 167 159
CGCRC291 10757 86 154 166 167 CGCRC291 5429 100 151 171 167
CGCRC292 8120 101 157 167 169 CGCRC292 10693 100 155 169 168
CGCRC292 7587 97 158 166 171 CGCRC293 7672 95 159 168 170 CGCRC294
7339 84 155 166 167 CGCRC294 12054 89 159 167 170 CGCRC295 5602 101
157 164 170 CGCRC295 8330 100 157 166 169 CGCRC296 8375 89 161 166
172 CGCRC297 3580 102 159 164 170 CGCRC298 13032 100 159 168 171
CGCRC298 13475 93 158 169 170 CGCRC298 5815 100 156 168 169
CGCRC299 11995 100 154 164 165 CGCRC299 15363 96 151 166 164
CGCRC300 7487 100 162 170 173 CGCRC301 5881 100 156 169 169
CGCRC302 24784 84 154 165 164 CGCRC302 11763 95 159 165 165
CGCRC303 13967 95 160 169 171 CGCRC303 10161 81 160 169 172
CGCRC303 10845 100 160 169 172 CGCRC304 16168 90 153 167 164
CGCRC304 10502 100 152 165 163 CGCRC304 12987 101 154 165 165
CGCRC305 12507 100 159 169 171 CGCRC305 10301 100 156 168 168
CGCRC306 8594 101 157 165 169 CGCRC306 9437 90 159 167 171 CGCRC306
8090 100 152 163 168 CGCRC306 4585 103 158 167 170 CGCRC306 7395 81
160 166 171 CGCRC306 4885 100 152 167 167 CGCRC306 3700 100 159 166
171 CGCRC307 6860 100 158 170 170 CGCRC307 10065 95 157 168 169
CGCRC307 7520 102 156 167 168 CGCRC307 6623 76 157 169 168 CGCRC307
10606 100 155 167 168 CGCRC307 13189 90 158 168 171 CGCRC308 16287
90 159 168 169 CGCRC308 7729 100 160 164 170 CGCRC308 14067 92 157
170 169 CGCRC309 13036 85 157 170 169 CGCRC309 9084 101 157 166 168
CGCRC310 7393 100 153 165 164 CGCRC310 11689 100 152 166 164
CGCRC310 10273 100 153 166 164 CGCRC311 8456 94 160 171 172
CGCRC312 4719 100 160 165 173 CGCRC312 3391 101 157 172 170
CGCRC313 5013 100 163 166 174 CGCRC313 8150 72 161 171 174 CGCRC314
4684 100 158 165 169 CGCRC314 6902 85 159 165 170 CGCRC314 7229 102
158 167 170 CGCRC315 8739 94 155 167 169 CGCRC315 9623 101 158 166
170 Stage at Amino Acid Patient Patient Type Diagnosis Alteration
Type Gene (Protein) CGCRC316 Colorectal Cancer III Tumor-derived
TP53 245G > S CGCRC316 Colorectal Cancer III Tumor-derived
CDKN2A 1M > R CGCRC316 Colorectal Cancer III Tumor-derived
CTNNB1 37S > C CGCRC316 Colorectal Cancer III Tumor-derived EGFR
2732 - 3C > T CGCRC316 Colorectal Cancer III Hematopoietic ATM
3008R > P CGCRC317 Colorectal Cancer III Tumor-derived TP53 220Y
> C CGCRC317 Colorectal Cancer III Tumor-derived ATM 1026W >
R CGCRC317 Colorectal Cancer III Tumor-derived APC 216R > X
CGCRC318 Colorectal Cancer I Hematopoietic DNMT3A 698W > X
CGCRC320 Colorectal Cancer I Germline KIT 18L > F CGCRC320
Colorectal Cancer I Tumor-derived ERBB4 78R > W CGCRC321
Colorectal Cancer I Tumor-derived CDKN2A 12S > L CGCRC321
Colorectal Cancer I Hernatopcietic DNMT3A 882R > H CGCRC321
Colorectal Cancer I Germline EGFR 511S > Y CGCRC332 Colorectal
Cancer IV Tumor-derived TP53 125T > R CGCRC333 Colorectal Cancer
IV Tumor-derived TP53 673 - 2A > G CGCRC333 Colorectal Cancer IV
Tumor-derived BRAF 600V > E CGCRC333 Colorectal Cancer IV
Tumor-derived ERBB4 891E > A CGCRC334 Colorectal Cancer IV
Tumor-derived TP53 245G > S CGCRC334 Colorectal Cancer IV
Germline EGFR 638T > M CGCRC334 Colorectal Cancer IV
Tumor-derived PIK3CA 104P > R CGCRC335 Colorectal Cancer IV
Tumor-derived BRAF 600V > E CGCRC336 Colorectal Cancer IV
Tumor-derived TP53 175R > H CGCRC336 Colorectal Cancer IV
Tumor-derived KRAS 12G > V CGCRC336 Colorectal Cancer IV
Tumor-derived APC 1286E > X CGCRC337 Colorectal Cancer IV
Tumor-derived STK11 734 + ST > A CGCRC337 Colorectal Cancer IV
Germline APC 485M > I OGORC338 Colorectal Cancer IV
Tumor-derived KRAS 12G > D CGCRC339 Colorectal Cancer IV
Tumor-derived KRAS 13G > D
CGCRC339 Colorectal Cancer IV Tumor-derived APC 876R > X
CGCRC339 Colorectal Cancer IV Tumor-derived PIK3CA 407C > F
CGCRC339 Colorectal Cancer IV Tumor-derived PIK3CA 1047H > L
CGCRC340 Colorectal Cancer IV Tumor-derived TP53 196R > X
CGCRC340 Colorectal Cancer IV Tumor-derived APC 1306E > X
CGPLBR38 Breast Cancer I Tumor-derived TP53 241S > P CGPLBR40
Breast Cancer III Germline AR 392P > R CGPLBR44 Breast Cancer
III Hematopoietic DNMT3A 882R > H CGPLBR44 Breast Cancer III
Hematopoietic DNMT3A 705I > T CGPLBR44 Breast Cancer III
Tumor-derived PDGFRA 859V > M CGPLBR48 Breast Cancer II Germline
ALK 1231R > Q CGPLBR48 Breast Cancer II Tumor-derived EGFR 669R
> Q CGPLBR55 Breast Cancer III Hematopoietic DNMT3A 743P > S
CGPLBR55 Breast Cancer III Tumor-derived GNAS 201R > H CGPLBR55
Breast Cancer III Tumor-derived PIK3CA 345N > K CGPLBR63 Breast
Cancer II Germline FGFR3 403K > E CGPLBR67 Breast Cancer II
Hematopoietic DNMT3A 882R > H CGPLBR67 Breast Cancer II
Tumor-derived PIK3CA 545E > K CGPLBR67 Breast Cancer II
Tumor-derived ERBB4 1000D > A CGPLBR69 Breast Cancer II
Hematopoietic DNMT3A 774E > V CGPLBR69 Breast Cancer II Germline
CTNNB1 30Y > S CGPLBR69 Breast Cancer II Germline IDH1 231Y >
N CGPLBR70 Breast Cancer II Tumor-derived ATM 2832R > H CGPLBR70
Breast Cancer II Germline APC 1577E > D CGPLBR71 Breast Cancer
II Tumor-derived TP53 273R > H CGPLBR72 Breast Cancer II
Germline APC 1532D > G CGPLBR73 Breast Cancer II Tumor-derived
ALK 708S > P CGPLBR73 Breast Cancer II Germline ERBB4 158A >
E CGPLBR74 Breast Cancer II Germline AR 20 + G1G > T CGPLBR75
Breast Cancer II Tumor-derived PIK3CA 1047H > R CGPLBR76 Breast
Cancer II Germline KDR 1290S > N CGPLBR76 Breast Cancer II
Tumor-derived PIK3CA 1047H > R CGPLBR77 Breast Cancer III
Tumor-derived PTEN 170S > I CGPLBR80 Breast Cancer II
Tumor-derived CDKN2A 12S > L CGPLBR83 Breast Cancer II Germline
AR 728N > D CGPLBR83 Breast Cancer II Tumor-derived ATM 322E
> K CGPLBR83 Breast Cancer II Germline ERBB4 539Y > S
CGPLBR86 Breast Cancer II Germline STK11 354F > L Alteration
Mutant Mutation Hotspot Detected Allele Patient Nucleotide Type
Alteration in Tissue Fraction CGCRC316 chr17_7577548-7577548_C_T
Substitution Yes Yes 6.52% CGCRC316 chr9_21974625-21974825_A_C
Substitution No Yes 5.74% CGCRC316 chr3_41266113-41266113_C_G
Substitution Yes Yes 5.47% CGCRC316 chr7_55266407-55266407_C_T
Substitution No No 0.11% CGCRC316 chr11_108236087-108236087_G_C
Substitution No Yes 0.13% CGCRC317 chr17_7578190-7578190_T_C
Substitution Yes Yes 0.36% CGCRC317 chr11_108142132-108142132_T_C
Substitution No Yes 0.23% CGCRC317 chr5_112128143-112128143_C_T
Substitution Yes No 0.29% CGCRC318 chr2_25463589-25463589_C_T
Substitution No Yes 0.25% CGCRC320 chr4_55524233-55524233_C_T
Substitution NA Yes 34.76% CGCRC320 chr2_212989479-212989479_G_A
Substitution No No 0.12% CGCRC321 chr9_21974792-21974792_C_T
Substitution No No 0.20% CGCRC321 chr2_25457242-25457242_C_A
Substitution You No 0.08% CGCRC321 chr7_55229225-55229225_G_C
Substitution NA Yes 41.86% CGCRC332 chr17_7579313-7579313_T_C
Substitution No Yes 19.98% CGCRC333 chr17_7577610-7577610_A_T
Substitution No Yes 43.03% CGCRC333 chr7_140453136-140453136_T_G
Substitution Yes Yes 22.26% CGCRC333 chr2_212495194-212495194_C_T
Substitution No No 1.00% CGCRC334 chr17_7577548-7577548_C_T
Substitution Yes Yes 13.44% CGCRC334 chr7_55238900-55238900_C_T
Substitution NA Yes 35.28% CGCRC334 chr3_178916924-178916924_C_G
Substitution No No 3.85% CGCRC335 chr7_140453136-140453136_A_T
Substitution Yes Yes 0.32% CGCRC336 chr17_7578406-7578406_C_T
Substitution Yes Yes 75.76% CGCRC336 chr12_25398284-25398284_C_A
Substitution Yes Yes 42.87% CGCRC336 chr5_112175147-112175147_G_T
Substitution No Yes 81.61% CGCRC337 chr19_1220718-1220718_T_A
Substitution No No 0.12% CGCRC337 chr5_112162851-112162851_G_A
Substitution NA Yes 46.26% OGORC338 chr12_25398284-25398284_C_T
Substitution Yes Yes 27.03% CGCRC339 chr12_25398281-25398281_C_T
Substitution Yes Yes 1.94% CGCRC339 chr5_112173917-112173917_C_T
Substitution Yes Yes 2.35% CGCRC339 chr3_178927457-178927457_G_T
Substitution No Yes 3.14% CGCRC339 chr3_178952085-178952085_A_T
Substitution Yes Yes 1.71% CGCRC340 chr17_7578263-7578263_G_A
Substitution Yes Yes 18.26% CGCRC340 chr5_112175207-112175207_G_T
Substitution Yes Yes 22.57% CGPLBR38 chr17_7577560-7577560_A_G
Substitution No Yes 0.53% CGPLBR40 chrX_66766163-66766163_C_G
Substitution NA Yes 28.99% CGPLBR44 chr2_25457242-25457242_C_T
Substitution Yes Yes 1.82% CGPLBR44 chr2_25463568-25463568_A_G
Substitution No Yes 0.41% CGPLBR44 chr4_55153609-55153609_G_A
Substitution No Yes 0.13% CGPLBR48 chr2_2936301-2936301_C_T
Substitution NA Yes 34.61% CGPLBR48 chr7_55240762-55240762_G_A
Substitution No No 0.18% CGPLBR55 chr2_25463266-25463266_G_A
Substitution No No 0.18% CGPLBR55 chr20_57484421-57484421_G_A
Substitution Yes Yes 0.68% CGPLBR55 chr_178921553-178921553_T_A
Substitution Yes Yes 0.42% CGPLBR63 chr3_1806188-1806188_A_G
Substitution NA Yes 34.82% CGPLBR67 chr4_25457242-25457242_C_T
Substitution Yes Yes 0.11% CGPLBR67 chr3_178936091-178936091_G_A
Substitution Yes Yes 0.68% CGPLBR67 chr2_212285302-212285302_T_G
Substitution No No 0.28% CGPLBR69 chr2_25463172-25463172_T_A
Substitution No No 0.29% CGPLBR69 chr3_41266092-41266092_A_C
Substitution NA Yes 41.74% CGPLBR69 chr2_209108158-209108158_A_T
Substitution NA Yes 41.86% CGPLBR70 chr11_108216546-108216546_G_A
Substitution No No 0.36% CGPLBR70 chr5_112176022-112176022_A_C
Substitution NA Yes 40.28% CGPLBR71 chr17_7577120-7577120_C_T
Substitution Yes Yes 0.10% CGPLBR72 chr5_112175886-112175886_A_G
Substitution NA Yes 44.03% CGPLBR73 chr2_29474053-29474053_A_G
Substitution No No 0.27% CGPLBR73 chr2_212652833-212652833_G_T
Substitution NA Yes 35.58% CGPLBR74 chrX_66788865-66788865_G_T
Substitution NA Yes 36.23% CGPLBR75 chr3_178952085-178952085_A_G
Substitution Yes Yes 0.14% CGPLBR76 chr4_55946310-55946310_C_T
Substitution NA Yes 36.57% CGPLBR76 chr3_178952085-178952085_A_G
Substitution Yes Yes 0.12% CGPLBR77 chr10_89711891-89711891_G_T
Substitution No Yes 2.29% CGPLBR80 chr9_21974792-21974792_G_A
Substitution No No 0.54% CGPLBR83 chrX_66937328-66937328_A_G
Substitution NA Yes 42.66% CGPLBR83 chr11_108117753-108117753_G_A
Substitution No No 0.28% CGPLBR83 chr2_212543783-212543783_T_G
Substitution NA Yes 44.91% CGPLBR86 chr19_1223125-1223125_C_G
Substitution NA Yes 42.32% Wild-type Fragments 25th Minimum
Percentile Mode Median cfDNA cfDNA cfDNA cfDNA Fragment Fragment
Fragment Fragment Distinct Size Size Size Size Patient Coverage
(bp) (bp) (bp) (bp) CGCRC316 12880 100 150 166 163 CGCRC316 7479 93
157 164 168 CGCRC316 13682 100 149 165 162 CGCRC316 16716 85 153
166 156 CGCRC316 17060 100 150 166 153 CGCRC317 14587 84 152 166
154 CGCRC317 10483 100 152 164 155 CGCRC317 3497 101 149 166 163
CGCRC318 16436 98 158 170 170 CGCRC320 6521 100 163 170 175
CGCRC320 11633 100 162 174 174 CGCRC321 6918 88 161 167 174
CGCRC321 9559 94 159 171 170 CGCRC321 5545 100 159 172 172 CGCRC332
605 104 164 170 176 CGCRC333 1265 89 159 165 171 CGCRC333 3338 102
153 165 169 CGCRC333 3008 102 153 169 109 CGCRC334 1725 105 160 170
175 CGCRC334 1168 100 159 164 174 CGCRC334 1798 103 159 166 173
CGCRC335 2411 99 155 167 167 CGCRC336 757 104 156 171 170 CGCRC336
1080 102 150 166 167 CGCRC336 391 102 161 165 171 CGCRC337 6497 72
153 169 177 CGCRC337 1686 100 147 170 153 OGORC338 1408 105 153 164
156 CGCRC339 1256 105 158 168 159 CGCRC339 1639 101 158 165 172
CGCRC339 1143 100 154 170 167 CGCRC339 1584 108 161 171 173
CGCRC340 876 101 162 170 175 CGCRC340 796 105 159 164 174 CGPLBR38
9684 95 156 166 168 CGPLBR40 10277 78 162 168 173 CGPLBR44 10715 99
162 171 173 CGPLBR44 10837 100 159 169 171 CGPLBR44 12640 100 159
168 171 CGPLBR48 5631 100 164 170 179 CGPLBR48 12467 101 167 174
180 CGPLBR55 10527 101 158 169 169 CGPLBR55 6011 101 153 166 167
CGPLBR55 3973 101 153 166 166 CGPLBR63 3405 97 165 170 176 CGPLBR67
10259 87 157 166 168 CGPLBR67 5163 100 151 167 165 CGPLBR67 6250
100 155 166 187 CGPLBR69 7558 100 159 166 170 CGPLBR69 3938 101 154
169 166 CGPLBR69 2387 101 157 166 168 CGPLBR70 6916 100 158 171 169
CGPLBR70 3580 107 160 169 173 CGPLBR71 7930 85 156 166 158 CGPLBR72
2389 100 157 160 170 CGPLBR73 11348 95 161 173 174 CGPLBR73 3422
102 157 168 169 CGPLBR74 9784 101 163 175 174 CGPLBR75 7290 103 162
173 172 CGPLBR76 4342 104 166 171 179 CGPLBR76 11785 100 165 168
177 CGPLBR77 6161 100 158 166 169 CGPLBR80 3643 96 166 166 185
CGPLBR83 3479 105 162 164 174 CGPLBR83 3496 103 165 170 177
CGPLBR83 1748 100 164 173 175 CGPLBR86 4241 98 160 168 175 Stage at
Amino Acid Patient Patient Type Diagnosis Alteration Type Gene
(Protein) CGPLBR86 Breast Cancer II Germline SMARCB1 795 + 3A >
G CGPLBR87 Breast Cancer II Tumor-derived JAK2 215R > X CGPLBR87
Breast Cancer II Hematopoietic DNMT3A 882R > H CGPLBR87 Breast
Cancer II Tumor-derived SMAD4 496R > C CGPLBR87 Breast Cancer II
Germline AR 651S > N CGPLBR88 Breast Cancer II Tumor-derived
CDK6 51E > K CGPLBR88 Breast Cancer II Germline APC 1125V > A
CGPLBR92 Breast Cancer II Tumor-derived TP53 257L > P CGPLBR96
Breast Cancer II Tumor-derived TP53 213R > X CGPLBR96 Breast
Cancer II Hematopoietic DNMT3A 531D > G CGPLBR96 Breast Cancer
II Tumor-derived AR 13R > Q CGPLBR97 Breast Cancer II
Hematopoietic DNMT3A 882R > H CGPLBR97 Breast Cancer II Germline
PDGFRA 401A > D CGPLBR97 Breast Cancer II Tumor-derived GNAS
201R > H CGPLLU144 Lung Cancer II Tumor-derived TP53 241S > F
CGPLLU144 Lung Cancer II Tumor-derived KRAS 12G > C CGPLLU144
Lung Cancer II Tumor-derived EGFR 373P > S CGPLLU144 Lung Cancer
II Tumor-derived ATM 292P > L CGPLLU144 Lung Cancer II
Tumor-derived PIK3CA 545E > K CGPLLU144 Lung Cancer II
Tumor-derived ERBB4 426R > K CGPLLU146 Lung Cancer II
Tumor-derived JAK2 617V > F CGPLLU146 Lung Cancer II
Tumor-derived TP53 282R > P CGPLLU146 Lung Cancer II
Tumor-derived DNMT3A 737L > H CGPLLU146 Lung Cancer II
Tumor-derived RB1 861 + 2T > C CGPLLU146 Lung Cancer II
Tumor-derived ATM 581L > F CGPLLU147 Lung Cancer III
Tumor-derived TP53 248R > Q CGPLLU147 Lung Cancer III
Tumor-derived TP53 201L > X CGPLLU147 Lung Cancer III
Tumor-derived ALK 1537G > E CGPLLU147 Lung Cancer III Germline
PDGFRA 200T > S CGPLLU162 Lung Cancer II Tumor-derived CDKN2A
12S > L CGPLLU162 Lung Cancer II Tumor-derived EGFR 858L > R
CGPLLU162 Lung Cancer II Tumor-derived BRAF 354R > Q CGPLLU163
Lung Cancer II Tumor-derived CDKN2A 12S > L CGPLLU163 Lung
Cancer II Hematopoietic DNMT3A 528Y > D CGPLLU164 Lung Cancer II
Tumor-derived STK11 216S > Y CGPLLU164 Lung Cancer II Germline
STK11 354F > L CGPLLU164 Lung Cancer II Tumor-derived GNA11 606
- 3C > T CGPLLU164 Lung Cancer II Tumor-derived TP53 278P > S
CGPLLU164 Lung Cancer II Tumor-derived TP53 161A > S CGPLLU164
Lung Cancer II Tumor-derived TP53 160M > I CGPLLU164 Lung Cancer
II Tumor-derived ERBB4 1299P > L CGPLLU164 Lung Cancer II
Tumor-derived ERBB4 253N > S CGPLLU165 Lung Cancer II
Tumor-derived STK11 354F > L CGPLLU165 Lung Cancer I
Tumor-derived GNAS 201R > H CGPLLU168 Lung Cancer I
Tumor-derived TP53 136Q > X CGPLLU168 Lung Cancer I
Hematopoietic DNMT3A 736R > S CGPLLU168 Lung Cancer I
Tumor-derived EGFR 858L > R CGPLLU174 Lung Cancer I
Tumor-derived STK11 597 + 1G > T CGPLLU174 Lung Cancer I
Tumor-derived JAK2 160D > Y CGPLLU174 Lung Cancer I
Tumor-derived KRAS 12G > C CGPLLU174 Lung Cancer I Hematopoietic
DNMT3A 891R > W CGPLLU174 Lung Cancer I Hematopoietic DNMT3A
715I > M CGPLLU175 Lung Cancer I Tumor-derived TP53 179H > R
CGPLLU175 Lung Cancer I Hematopoietic DNMT3A 2598 - 1I > A
CGPLLU175 Lung Cancer I Hematopoietic DNMT3A 755F > L CGPLLU175
Lung Cancer I Germline ATM 337R > C CGPLLU175 Lung Cancer I
Tumor-derived ERBB4 941Q > X CGPLLU176 Lung Cancer I
Hematopoietic DNMT3A 750P > S CGPLLU176 Lung Cancer I
Hematopoietic DNMT3A 735Y > C CGPLLU177 Lung Cancer II
Tumor-derived KRAS 12G > V CGPLLU177 Lung Cancer II
Hematopoietic DNMT3A 897V > G
CGPLLU177 Lung Cancer II Hematopoietic DNMT3A 862R > C CGPLLU177
Lung Cancer II Hematopoietic DNMT3A 2173 + 1 > A CGPLLU178 Lung
Cancer I Tumor-derived CDH1 251 > M CGPLLU178 Lung Cancer I
Tumor-derived PIK3CA 861Q > X CGPLLU179 Lung Cancer I
Hematopoietic DNMT3A 879N > D CGPLLU179 Lung Cancer I Germline
APC 2611T > I Alteration Mutant Mutation Hotspot Detected Allele
Patient Nucleotide Type Alteration in Tissue Fraction CGPLBR86
chr22_24159126-24159124_A_G Substitution NA Yes 42.38% CGPLBR87
chr9_5054591-5054591_C_T Substitution No No 0.35% CGPLBR87
chr2_25457242-25457242_C_T Substitution You No 0.31% CGPLBR87
chr18_48604664-48604664_C_T Substitution No No 0.40% CGPLBR87
chrX_66931310-66931310_G_A Substitution NA Yes 42.94% CGPLBR88
chr7_92462487-92462487_C_T Substitution No No 0.13% CGPLBR88
chr5_112174665-112174665_T_C Substitution NA Yes 31.19% CGPLBR92
chr17_7577511-7577511_A_G Substitution No Yes 0.20% CGPLBR96
chr17.fa:7578212-7578212_G_A Substitution Yes No 0.10% CGPLBR96
chr2_25467484-25467484_C_T Substitution No Yes 5.81% CGPLBR96
chrX_66765026-66765026_G_A Substitution No No 0.60% CGPLBR97
chr2_25457242-25457242_C_T Substitution Yes Yes 0.11% CGPLBR97
chr4_55136880-55136880_C_A Substitution NA Yes 34.12% CGPLBR97
chr20_57484421-57484421_G_A Substitution Yes Yes 0.13% CGPLLU144
chr17_7577559-7577559_G_A Substitution Yes Yes 1.95% CGPLLU144
chr12_25398285-25398285_C_A Substitution Yes Yes 5.10% CGPLLU144
chr7_55224336-55224336_C_T Substitution No Yes 0.16% CGPLLU144
chr11_108115727-108115727_C_T Substitution No No 0.22% CGPLLU144
chr3_178936091-178936091_G_A Substitution Yes Yes 2.94% CGPLLU144
chr2_212568841-212568841_C_T Substitution No No 0.18% CGPLLU146
chr9_5073770-5073770_G_T Substitution Yes No 0.25% CGPLLU146
chr17_7577093-7577093_C_G Substitution No Yes 1.30% CGPLLU146
chr2_25463283-25463283_A_T Substitution No Yes 0.84% CGPLLU146
chr13_48937095-48937095_T_C Substitution No Yes 0.87% CGPLLU146
chr11_108122699-108122699_A_T Substitution No No 0.20% CGPLLU147
chr17_7577538-7577538_C_T Substitution Yes No 0.15% CGPLLU147
chr17_7578247-7578247_A_T Substitution No Yes 0.55% CGPLLU147
chr2_29416343-29416343_C_T Substitution No Yes 0.94% CGPLLU147
chr4_55130065-55130065_C_G Substitution NA Yes 43.47% CGPLLU162
chr9_21974792-21974792_G_A Substitution No No 0.22% CGPLLU162
chr7_55259515-55259515_T_G Substitution Yes Yes 0.22% CGPLLU162
chr7_140494187-140494187_C_T Substitution No No 0.14% CGPLLU163
chr9_21974792-21974792_G_A Substitution No No 0.21% CGPLLU163
chr2_25467494-25467494_A_C Substitution No Yes 0.15% CGPLLU164
chr19_1220629-1220629_C_A Substitution No Yes 1.23% CGPLLU164
chr19_1223125-1223125_C_G Substitution NA Yes 45.52% CGPLLU164
chr19_3118919-3118919_C_T Substitution No No 0.20% CGPLLU164
chr17_7577106-7577106_G_A Substitution Yes No 0.10% CGPLLU164
chr17_7578449-7578449_C_A Substitution No Yes 1.78% CGPLLU164
chr17_7578450-7578450_C_A Substitution No Yes 1.86% CGPLLU164
chr2_212248371-212248371_G_A Substitution No Yes 0.96% CGPLLU164
chr2_212587243-212587243_T_C Substitution No No 0.22% CGPLLU165
chr19_1223125-1223125_C_G Substitution NA Yes 36.62% CGPLLU165
chr20_57484421-57484421_G_A Substitution Yes Yes 0.16% CGPLLU168
chr17.fa:7578524-7578524_G_A Substitution Yes Yes 0.06% CGPLLU168
chr2_25463287-25463287_G_T Substitution No No 0.39% CGPLLU168
chr7.fa:55259515-55259515_T_G Substitution Yes Yes 0.07% CGPLLU174
chr19_1220505-1220505_G_T Substitution No Yes 0.33% CGPLLU174
chr9_5050695-5050695_G_T Substitution No Yes 0.40% CGPLLU174
chr12_25398285-25398285_C_A Substitution Yes Yes 0.16% CGPLLU174
chr2_25457216-25457216_G_A Substitution No Yes 0.29% CGPLLU174
chr2_25463537-25463537_G_C Substitution No Yes 0.26% CGPLLU175
chr17_7578394-7578394_T_C Substitution Yes Yes 8.03% CGPLLU175
chr2_25457216-25457216_C_T Substitution No No 0.21% CGPLLU175
chr2_25463230-25463230_A_G Substitution No No 0.15% CGPLLU175
chr11_108117798-108117798_C_T Substitution NA Yes 43.84% CGPLLU175
chr2_212288925-212288925_G_A Substitution No Yes 3.64% CGPLLU176
chr2_25463245-25463245_G_A Substitution No Yes 0.92% CGPLLU176
chr2_25463289-25463289_T_C Substitution No Yes 0.12% CGPLLU177
chr12_25398284-25398284_C_A Substitution Yes Yes 2.49% CGPLLU177
chr2_25457197-25457197_A_C Substitution No Yes 1.53% CGPLLU177
chr2_25457243-25457243_G_A Substitution Yes No 0.29% CGPLLU177
chr2_25463508-25463508_C_T Substitution No No 0.13% CGPLLU178
chr16_68844164-68844164_C_T Substitution No No 0.29% CGPLLU178
chr3_178947145-178947145_C_T Substitution No No 0.17% CGPLLU179
chr2_25457252-25457252_T_C Substitution No Yes 0.38% CGPLLU179
chr5_112179123-112179123_C_T Substitution NA Yes 39.91% Wild-type
Fragments 25th Minimum Percentile Mode Median cfDNA cfDNA cfDNA
cfDNA Fragment Fragment Fragment Fragment Distinct Size Size Size
Size Patient Coverage (bp) (bp) (bp) (bp) CGPLBR86 3096 88 160 167
174 CGPLBR87 3680 101 162 168 175 CGPLBR87 6180 101 163 164 175
CGPLBR87 7746 86 160 167 175 CGPLBR87 2286 106 160 166 172 CGPLBR88
17537 89 185 200 223 CGPLBR88 5919 101 162 172 173 CGPLBR92 15530
77 150 164 152 CGPLBR96 9893 100 159 164 171 CGPLBR96 8620 95 162
167 173 CGPLBR96 8036 85 162 169 175 CGPLBR97 14856 93 160 168 170
CGPLBR97 5329 100 161 165 171 CGPLBR97 7010 97 158 169 170
CGPLLU144 11371 100 156 165 167 CGPLLU144 7641 100 155 167 166
CGPLLU144 9996 100 158 168 169 CGPLLU144 4956 101 159 166 169
CGPLLU144 6540 100 153 170 168 CGPLLU144 7648 101 156 164 166
CGPLLU146 5920 100 155 164 168 CGPLLU146 9356 100 155 166 168
CGPLLU146 7284 101 158 165 170 CGPLLU146 4183 103 160 166 170
CGPLLU146 6778 100 157 166 158 CGPLLU147 4807 100 155 166 170
CGPLLU147 5282 100 156 167 171 CGPLLU147 7122 100 158 174 173
CGPLLU147 2825 101 160 165 173 CGPLLU162 9940 95 161 164 174
CGPLLU162 13855 87 160 174 173 CGPLLU162 11251 100 153 167 165
CGPLLU163 10805 85 159 165 173 CGPLLU163 20185 83 158 166 170
CGPLLU164 8795 91 156 161 169 CGPLLU164 4561 92 157 164 169
CGPLLU164 8097 100 158 170 170 CGPLLU164 9241 100 155 165 157
CGPLLU164 10806 100 157 168 159 CGPLLU164 10919 100 157 168 159
CGPLLU164 5412 103 159 175 170 CGPLLU164 5151 101 160 166 169
CGPLLU165 7448 95 155 167 167 CGPLLU165 5822 102 154 166 166
CGPLLU168 15985 97 152 165 166 CGPLLU168 11070 100 156 165 168
CGPLLU168 11063 83 157 166 169 CGPLLU174 5881 88 162 165 174
CGPLLU174 3696 100 162 167 172 CGPLLU174 4941 101 162 167 172
CGPLLU174 7527 100 163 168 173 CGPLLU174 8353 101 162 168 173
CGPLLU175 10214 100 160 166 170 CGPLLU175 9739 100 157 168 158
CGPLLU175 9509 100 157 165 158 CGPLLU175 2710 101 157 165 157
CGPLLU175 6565 100 158 166 158 CGPLLU176 6513 101 164 168 175
CGPLLU176 5962 100 164 174 175 CGPLLU177 7044 102 160 165 170
CGPLLU177 9950 88 160 169 171 CGPLLU177 11233 100 160 168 171
CGPLLU177 10966 75 160 169 172 CGPLLU178 5378 100 162 176 172
CGPLLU178 7235 101 159 167 170 CGPLLU179 6350 103 161 169 171
CGPLLU179 2609 108 162 171 173 Stage at Amino Acid Patient Patient
Type Diagnosis Alteration Type Gene (Protein) CGPLLU180 Lung Cancer
I Tumor-derived STK11 237D > Y CGPLLU180 Lung Cancer I
Tumor-derived TP53 293G > V CGPLLU180 Lung Cancer I
Tumor-derived TP53 282R > P CGPLLU180 Lung Cancer I
Tumor-derived TP53 177P > L CGPLLU180 Lung Cancer I
Tumor-derived RB1 565S > X CGPLLU197 Lung Cancer I Hematopoietic
DNMT3A 882R > C CGPLLU197 Lung Cancer I Hematopoietic DNMT3A
879N > D CGPLLU198 Lung Cancer I Tumor-derived TP53 162I > N
CGPLLU198 Lung Cancer I Tumor-derived EGFR 858L > R CGPLLU202
Lung Cancer I Tumor-derived EGFR 790T > M CGPLLU202 Lung Cancer
I Tumor-derived EGFR 868E > X CGPLLU204 Lung Cancer I
Tumor-derived KIT 956R > Q CGPLLU205 Lung Cancer II
Hematopoietic DNMT3A 736R > C CGPLLU205 Lung Cancer II
Hematopoietic DNMT3A 696Q > X CGPLLU206 Lung Cancer III
Tumor-derived TP53 672 + 1G > A CGPLLU206 Lung Cancer III
Tumor-derived TP53 131N > S CGPLLU207 Lung Cancer II
Tumor-derived TP53 376 - 1G > A CGPLLU207 Lung Cancer II
Germline ALK 419P > L CGPLLU207 Lung Cancer II Tumor-derived
EGFR 790T > M CGPLLU208 Lung Cancer II Tumor-derived TP53 250P
> L CGPLLU208 Lung Cancer II Germline EGFR 224R > H CGPLLU208
Lung Cancer II Tumor-derived EGFR 858L > R CGPLLU208 Lung Cancer
II Tumor-derived MYC 98R > W CGPLLU209 Lung Cancer II Germline
STK11 354F > L CGPLLU209 Lung Cancer II Tumor-derived TP53 100Q
> X CGPLLU209 Lung Cancer II Tumor-derived CDKN2A 88E > X
CGPLLU209 Lung Cancer II Tumor-derived PDGFRA 921A > T CGPLLU209
Lung Cancer II Germline EGFR 567M > V CGPLOV10 Ovarian Cancer I
Tumor-derived TP53 342R > X CGPLOV11 Ovarian Cancer IV
Tumor-derived TP53 248R > Q CGPLOV11 Ovarian Cancer IV Germline
TP53 63A > V CGPLOV13 Ovarian Cancer IV Tumor-derived ALK 444W
> C CGPLOV13 Ovarian Cancer IV Germline PDGFRA 401A > D
CGPLOV13 Ovarian Cancer IV Tumor-derived KIT 135R > H CGPLOV14
Ovarian Cancer I Tumor-derived HNF1A 230E > K CGPLOV15 Ovarian
Cancer III Tumor-derived TP53 278P > S CGPLOV15 Ovarian Cancer
III Tumor-derived EGFR 433H > D CGPLOV17 Ovarian Cancer I
Tumor-derived TP53 248R > Q CGPLOV17 Ovarian Cancer I Germline
PDGFRA 1071D > N CGPLOV18 Ovarian Cancer I Germline APC 1125V
> A CGPLOV19 Ovarian Cancer II Germline FGFR3 403K > E
CGPLOV19 Ovarian Cancer II Tumor-derived TP53 273R > H CGPLOV19
Ovarian Cancer II Germline AR 176S > R CGPLOV19 Ovarian Cancer
II Tumor-derived APC 1378Q > X CGPLOV20 Ovarian Cancer II
Tumor-derived TP53 195I > T CGPLOV20 Ovarian Cancer II Germline
EGFR 253K > R CGPLOV21 Ovarian Cancer IV Germline STK11 354F
> L CGPLOV21 Ovarian Cancer IV Tumor-derived TP53 275C > Y
CGPLOV21 Ovarian Cancer IV Tumor-derived ERBB4 602S > T CGPLOV22
Ovarian Cancer III Tumor-derived TP53 193H > P CGPLOV22 Ovarian
Cancer III Tumor-derived CTNNB1 41T > A Alteration Mutant
Mutation Hotspot Detected Allele Patient Nucleotide Type Alteration
in Tissue Fraction CGPLLU180 chr19_1220691-1220691_G_T Substitution
No You 2.43% CGPLLU180 chr17_7577060-7577060_C_A Substitution No
Yes 2.07% CGPLLU180 chr17_7577093-7577093_C_G Substitution No Yes
1.94% CGPLLU180 chr17:fa_7578400-7578400_G_A Substitution Yes No
0.08% CGPLLU180 chr13_48955578-48955578_C_G Substitution No Yes
1.01% CGPLLU197 chr2_25457243-25457243_G_A Substitution Yes No
0.16% CGPLLU197 chr2_25457252-25457252_T_C Substitution No No 0.38%
CGPLLU198 chr17_7578445-7578445_A_T Substitution No Yes 0.87%
CGPLLU198 chr7_55259515-55259515_T_G Substitution Yes Yes 0.52%
CGPLLU202 chr7:fa_55249071-55249071_C_T Substitution Yes Yes 0.05%
CGPLLU202 chr7_55259544-55259544_G_T Substitution No No 0.13%
CGPLLU204 chr4_55604659-55604659_G_A Substitution No No 0.26%
CGPLLU205 chr2_25463287-25463287_G_A Substitution No Yes 0.70%
CGPLLU205 chr2_25463598-25463598_G_A Substitution No Yes 3.47%
CGPLLU206 chr17_7578176-7578176_C_T Substitution Yes Yes 26.13%
CGPLLU206 chr17_7578538-7578538_T_C Substitution No No 0.21%
CGPLLU207 chr17_7578555-7578555_C_T Substitution Yes Yes 0.32%
CGPLLU207 chr2_29606625-29606625_A_G Substitution NA Yes 34.38%
CGPLLU207 chr7:fa_55249071-55249071_C_T Substitution Yes No 0.09%
CGPLLU208 chr17_7577532-7577532_G_A Substitution Yes Yes 1.33%
CGPLLU208 chr7_55220281-55220281_G_A Substitution NA Yes 39.34%
CGPLLU208 chr7_55259515-55259515_T_G Substitution Yes Yes 0.86%
CGPLLU208 chr8_128750755-128750755_C_T Substitution No No 0.17%
CGPLLU209 chr19_1223125-1223125_C_G Substitution NA Yes 26.84%
CGPLLU209 chr17_7579389-7579389_G_A Substitution No Yes 9.97%
CGPLLU209 chr9_21971096-21971096_C_A Substitution Yes Yes 9.13%
CGPLLU209 chr4_55155052-55155052_G_A Substitution No Yes 9.82%
CGPLLU209 chr7_55231493-55231493_A_G Substitution NA Yes 30.41%
CGPLOV10 chr17_7574003-7574003_G_A Substitution Yes Yes 3.14%
CGPLOV11 chr17_7577538-7577538_C_T Substitution Yes Yes 0.87%
CGPLOV11 chr17_7579499-7579499_G_A Substitution NA Yes 37.77%
CGPLOV13 chr2_29551296-29551296_C_A Substitution No Yes 0.12%
CGPLOV13 chr4_55136880-55136880_C_A Substitution NA Yes 37.98%
CGPLOV13 chr4_55564516-55564516_G_A Substitution No Yes 0.35%
CGPLOV14 chr12_121431484-121431484_G_A Substitution No No 0.14%
CGPLOV15 chr17_7577106-7577106_G_A Substitution Yes Yes 3.54%
CGPLOV15 chr7_55225445-55225445_C_G Substitution No No 0.19%
CGPLOV17 chr17_7577538-7577538_C_T Substitution Yes Yes 0.32%
CGPLOV17 chr4_55161382-55161382_G_A Substitution NA Yes 44.10%
CGPLOV18 chr5_112174665-112174665_T_C Substitution NA Yes 40.81%
CGPLOV19 chr4_1806186-1806186_A_G Substitution NA Yes 23.80%
CGPLOV19 chr17_7577120-7577120_C_T Substitution Yes Yes 36.83%
CGPLOV19 chrX_66765516-66765516_C_A Substitution NA Yes 65.29%
CGPLOV19 chr5_112175423-112175423_C_T Substitution Yes Yes 46.35%
CGPLOV20 chr17_7578265-7578265_A_G Substitution Yes Yes 0.21%
CGPLOV20 chr7_55221714-55221714_A_G Substitution NA Yes 44.05%
CGPLOV21 chr19_1223125-1223125_C_G Substitution NA Yes 7.68%
CGPLOV21 chr17_7577114-7577114_C_T Substitution No Yes 2.04%
CGPLOV21 chr2_212530114-212530114_C_G Substitution No No 14.36%
CGPLOV22 chr17_7578271-7578271_T_G Substitution No Yes 0.49%
CGPLOV22 chr3_41266124-41266124_A_G Substitution Yes Yes 0.34%
Wild-type Fragments 25th Minimum Percentile Mode Median cfDNA cfDNA
cfDNA cfDNA Fragment Fragment Fragment Fragment Distinct Size Size
Size Size Patient Coverage (bp) (bp) (bp) (bp) CGPLLU180 6065 91
158 165 170 CGPLLU180 6680 92 158 164 169 CGPLLU180 7790 92 158 167
168 CGPLLU180 9036 101 160 169 171 CGPLLU180 4679 100 157 169 158
CGPLLU197 7196 102 162 166 172 CGPLLU197 7147 100 161 166 172
CGPLLU198 9322 97 157 165 158 CGPLLU198 8303 100 160 173 172
CGPLLU202 14197 90 151 165 166 CGPLLU202 9279 51 150 168 167
CGPLLU204 7185 100 157 165 168 CGPLLU205 10739 96 156 165 166
CGPLLU205 12065 100 154 165 165 CGPLLU206 6746 94 148 165 164
CGPLLU206 11225 100 147 167 164 CGPLLU207 11224 100 159 165 170
CGPLLU207 4960 101 160 166 170 CGPLLU207 13216 85 161 165 172
CGPLLU208 9211 101 156 166 168 CGPLLU208 5253 100 159 164 170
CGPLLU208 10733 100 160 170 171 CGPLLU208 11421 100 158 165 171
CGPLLU209 11695 96 153 166 159 CGPLLU209 12771 94 155 163 168
CGPLLU209 16557 92 157 169 170 CGPLLU209 13057 97 158 167 171
CGPLLU209 8521 100 155 167 169 CGPLOV10 4421 101 161 165 172
CGPLOV11 7987 100 157 164 169 CGPLOV11 3782 97 160 166 171 CGPLOV13
12072 88 157 165 169 CGPLOV13 4107 103 159 166 169 CGPLOV13 6427
100 161 165 171 CGPLOV14 11418 92 154 166 171 CGPLOV15 7689 102 157
164 169 CGPLOV15 7617 101 159 167 171 CGPLOV17 4463 96 156 168 169
CGPLOV17 2884 110 157 170 170 CGPLOV18 2945 101 159 164 169
CGPLOV19 9727 95 158 167 172 CGPLOV19 4387 100 158 165 169 CGPLOV19
2775 93 161 171 171 CGPLOV19 3616 102 156 170 170 CGPLOV20 5404 94
159 165 170 CGPLOV20 3744 102 158 166 169 CGPLOV21 21823 81 158 166
169 CGPLOV21 18806 101 159 165 169 CGPLOV21 10801 89 160 166 169
CGPLOV22 11952 100 155 165 167 CGPLOV22 12399 92 150 165 164 Mutant
Fragments 75th 25th Mean Percentile Maximum Minimum Percentile
cfDNA cfDNA cfDNA cfDNA cfDNA Fragment Fragment Fragment Fragment
Fragment Size Size Size Distinct Size Size (bp) (bp) (bp) Coverage
(bp) (bp) 179 186 400 19 100 142 182 185 400 21 132 166 180 183 400
5411 92 152 177 182 400 1903 100 148 184 185 400 1344 108 155 181
182 400 2108 100 153 176 180 400 1951 101 149 176 183 399 75 123
162 177 182 400 28 101 130 183 188 399 6863 100 160 188 186 400 34
77 154 175 179 396 9 138 147 184 185 400 21 115 145 179 185 397 30
137 149 179 182 397 44 125 155 185 186 400 8167 101 180 187 186 400
3552 102 158 184 187 399 15 93 137 183 185 400 26 137 163 181 182
397 35 118 147 172 175 400 71 133 152 169 174 400 55 130 153 189
187 390 17 149 155 176 183 400 18 156 170 169 175 397 51 108 143
166 173 397 26 118 147 184 186 400 45 116 151 185 186 400 25 157
165 185 187 400 25 124 168 167 175 394 86 121 155 167 173 397 45
124 143 170 175 396 108 126 147 190 189 400 23 131 148 182 182 399
42 138 155 189 187 399 25 126 153 192 193 400 977 101 149 173 179
391 525 102 140 181 185 399 4010 100 158 178 184 399 625 100 140
175 179 398 37 111 143 181 186 398 3184 102 159 180 183 399 47 111
148 183 184 397 39 111 146 185 184 400 24 110 146 176 180 400 32
117 146 180 184 399 43 111 143 185 187 400 29 109 140 179 182 399
20 128 152 176 184 396 7515 101 160 182 182 399 31 85 145 181 182
395 428 100 135 176 180 397 352 97 136 165 172 397 15 131 137 170
173 398 25 107 138 171 173 400 27 122 147 189 169 400 91 112 165
189 169 400 27 124 144 178 184 399 24 105 143 188 189 399 8 122 143
194 192 400 17 144 163 180 183 394 15 132 159 183 185 399 233 131
162 186 186 398 27 136 155 192 195 399 23 137 144 182 184 399 29
131 157 Difference Difference Adjusted P between between Value of
Median Mean Difference Mutant Fragments Mutant Mutant between 75th
and and Mutant Mode Median Mean Percentile Maximum Wild type
Wild-type and cfDNA cfDNA cfDNA cfDNA cfDNA cfDNA cfDNA Wild-type
Fragment Fragment Fragment Fragment Fragment Fragment Fragment
cfDNA Size Size Size Size Size Size Size Fragment (bp) (bp) (bp)
(bp) (bp) (bp) (bp) Size 233 165 180 230 305 -4.0 1.54 0.475 182
176 191 198 309 7.0 8.33 0.250 167 169 186 191 399 0.0 5.89 0.000
166 166 177 183 383 -1.0 -0.25 0.874 167 170 189 191 398 1.0 5.37
0.009 166 168 185 187 386 1.0 3.80 0.025 175 167 179 182 397 0.0
2.65 0.148 167 172 182 190 370 3.0 5.31 0.368 130 139 164 155 345
-29.5 -12.79 0.000 165 173 185 159 400 2.0 3.13 0.002 171 170 177
192 335 -0.5 -11.46 0.571 176 171 177 176 290 4.0 1.22 0.475 155
159 176 175 368 -11.0 -7.99 0.052 181 162 182 161 369 -8.0 3.49
0.061 155 169 185 194 338 0.0 5.78 0.623 166 171 184 187 400 -1.0
-1.27 0.212 168 170 185 185 399 0.0 -2.62 0.114 127 174 173 193 261
3.0 -11.00 0.507 166 167 179 180 364 -3.0 -4.34 0.430 176 163 172
176 336 -6.0 -9.35 0.166 170 165 169 173 301 0.0 3.57 0.668 165 164
166 166 325 0.0 -2.15 0.630 326 170 221 301 387 -3.0 32.43 0.453
174 174 210 219 372 5.0 33.84 0.368 268 152 164 176 268 -12.0 -5.12
0.000 153 156 174 158 327 -9.5 8.37 0.036 168 163 175 177 346 -8.0
-8.84 0.057 191 175 207 199 350 3.0 22.93 0.456 180 180 189 191 338
8.0 4.06 0.154 169 166 168 175 309 2.0 0.46 0.445 197 162 166 168
377 -1.0 -0.91 0.482 162 162 164 174 302 -3.0 -6.74 0.064 145 166
189 205 333 -5.0 -0.80 0.297 155 174 177 187 343 5.5 -4.51 0.171
176 176 188 229 305 7.0 -0.19 0.234 189 170 182 192 380 -1.0 -9.76
0.000 168 159 168 176 382 -7.0 -5.57 0.052 166 170 181 185 398 0.0
0.37 0.770 167 162 172 181 380 -9.0 -6.68 0.009 142 166 172 186 321
-1.0 -2.36 0.572 168 172 182 187 400 0.5 0.95 0.564 144 169 176 153
353 -1.0 -4.83 0.598 182 162 182 155 337 -7.0 -0.44 0.064 309 182
208 284 355 14.0 22.31 0.031 154 157 167 166 298 -11.0 -8.94 0.013
144 177 187 212 319 9.0 7.22 0.062 204 159 186 204 387 -12.0 3.32
0.031 180 163 166 180 219 -6.5 -13.04 0.155 170 171 177 185 400 1.0
1.08 0.166 137 166 167 176 316 -3.0 -14.62 0.469 138 149 158 166
340 -20.0 -23.47 0.000 132 147 149 159 326 21.0 26.04 0.000 132 144
163 171 323 -20.0 -1.73 0.000 159 161 175 190 299 -3.0 4.83 0.384
161 161 173 171 342 -3.0 2.54 0.354 168 173 196 192 397 1.0 6.83
0.571 154 154 167 172 320 -19.0 -22.39 0.000 132 159 183 190 367
-11.0 4.67 0.054 122 161 168 195 241 -13.0 -19.21 0.100 173 173 213
261 372 1.0 19.22 0.587 186 166 174 185 265 -3.0 -5.62 0.461 167
172 190 187 394 2.0 7.27 0.137 183 163 170 178 262 -7.0 -16.03
0.131 175 152 190 212 327 -17.0 -1.78 0.018 177 171 183 179 319
-1.0 -0.74 0.564 Mutant Fragments 75th 25th Mean Percentile Maximum
Minimum Percentile cfDNA cfDNA cfDNA cfDNA cfDNA Fragment Fragment
Fragment Fragment Fragment Size Size Size Distinct Size Size (bp)
(bp) (bp) Coverage (bp) (bp) 166 172 396 1616 100 146 175 180 400
806 96 158 165 172 399 1410 102 140 170 177 397 49 99 153 166 173
398 33 140 155 180 178 400 73 95 140 172 177 400 38 115 160 171 174
386 6 124 137 180 183 400 70 124 151 191 199 399 6586 96 162 184
188 400 41 112 172 181 198 399 35 149 168 182 184 399 20 166 180
183 186 397 5338 102 159 202 203 393 178 101 150 195 195 397 1350
104 153 185 189 400 1257 100 153
185 189 396 30 117 163 203 210 391 336 105 153 188 194 399 741 101
161 193 193 396 89 100 145 172 179 396 12 129 143 186 188 387 3559
91 155 177 183 392 873 102 149 194 200 377 1909 100 158 202 259 400
27 122 157 171 178 395 1818 103 147 178 182 374 546 102 151 179 184
397 26 132 142 195 194 400 53 117 157 176 179 397 40 124 150 188
191 390 38 107 153 205 207 399 217 102 146 196 195 397 266 111 147
186 184 400 76 123 157 179 186 400 9832 93 161 191 190 400 277 104
162 191 189 400 65 123 165 187 189 400 31 136 163 202 202 400 5286
102 166 196 201 400 102 138 166 181 182 397 30 138 158 181 181 400
64 113 158 176 179 398 27 121 163 191 192 398 2943 100 165 179 181
399 25 138 153 171 177 399 60 110 136 172 179 399 26 139 147 186
184 398 35 121 149 176 178 397 4000 103 155 176 178 385 2390 99 157
182 184 400 28 131 160 194 193 400 3545 100 161 179 180 398 15 121
146 188 187 400 2587 103 158 189 192 400 86 121 165 178 184 399
3339 101 157 179 187 391 3193 101 163 183 186 398 13 111 153 197
201 400 4140 102 166 191 194 400 16 130 143 183 183 400 209 125 154
211 230 400 41 158 176 193 193 400 3445 94 162 197 199 400 23 123
182 193 195 399 1787 100 163 204 207 400 4100 100 159 Difference
Difference Adjusted P between between Value of Median Mean
Difference Mutant Fragments Mutant Mutant between 75th and and
Mutant Mode Median Mean Percentile Maximum Wild type Wild-type and
cfDNA cfDNA cfDNA cfDNA cfDNA cfDNA cfDNA Wild-type Fragment
Fragment Fragment Fragment Fragment Fragment Fragment cfDNA Size
Size Size Size Size Size Size Fragment (bp) (bp) (bp) (bp) (bp)
(bp) (bp) Size 164 159 163 170 354 -3.5 -3.57 0.000 169 169 173 184
366 1.0 3.80 0.054 149 154 164 170 398 -8.0 -0.35 0.816 143 182 206
284 333 16.0 36.25 0.000 154 170 108 180 296 7.0 14.38 0.104 140
155 173 178 324 -9.0 -6.66 0.000 164 167 182 179 329 1.5 10.09
0.479 170 156 153 168 178 -7.5 -18.98 0.411 151 164 182 183 385
-6.0 1.71 0.064 168 175 193 196 399 0.0 -1.79 0.166 176 177 195 195
373 3.0 11.02 0.397 175 175 181 186 312 1.0 -13.40 0.587 185 191
205 219 357 21.0 23.48 0.013 175 171 183 185 394 -1.0 0.03 0.984
168 171 198 240 357 -5.0 -4.34 0.571 163 171 201 258 400 0.0 5.94
0.066 168 170 189 202 392 1.0 4.37 0.064 164 172 175 179 372 3.0
-10.29 0.463 141 171 200 240 399 4.0 3.10 0.571 169 176 190 194 400
2.0 1.96 0.571 171 171 197 229 393 -2.0 3.42 0.479 143 153 163 166
275 -14.0 -8.99 0.084 164 173 195 211 398 3.0 5.92 0.001 163 164
177 181 400 -3.0 -0.39 0.880 167 176 202 242 398 5.0 7.98 0.061 164
179 199 231 350 2.0 -3.82 0.685 169 162 173 180 396 1.0 1.92 0.372
166 166 180 182 381 0.0 2.87 0.416 138 171 183 188 351 1.5 3.29
0.572 165 169 192 198 336 -3.0 -2.86 0.451 169 166 181 176 309 -1.0
4.53 0.539 180 174 185 210 326 0.5 -2.59 0.576 144 163 188 212 360
-12.0 -17.11 0.004 150 166 188 204 379 -8.0 -7.53 0.208 171 169 182
182 346 1.0 -3.64 0.479 166 172 180 186 399 -1.0 1.04 0.155 160 176
201 200 384 3.0 9.95 0.061 166 172 198 192 371 1.0 7.08 0.560 171
167 201 199 387 -4.0 14.14 0.341 168 181 201 203 400 2.0 -0.86
0.587 161 179 199 209 372 -1.5 2.90 0.679 189 185 191 191 311 16.0
9.25 0.000 163 167 179 176 318 0.0 -2.85 0.679 200 171 187 190 392
5.0 10.89 0.314 176 176 187 192 398 0.0 -3.83 0.015 138 167 181 184
340 -1.0 2.00 0.571 147 147 161 159 327 -19.0 -9.77 0.000 180 176
176 184 344 9.0 3.52 0.015 360 161 197 195 360 -9.0 10.77 0.314 166
167 176 178 397 0.5 0.65 0.610 164 168 178 180 400 0.0 1.78 0.314
168 167 177 179 338 -2.0 -5.83 0.463 169 173 194 192 399 0.0 0.40
0.825 166 166 172 204 221 -2.0 -7.32 0.564 162 169 189 186 399 -1.0
1.12 0.598 183 177 189 193 373 3.0 -0.01 0.293 165 169 177 184 400
0.0 -1.73 0.598 178 173 180 186 389 1.0 0.22 0.839 153 161 171 179
323 -11.0 -12.36 0.061 169 179 197 200 400 0.0 -0.32 0.839 143 157
173 173 325 -20.0 -18.40 0.000 175 170 196 233 357 1.0 12.55 0.025
197 186 215 220 374 1.0 3.72 0.603 175 174 194 194 399 0.0 0.65
0.714 248 224 232 260 359 47.0 34.97 0.000 163 176 192 194 400 1.0
-0.85 0.718 164 173 200 202 400 -2.0 -3.65 0.062 Mutant Fragments
75th 25th Mean Percentile Maximum Minimum Percentile cfDNA cfDNA
cfDNA cfDNA cfDNA Fragment Fragment Fragment Fragment Fragment Size
Size Size Distinct Size Size (bp) (bp) (bp) Coverage (bp) (bp) 196
195 400 3096 79 159 202 203 400 73 142 178 205 203 400 23 161 168
195 196 400 170 125 158 195 192 400 2089 101 162 238 280 400 125 84
192 197 194 400 5715 108 163 172 173 398 109 78 148 196 191 399 35
119 161 189 190 400 826 102 162 194 195 400 95 135 160 184 184 400
27 128 150 179 184 399 4771 103 161 187 185 399 7 417 154 179 179
395 330 106 152 172 177 399 536 106 151 179 183 400 45 136 163 182
182 397 16 138 146 172 177 397 293 101 152 171 177 399 23 130 152
180 183 399 54 104 161 184 184 400 154 96 149 186 187 399 79 102
163 183 185 400 44 118 149 182 184 400 35 136 164 192 191 400 13
138 164 199 205 400 50 128 155 191 193 400 81 108 150 190 191 389
2597 101 159 192 197 400 58 92 173 183 189 400 74 90 147 175 178
400 37 144 163 194 202 400 61 93 164 184 186 400 66 104 158 191 190
396 101 126 155 188 185 394 4718 100 156 186 186 399 30 134 161 180
180 397 34 139 163 182 182 400 262 101 150 182 182 400 277 101 150
180 182 395 65 121 158 177 182 400 16 144 172 185 184 399 7186 100
154 181 179 394 21 108 164 177 180 400 18 111 127 179 181 400 72
121 156 177 182 400 30 106 160 200 199 399 36 131 147 184 185 392
20 144 173 182 184 395 16 147 156 186 187 399 34 159 168 186 186
396 5 116 182 185 183 399 1073 100 142 179 180 400 46 109 151 181
181 400 30 146 154 176 179 392 2742 102 154 174 180 399 298 103 140
197 194 399 67 115 164 195 194 399 19 156 165 178 182 395 189 105
138 183 185 398 227 123 160 185 184 397 53 78 161 190 188 395 50
130 161 186 187 398 28 139 150 179 184 400 24 130 153 185 185 394
48 111 154 189 187 398 2337 100 163 Difference Difference Adjusted
P between between Value of Median Mean Difference Mutant Fragments
Mutant Mutant between 75th and and Mutant Mode Median Mean
Percentile Maximum Wild type Wild-type and cfDNA cfDNA cfDNA cfDNA
cfDNA cfDNA cfDNA Wild-type Fragment Fragment Fragment Fragment
Fragment Fragment Fragment cfDNA Size Size Size Size Size Size Size
Fragment (bp) (bp) (bp) (bp) (bp) (bp) (bp) Size 161 173 194 191
397 -1.0 -2.45 0.251 178 184 237 338 377 9.0 35.30 0.114 168 171
189 186 380 -4.0 -16.38 0.435 173 173 188 190 400 -2.0 -6.17 0.293
169 176 203 203 400 4.5 8.80 0.000 194 207 243 324 400 -16.0 5.51
0.574 164 174 200 196 400 1.0 2.87 0.065 149 158 166 173 302 -4.0
-5.94 0.190 172 171 191 180 390 0.0 -4.34 0.627 166 171 187 187 395
-2.0 -1.94 0.475 161 170 182 184 400 -5.0 -11.54 0.155 150 169 174
185 319 -1.0 -9.68 0.571 168 171 179 183 400 0.0 0.15 0.880 154 167
164 174 117 -3.0 -22.90 0.155 165 166 178 178 361 -1.0 -1.35 0.685
167 163 172 175 363 -3.0 -0.34 0.880 175 172 185 191 380 3.0 6.52
0.368 146 155 162 170 224 -14.0 -19.82 0.007 169 164 170 174 392
2.0 1.37 0.646 162 162 163 177 232 -4.0 -7.62 0.252 154 176 195 206
383 7.5 14.58 0.064 157 163 176 185 347 -5.5 -7.87 0.154 177 174
200 203 372 4.0 14.61 0.270 163 163 185 186 338 -7.0 1.98 0.039 204
181 194 203 369 13.0 11.80 0.039 169 169 198 173 333 -1.0 6.05
0.610 161 171 216 301 360 0.0 17.02 0.623 108 173 198 224 385 0.0
6.48 0.624 165 172 185 187 397 -1.0 -5.17 0.005 192 192 202 200 397
18.0 9.79 0.007 142 167 176 182 391 -6.5 -6.78 0.061 185 172 192
186 375 6.0 17.15 0.005 181 181 197 211 370 8.0 3.34 0.169 194 174
189 194 379 3.5 4.60 0.270
176 176 194 213 331 7.0 2.50 0.718 164 168 190 187 393 -1.0 2.54
0.113 175 175 190 208 339 5.0 4.07 0.302 165 170 178 175 349 3.0
-1.65 0.407 152 165 181 186 393 -4.0 -0.65 0.876 147 166 182 185
393 -3.0 0.36 0.926 161 167 186 188 338 -4.0 6.15 0.234 179 179 187
180 376 10.0 9.98 0.130 167 166 183 181 396 -1.0 -1.73 0.154 164
173 196 200 357 7.0 14.95 0.213 127 158 189 186 352 -8.0 12.47
0.179 173 166 183 179 396 -2.0 4.31 0.427 174 174 180 156 282 5.0
3.09 0.252 143 177 196 227 298 2.5 -4.24 0.479 266 178 199 215 269
6.0 15.13 0.252 156 164 177 169 302 8.0 4.82 0.119 168 176 206 196
365 3.0 20.55 0.415 182 185 201 192 329 12.0 14.62 0.263 164 152
157 164 346 -18.0 -27.67 0.000 143 175 174 183 325 7.0 -5.22 0.054
146 168 186 181 367 -0.5 5.19 0.568 164 166 176 176 387 -1.0 -0.24
0.874 148 150 152 162 288 -18.0 -22.25 0.000 250 173 187 201 366
2.0 9.89 0.425 165 185 197 199 361 10.0 2.20 0.154 141 150 164 175
348 -20.0 -14.58 0.000 168 169 185 184 396 -2.0 1.68 0.706 175 175
189 158 392 4.0 3.80 0.241 168 168 184 175 377 -4.5 -5.86 0.234 173
170 170 173 354 -2.5 -15.88 0.416 176 170 193 199 359 0.0 13.13
0.598 170 168 173 183 295 -3.0 -11.80 0.270 166 172 187 185 394
-1.0 -1.27 0.564 Mutant Fragments 75th 25th Mean Percentile Maximum
Minimum Percentile cfDNA cfDNA cfDNA cfDNA cfDNA Fragment Fragment
Fragment Fragment Fragment Size Size Size Distinct Size Size (bp)
(bp) (bp) Coverage (bp) (bp) 198 200 396 172 83 152 190 188 400 215
123 151 184 184 400 207 121 151 191 189 397 17 143 170 181 182 398
52 122 152 191 189 399 17 109 161 191 189 399 40 136 164 180 181
399 127 88 149 181 186 400 68 141 166 169 179 398 10 81 167 170 181
398 33 107 162 175 181 391 23 112 156 175 177 400 109 130 153 172
176 400 684 105 153 179 178 398 2946 100 138 175 178 399 30 121 165
187 186 400 63 140 155 181 184 400 4754 101 160 182 187 400 31 131
162 181 183 400 150 110 144 179 184 400 5290 95 159 181 186 400 140
101 155 187 190 397 20 92 141 190 192 400 8065 85 156 174 182 400
2586 101 147 185 188 400 2808 100 150 182 187 400 2227 100 154 176
183 396 8425 100 155 186 188 399 142 112 146 186 185 399 104 132
158 183 185 392 3462 101 160 182 183 399 25 94 140 177 181 399 3789
101 159 181 184 400 57 131 152 183 191 400 36 118 154 187 185 399
362 110 152 182 188 400 20 158 163 185 187 397 23 126 151 188 189
400 2980 100 158 183 163 391 2793 91 158 185 189 395 7357 100 158
184 184 398 5186 101 157 182 187 400 15595 64 159 186 185 400 6749
101 158 193 190 400 23 127 148 182 185 394 3901 101 160 179 180 400
4633 100 158 175 179 400 734 101 151 175 180 394 4022 101 159 184
182 400 117 116 156 172 176 395 65 109 145 Difference Difference
Adjusted P between between Value of Median Mean Difference Mutant
Fragments Mutant Mutant between 75th and and Mutant Mode Median
Mean Percentile Maximum Wild type Wild-type and cfDNA cfDNA cfDNA
cfDNA cfDNA cfDNA cfDNA Wild-type Fragment Fragment Fragment
Fragment Fragment Fragment Fragment cfDNA Size Size Size Size Size
Size Size Fragment (bp) (bp) (bp) (bp) (bp) (bp) (bp) Size 160 166
193 226 396 -4.0 -4.93 0.490 159 163 188 196 365 -6.0 -1.72 0.735
157 161 181 179 365 -7.0 -3.01 0.571 217 214 198 217 294 43.0 7.08
0.000 167 164 179 173 372 -4.5 -2.07 0.137 173 171 181 174 392 -1.0
-9.24 0.576 166 171 185 185 335 -1.0 -5.86 0.571 131 162 168 178
311 -6.0 -11.80 0.005 175 176 198 207 387 4.0 17.11 0.184 167 167
159 176 182 1.0 -10.20 0.589 167 167 174 185 322 0.0 4.57 0.636 190
164 175 190 349 -4.0 -0.92 0.308 169 166 175 178 382 0.0 -0.09
0.987 167 166 172 175 385 1.0 0.00 0.999 157 155 172 174 398 -9.0
-7.28 0.000 165 176 198 219 325 12.0 22.37 0.007 154 167 201 215
372 -3.0 13.70 0.286 170 170 179 161 393 0.0 -1.72 0.154 162 174
180 185 352 2.0 2.26 0.494 166 162 176 173 385 -6.0 -5.86 0.314 167
169 179 164 400 -1.0 0.11 0.909 175 167 179 180 352 -4.5 -2.77
0.589 241 168 178 209 283 -3.0 -9.82 0.479 164 169 190 190 399 0.0
-0.08 0.942 165 165 169 179 386 -3.5 -4.59 0.000 158 167 189 200
399 -3.0 4.17 0.007 162 171 183 190 398 0.0 1.00 0.564 165 169 176
184 400 0.0 0.54 0.568 140 159 180 193 352 -13.0 -5.41 0.463 159
167 189 180 331 -2.0 3.05 0.657 173 172 184 167 396 1.0 0.82 0.576
140 158 159 163 341 -11.0 -23.47 0.027 168 169 176 161 395 0.0
-0.66 0.576 170 170 179 184 327 -1.0 -2.41 0.568 201 182 187 201
328 11.0 3.60 0.114 143 180 207 268 389 11.0 20.70 0.000 311 174
198 209 311 3.0 15.25 0.475 184 168 185 185 328 -1.0 -1.49 0.571
169 170 187 189 398 0.0 -0.84 0.637 167 170 161 182 389 1.0 -2.30
0.171 175 171 162 187 399 -1.0 -2.37 0.008 165 170 185 186 400 1.0
1.72 0.240 167 170 181 185 397 -1.0 -1.39 0.245 167 170 185 187 400
0.0 -0.52 0.702 148 194 222 292 378 24.0 29.58 0.027 167 171 182
155 398 2.0 0.32 0.821 169 170 185 157 400 1.0 6.16 0.000 155 165
176 178 366 -4.0 0.48 0.823 167 168 172 178 399 -1.0 -2.84 0.000
156 172 199 184 399 5.0 15.08 0.084 177 167 181 181 306 3.0 9.11
0.293
TABLE-US-00006 APPENDIX-D Table 4 Summary of whole genome cfDNA
analyses High Total Quality Analysis Patient Read Bases Bases
Patient Timepoint type Type Length Sequenced Analyzed Coverage
CGCRC291 Preoperative treatment naive WGS Colorectal Cancer 100
7232125000 4695396600 1.86 CGCRC292 Preoperative treatment naive
WGS Colorectal Cancer 100 6794092800 4471065400 1.77 CGCRC293
Preoperative treatment naive WGS Colorectal Cancer 100 8373899600
5686176000 2.26 CGCRC294 Preoperative treatment naive WGS
Colorectal Cancer 100 3081312000 5347045800 2.12 CGCRC296
Preoperative treatment naive WGS Colorectal Cancer 100 10072029200
6770998200 2.69 CGCRC299 Preoperative treatment naive WGS
Colorectal Cancer 100 10971591600 7632723200 3.03 CGCRC300
Preoperative treatment naive WGS Colorectal Cancer 100 9894332600
6699951000 2.66 CGCRC301 Preoperative treatment naive WGS
Colorectal Cancer 100 7357346200 5021002000 1.99 CGCRC302
Preoperative treatment naive WGS Colorectal Cancer 100 11671913000
8335275800 3.31 CGCRC304 Preoperative treatment naive WGS
Colorectal Cancer 100 19011739200 12957614200 5.14 CGCRC305
Preoperative treatment naive WGS Colorectal Cancer 100 7177341400
4809957200 1.91 CGCRC306 Preoperative treatment naive WGS
Colorectal Cancer 100 8302233200 5608043600 2.23 CGCRC307
Preoperative treatment naive WGS Colorectal Cancer 100 8034720400
5342620000 2.12 CGCRC308 Preoperative treatment naive WGS
Colorectal Cancer 100 8670084800 5934037200 2.35 CGCRC311
Preoperative treatment naive WGS Colorectal Cancer 100 6947634400
4704601800 1.87 CGCRC315 Preoperative treatment naive WGS
Colorectal Cancer 100 5205544000 3419565400 1.36 CGCRC316
Preoperative treatment naive WGS Colorectal Cancer 100 6405388600
4447534800 1.76 CGCRC317 Preoperative treatment naive WGS
Colorectal Cancer 100 6060390400 4104616600 1.63 CGCRC318
Preoperative treatment naive WGS Colorectal Cancer 100 6848768600
4439404800 1.76 CGCRC319 Preoperative treatment naive WGS
Colorectal Cancer 100 10545294400 7355181600 2.92 CGCRC320
Preoperative treatment naive WGS Colorectal Cancer 100 5961999200
3945054000 1.57 CGCRC321 Preoperative treatment naive WGS
Colorectal Cancer 100 8248095400 5614355000 2.23 CGCRC333
Preoperative treatment naive WGS Colorectal Cancer 100 10540267600
6915490600 2.74 CGCRC336 Preoperative treatment naive WGS
Colorectal Cancer 100 10675581800 7087691800 2.81 CGCRC338
Preoperative treatment naive WGS Colorectal Cancer 100 13788172600
8970308600 3.56 CGCRC341 Preoperative treatment naive WGS
Colorectal Cancer 100 10753467600 7311539200 2.90 CGCRC342
Preoperative treatment naive WGS Colorectal Cancer 100 11836966000
7552793200 3.00 CGH14 Human adult elutriated lymphocytes WGS
Healthy 100 36525427600 24950300200 9.90 CGH15 Human adult
elutriated lymphocytes WGS Healthy 100 29930855000 23754049400 9.43
CGLU316 Pre-treatment, Day-53 WGS Lung Cancer 100 10354123200
6896471400 2.74 CGLU316 Pre-treatment, Day-4 WGS Lung Cancer 100
7870039200 5254938800 2.09 CGLU316 Post-treatment, Day 18 WGS Lung
Cancer 100 8155322000 5416262400 2.15 CGLU316 Post-treatment, Day
81 WGS Lung Cancer 100 9442310400 6087893400 2.42 CGLU344
Pre-treatment, Day-21 WGS Lung Cancer 100 8728318600 5769097200
2.29 CGLU344 Pre-treatment, Day 0 WGS Lung Cancer 100 11710246400
7826902600 3.11 CGLU344 Post-treatment, Day 0.1875 WGS Lung Cancer
100 11569683000 7654701600 3.04 CGLU344 Post-treatment, Day 59 WGS
Lung Cancer 100 11042459200 6320133800 2.51 CGLU369 Pre-treatment,
Day-2 WGS Lung Cancer 100 8630932800 5779595800 2.29 CGLU369
Post-treatment, Day 12 WGS Lung Cancer 100 9227709600 6136755200
2.44 CGLU369 Post-treatment, Day 68 WGS Lung Cancer 100 7995282600
5239077200 2.08 CGLU369 Post-treatment, Day 110 WGS Lung Cancer 100
8750541000 5626139000 2.23 CGLU373 Pre-treatment, Day-2 WGS Lung
Cancer 100 11746059600 7547485800 3.00 CGLU373 Post-treatment, Day
0.125 WGS Lung Cancer 100 13801136800 9255579400 3.67 CGLU373
Post-treatment, Day 7 WGS Lung Cancer 100 11537896800 7654111200
3.04 CGLU373 Post-treatment, Day 47 WGS Lung Cancer 100 8046326400
5397702400 2.14 CGPLBR100 Preoperative treatment naive WGS Breast
Cancer 100 8440532400 5729474800 2.27 CGPLBR101 Preoperative
treatment naive WGS Breast Cancer 100 9786253600 6673495200 2.65
CGPLBR102 Preoperative treatment naive WGS Breast Cancer 100
8664980400 5669781600 2.25 CGPLBR103 Preoperative treatment naive
WGS Breast Cancer 100 9346936200 6662883400 2.64 CGPLBR104
Preoperative treatment naive WGS Breast Cancer 100 9443375400
6497061000 2.58 CGPLBR12 Preoperative treatment naive WGS Breast
Cancer 100 7017577800 4823327400 1.91 CGPLBR18 Preoperative
treatment naive WGS Breast Cancer 100 10309652800 7130386000 2.83
CGPLBR23 Preoperative treatment naive WGS Breast Cancer 100
9034484800 6219625800 2.47 CGPLBR24 Preoperative treatment naive
WGS Breast Cancer 100 9891454200 6601857400 2.62 CGPLBR28
Preoperative treatment naive WGS Breast Cancer 100 7997607200
5400803200 2.14 CGPLBR30 Preoperative treatment naive WGS Breast
Cancer 100 5502597200 5885822400 2.34 CGPLBR31 Preoperative
treatment naive WGS Breast Cancer 100 12660085600 8551995600 3.39
CGPLBR32 Preoperative treatment naive WGS Breast Cancer 100
8773498600 5839034600 2.32 CGPLBR33 Preoperative treatment naive
WGS Breast Cancer 100 10931742800 6967030600 2.76 CGPLBR34
Preoperative treatment naive WGS Breast Cancer 100 10861398600
7453225800 2.96 CGPLBR35 Preoperative treatment naive WGS Breast
Cancer 100 9180193600 6158440200 2.44 CGPLBR36 Preoperative
treatment naive WGS Breast Cancer 100 9159948400 6091817800 2.42
CGPLBR37 Preoperative treatment naive WGS Breast Cancer 100
10307505800 6929530600 2.75 CGPLBR38 Preoperative treatment naive
WGS Breast Cancer 100 9983824000 6841725400 2.71 CGPLBR40
Preoperative treatment naive WGS Breast Cancer 100 10148823800
7024345400 2.79 CGPLBR41 Preoperative treatment naive WGS Breast
Cancer 100 11168192000 7562945800 3.00 CGPLBR45 Preoperative
treatment naive WGS Breast Cancer 100 8793780600 6011109400 2.39
CGPLBR46 Preoperative treatment naive WGS Breast Cancer 100
7228607600 4706130000 1.87 CGPLBR47 Preoperative treatment naive
WGS Breast Cancer 100 7906911400 5341655000 2.12 CGPLBR48
Preoperative treatment naive WGS Breast Cancer 100 6992032000
4428636200 1.76 CGPLBR49 Preoperative treatment naive WGS Breast
Cancer 100 7311195000 4559460200 1.81 CGPLBR50 Preoperative
treatment naive WGS Breast Cancer 100 11107960600 7582776600 3.01
CGPLBR51 Preoperative treatment naive WGS Breast Cancer 100
8393547400 5102069000 2.02 CGPLBR52 Preoperative treatment naive
WGS Breast Cancer 100 9491894800 6141729000 2.44 CGPLBR55
Preoperative treatment naive WGS Breast Cancer 100 9380109800
6518855200 2.59 CGPLBR56 Preoperative treatment naive WGS Breast
Cancer 100 12191816800 8293011200 3.29 CGPLBR57 Preoperative
treatment naive WGS Breast Cancer 100 9847584400 6713638000 2.66
CGPLBR59 Preoperative treatment naive WGS Breast Cancer 100
7476477000 5059873200 2.01 CGPLBR60 Preoperative treatment naive
WGS Breast Cancer 100 6531354600 4331253800 1.72 CGPLBR61
Preoperative treatment naive WGS Breast Cancer 100 9311029200
6430920800 2.55 CGPLBR63 Preoperative treatment naive WGS Breast
Cancer 100 8971949000 6044009600 2.40 CGPLBR65 Preoperative
treatment naive WGS Breast Cancer 100 7197301400 4835015200 1.92
CGPLBR63 Preoperative treatment naive WGS Breast Cancer 100
10003774000 6974918800 2.77 CGPLBR69 Preoperative treatment naive
WGS Breast Cancer 100 10080881800 6903459200 2.74 CGPLBR70
Preoperative treatment naive WGS Breast Cancer 100 8824002800
6002533800 2.38 CGPLBR71 Preoperative treatment naive WGS Breast
Cancer 100 10164136800 6994668600 2.78 CGPLBR72 Preoperative
treatment naive WGS Breast Cancer 100 18418841400 12328783000 4.89
CGPLBR73 Preoperative treatment naive WGS Breast Cancer 100
10281460200 7078613200 2.81 CGPLBR76 Preoperative treatment naive
WGS Breast Cancer 100 10105270400 6800705000 2.70 CGPLBR81
Preoperative treatment naive WGS Breast Cancer 100 5087126000
3273367200 1.30 CGPLBR82 Preoperative treatment naive WGS Breast
Cancer 100 10576496600 7186662600 2.85 CGPLBR83 Preoperative
treatment naive WGS Breast Cancer 100 8977124400 5947525000 2.36
CGPLBR84 Preoperative treatment naive WGS Breast Cancer 100
6272538600 4066870600 1.61 CGPLBR87 Preoperative treatment naive
WGS Breast Cancer 100 8460954800 5375710200 2.13 CGPLBR83
Preoperative treatment naive WGS Breast Cancer 100 8665810400
5499893200 2.18 CGPLBR90 Preoperative treatment naive WGS Breast
Cancer 100 6663469200 4392442400 1.74 CGPLBR91 Preoperative
treatment naive WGS Breast Cancer 100 10933002400 7647842000 3.03
CGPLBR92 Preoperative treatment naive WGS Breast Cancer 100
10392674000 6493593000 2.58 CGPLBR93 Preoperative treatment naive
WGS Breast Cancer 100 5659836000 3931106800 1.56 CGPLH189
Preoperative treatment naive WGS Healthy 100 11400610400 7655568800
3.04 CGPLH190 Preoperative treatment naive WGS Healthy 100
11444671600 7581175200 3.01 CGPLH192 Preoperative treatment naive
WGS Healthy 100 12199010800 8126804800 3.22 CGPLH193 Preoperative
treatment naive WGS Healthy 100 10201897600 6635285400 2.63
CGPLH194 Preoperative treatment naive WGS Healthy 100 11005087400
7081652600 2.81 CGPLH196 Preoperative treatment naive WGS Healthy
100 12891462800 8646881800 3.43 CGP6H197 Preoperative treatment
naive WGS Healthy 100 11961841600 3052855200 3.20 CGPLH193
Preoperative treatment naive WGS Healthy 100 13605489000 8885716000
3.53 CGPLH199 Preoperative treatment naive WGS Healthy 100
1818090200 5615316000 2.23 CGPLH200 Preoperative treatment naive
WGS Healthy 100 14400027600 9310342000 3.69 CGPLH201 Preoperative
treatment naive WGS Healthy 100 6208766806 4171843400 1.66 CGPLH202
Preoperative treatment naive WGS Healthy 100 11282922800 7363530600
2.92 CGPLH203 Preoperative treatment naive WGS Healthy 100
13540689600 9068747600 3.60 CGPLH205 Preoperative treatment naive
WGS Healthy 100 10343537800 6696983600 2.66 CGPLH208 Preoperative
treatment naive WGS Healthy 100 12796300000 3272073400 3.28
CGPLH209 Preoperative treatment naive WGS Healthy 100 13123035400
3531813600 3.39 CGPLH210 Preoperative treatment naive WGS Healthy
100 10184218800 6832204600 2.71 CGPLH211 Preoperative treatment
naive WGS Healthy 100 14655260200 3887067600 3.53 CGPLH300
Preoperative treatment naive WGS Healthy 100 7062083400 4553351200
1.81 CGPLH307 Preoperative treatment naive WGS Healthy 100
7239128200 4547697200 1.80 CGPLH308 Preoperative treatment naive
WGS Healthy 100 8512551400 5526653600 2.19 CGPLH309 Preoperative
treatment naive WGS Healthy 100 11664474200 7431836600 2.95
CGPLH310 Preoperative treatment naive WGS Healthy 100 11045691000
7451506200 2.96 CGPLH311 Preoperative treatment naive WGS Healthy
100 10406803200 6786479600 2.69 CGPLH314 Preoperative treatment
naive WGS Healthy 100 10371343800 6925866600 2.75 CGPLH315
Preoperative treatment naive WGS Healthy 100 9508538400 6208744600
2.46 CGPLH316 Preoperative treatment naive WGS Healthy 100
10131063600 6891181000 2.73 CGPLH317 Preoperative treatment naive
WGS Healthy 100 8364314400 5302232600 2.10 CGPLH319 Preoperative
treatment naive WGS Healthy 100 8780528200 5585897000 2.22 CGPLH320
Preoperative treatment naive WGS Healthy 100 8956232600 5784619200
2.30 CGPLH322 Preoperative treatment naive WGS Healthy 100
9563837800 6445517800 2.56 CGPLH324 Preoperative treatment naive
WGS Healthy 100 6765038600 4469201600 1.77 CGPLH325 Preoperative
treatment naive WGS Healthy 100 8008213400 5099262800 2.02 CGPLH326
Preoperative treatment naive WGS Healthy 100 9554226200 6112544000
2.43 CGPLH327 Preoperative treatment naive WGS Healthy 100
8239168800 5351280200 2.12 CGPLH328 Preoperative treatment naive
WGS Healthy 100 7197086300 4516894800 1.79 CGPLH329 Preoperative
treatment naive WGS Healthy 100 8921554800 5493709800 2.18 CGPLH330
Preoperative treatment naive WGS Healthy 100 10693603400 7077793600
2.81 CGPLH331 Preoperative treatment naive WGS Healthy 100
8982792000 5538096200 2.20 CGPLH333 Preoperative treatment naive
WGS Healthy 100 7856985400 5178829600 2.06 CGPLH335 Preoperative
treatment naive WGS Healthy 100 9370663400 6035739400 2.40 CGPLH336
Preoperative treatment naive WGS Healthy 100 8002498200 5340331400
2.12 CGPLH337 Preoperative treatment naive WGS Healthy 100
7399022000 4954467600 1.97 CGPLH338 Preoperative treatment naive
WGS Healthy 100 8917121600 6170927200 2.45 CGPLH339 Preoperative
treatment naive WGS Healthy 100 8591130800 5866411400 2.33 CGPLH340
Preoperative treatment naive WGS Healthy 100 8046351000 5368062000
2.13 CGPLH341 Preoperative treatment naive WGS Healthy 100
7914788600 5200304800 2.06 CGPLH342 Preoperative treatment naive
WGS Healthy 100 8633413000 5701972400 2.26 CGPLH343 Preoperative
treatment naive WGS Healthy 100 6694769800 4410670860 1.75 CGPLH344
Preoperative treatment naive WGS Healthy 100 7628192400 4961476600
1.97 CGPLH345 Preoperative treatment naive WGS Healthy 100
7121569406 4747223000 1.88 CGPLH346 Preoperative treatment naive
WGS Healthy 100 7707924600 4873321600 1.93 CGPLH35 Preoperative
treatment naive WGS Healthy 100 47305985200 4774186200 12.63
CGPLH350 Preoperative treatment naive WGS Healthy 100 9745839800
6054055200 2.40 CGPLH351 Preoperative treatment naive WGS Healthy
100 13317435800 8714465000 3.46 CGPLH352 Preoperative treatment
naive WGS Healthy 100 7059351600 4752309400 1.89 CGPLH353
Preoperative treatment naive WGS Healthy 100 8435782400 5215098200
2.09 CGPLH354 Preoperative treatment naive WGS Healthy 100
8018644000 4857577660 1.93 CGPLH355 Preoperative treatment naive
WGS Healthy 100 8624675800 5709726400 2.27 CGPLH356 Preoperative
treatment naive WGS Healthy 100 8817952800 5729595200 2.27 CGPLH357
Preoperative treatment naive WGS Healthy 100 11931696200 7690004400
3.05 CGPLH358 Preoperative treatment naive WGS Healthy 100
12802561200 8451274800 3.35 CGPLH36 Preoperative treatment naive
WGS Healthy 100 40173545600 3914810400 10.52 CGPLH360 Preoperative
treatment naive WGS Healthy 100 7280078400 4918566200 1.95 CGPLH361
Preoperative treatment naive WGS Healthy 100 7493498400 4966813800
1.97 CGPLH362 Preoperative treatment naive WGS Healthy 100
11345644200 7532133600 2 99 CGPLH363 Preoperative treatment naive
WGS Healthy 100 6111382800 3965952400 1.57 CGPLH364 Preoperative
treatment naive WGS Healthy 100 10823490400 7195657000 2.86
CGPLH365 Preoperative treatment naive WGS Healthy 100 5938367400
3954556200 1.57 CGPLH366 Preoperative treatment naive WGS Healthy
100 7063168600 4731853060 1.88 CGPLH367 Preoperative treatment
naive WGS Healthy 100 7119631800 4627888200 1.84 CGPLH368
Preoperative treatment naive WGS Healthy 100 7726718400 4975233400
1.97 CGPLH369 Preoperative treatment naive WGS Healthy 100
10967584200 7130956800 2.83 CGPLH37 Preoperative treatment naive
WGS Healthy 100 45970545400 4591328800 12.15 CGPLH370 Preoperative
treatment naive WGS Healthy 100 9237170006 6106373800 2.42 CGPLH371
Preoperative treatment naive WGS Healthy 100 8077798800 5237070600
2.08 CGPLH380 Preoperative treatment naive WGS Healthy 100
14049589200 8614241200 3.42 CGPLH381 Preoperative treatment naive
WGS Healthy 100 16743792000 10767862800 4.27 CGPLH382 Preoperative
treatment naive WGS Healthy 100 18474025200 12276437200 4.87
CGPLH383 Preoperative treatment naive WGS Healthy 100 13215954000
8430420600 3.36 CGPLH384 Preoperative treatment naive WGS Healthy
100 8481814000 5463636260 2.17 CGPLH385 Preoperative treatment
naive WGS Healthy 100 9596118800 6445445600 2.56 CGPLH386
Preoperative treatment naive WGS Healthy 100 7399540400 4915484800
1.95 CGPLH387 Preoperative treatment naive WGS Healthy 100
6860332600 4339724400 1.72 CGPLH388 Preoperative treatment naive
WGS Healthy 100 8679705600 5463945400 2.17 CGPLH389 Preoperative
treatment naive WGS Healthy 100 7266863600 4702386000 1.87 CGPLH390
Preoperative treatment naive WGS Healthy 100 7509035600 4913901800
1.95 CGPLH391 Preoperative treatment naive WGS Healthy 100
7252286000 4702404800 1.87 CGPLH392 Preoperative treatment naive
WGS Healthy 100 7302618200 4722407000 1.87 CGPLH393 Preoperative
treatment naive WGS Healthy 100 8879138000 5947871800 2.36 CGPLH394
Preoperative treatment naive WGS Healthy 100 8737031000 5599777400
2.22 CGPLH395 Preoperative treatment naive WGS Healthy 100
7783904800 4907146000 1.95 CGPLH396 Preoperative treatment naive
WGS Healthy 100 7585567200 5076638200 2.01 CGPLH393 Preoperative
treatment naive WGS Healthy 100 13001418200 8607025000 3.42
CGPLH399 Preoperative treatment naive WGS Healthy 100 9867699200
5526646000 2.19 CGPLH400 Preoperative treatment naive WGS Healthy
100 10573939000 6290438200 2.50 CGPLH401 Preoperative treatment
naive WGS Healthy 100 9415150000 6139638000 2.44 CGPLH402
Preoperative treatment naive WGS Healthy 100 5541458000 2912027800
1.18 CGPLH403 Preoperative treatment naive WGS Healthy 100
6470913200 3549172600 1.41 CGPLH404 Preoperative treatment naive
WGS Healthy 100 7369651800 4120205000 1.64 CGPLH405 Preoperative
treatment naive WGS Healthy 100 7360239000 4293522600 1.70 CGPLH406
Preoperative treatment naive WGS Healthy 100 6026125400 3426007400
1.36 CGPLH407 Preoperative treatment naive WGS Healthy 100
7073375200 4079286800 1.62 CGPLH408 Preoperative treatment naive
WGS Healthy 100 8006103200 5121285600 2.03 CGPLH409 Preoperative
treatment naive WGS Healthy 100 7343124600 4432335600 1.76 CGPLH410
Preoperative treatment naive WGS Healthy 100 7551842000 4818779600
1.91 CGPLH411 Preoperative treatment naive WGS Healthy 100
6119676400 3636478400 1.44 CGPLH412 Preoperative treatment naive
WGS Healthy 100 7960821200 4935752200 1.96 CGPLH413 Preoperative
treatment naive WGS Healthy 100 7623405400 4827888400 1.92 CGPLH414
Preoperative treatment naive WGS Healthy 100 7381312400 4743337200
1.88 CGPLH415 Preoperative treatment naive WGS Healthy 100
7240754200 4162208800 1.65 CGPLH416 Preoperative treatment naive
WGS Healthy 100 7745658600 4670226000 1.85 CGPLH417 Preoperative
treatment naive WGS Healthy 100 7627498600 4403085600 1.75 CGPLH418
Preoperative treatment naive WGS Healthy 100 9090285000 5094814000
2.02 CGPLH419 Preoperative treatment naive WGS Healthy 100
7914120200 5078389800 2.02 CGPLH42 Preoperative treatment naive WGS
Healthy 100 39492040600 3901039400 10.32 CGPLH420 Preoperative
treatment naive WGS Healthy 100 70143072800 4711393600 1.87
CGPLH422 Preoperative treatment naive WGS Healthy 100 9103972800
6053559800 2.40 CGPLH423 Preoperative treatment naive WGS Healthy
100 10154714200 6128800200 2.43 CGPLH424 Preoperative treatment
naive WGS Healthy 100 11002394000 6573756000 2.61 CGPLH425
Preoperative treatment naive WGS Healthy 100 14681352600 9272557000
3.68 CGPLH426 Preoperative treatment naive WGS Healthy 100
8336731000 5177430800 2.05 CGPLH427 Preoperative treatment naive
WGS Healthy 100 8242924400 5632991800 2.24 CGPLH428 Preoperative
treatment naive WGS Healthy 100 8512550400 5604756600 2.22 CGPLH429
Preoperative treatment naive WGS Healthy 100 8369802800 5477121400
2.17 CGPLH43 Preoperative treatment naive WGS Healthy 100
38513193400 3815698400 10.10 CGPLH430 Preoperative treatment naive
WGS Healthy 100 10357365400 6841611000 2.71 CGPLH431 Preoperative
treatment naive WGS Healthy 100 7599875800 5006909000 1.99 CGPLH432
Preoperative treatment naive WGS Healthy 100 7932532400 4932304200
1.96 CGPLH434 Preoperative treatment naive WGS Healthy 100
10417028600 6965093800 2.76 CGPLH435 Preoperative treatment naive
WGS Healthy 100 6747793800 5677115290 2.29 CGPLH436 Preoperative
treatment naive WGS Healthy 100 7990589400 5228737800 2.07 GGPLH437
Preoperative treatment naive WGS Healthy 100 10156991200 6935537200
2.75 CGPLH438 Preoperative treatment naive WGS Healthy 100
9473604000 6445455600 2.56 CGPLH439 Preoperative treatment naive
WGS Healthy 100 8303723400 5439877200 2.16 CGPLH440 Preoperative
treatment naive WGS Healthy 100 9055233800 6018631400 2.39 CGPLH441
Preoperative treatment naive WGS Healthy 100 10290682000 6896415200
2.74 CGPLH442 Preoperative treatment naive WGS Healthy 100
9876551600 6591249800 2.62 CGPLH443 Preoperative treatment naive
WGS Healthy 100 9837225800 6360740800 2.52 CGPLH444 Preoperative
treatment naive WGS Healthy 100 9199271400 5795941660 2.26 CGPLH445
Preoperative treatment naive WGS Healthy 100 8089236400 5218259800
2.07 CGPLH446 Preoperative treatment naive WGS Healthy 100
7890664200 5181606000 2.06 CGPLH447 Preoperative treatment naive
WGS Healthy 100 7775775000 5120239800 2.03 CGPLH448 Preoperative
treatment naive WGS Healthy 100 8686964800 5605079200 2.22 CGPLH449
Preoperative treatment naive WGS Healthy 100 8604545400 5527726600
2.19 CGPLH45 Preoperative treatment naive WGS Healthy 100
39029653000 3771601200 9.98 CGPLH450 Preoperative treatment naive
WGS Healthy 100 8428254800 5439950000 2.16 CGPLH451 Preoperative
treatment naive WGS Healthy 100 8128977600
5186265600 2.06 CGPLH452 Preoperative treatment naive WGS Healthy
100 6474313400 4216316400 1.67 CGPLH453 Preoperative treatment
naive WGS Healthy 100 9831832800 6224917600 2.47 CGPLH455
Preoperative treatment naive WGS Healthy 100 7373753000 4593473600
1.82 CGPLH456 Preoperative treatment naive WGS Healthy 100
8455416200 5457148200 2.17 CGPLH457 Preoperative treatment naive
WGS Healthy 100 8647618000 5534503800 2.20 CGPLH458 Preoperative
treatment naive WGS Healthy 100 6633156400 4415186060 1.79 CGPLH459
Preoperative treatment naive WGS Healthy 100 8361048200 5497193800
2.18 CGPLH46 Preoperative treatment naive WGS Healthy 100
35361484600 3516232800 9.30 CGPLH460 Preoperative treatment naive
WGS Healthy 100 6788835400 4472282800 1.77 CGPLH463 Preoperative
treatment naive WGS Healthy 100 8534880800 5481759200 2.18 CGPLH464
Preoperative treatment naive WGS Healthy 100 6692520006 4184463400
1.66 CGPLH465 Preoperative treatment naive WGS Healthy 100
7772884600 4878430800 1.94 CGPLH466 Preoperative treatment naive
WGS Healthy 100 9056275000 5830877400 2.31 CGPLH467 Preoperative
treatment naive WGS Healthy 100 6931419200 4585861000 1.82 CGPLH468
Preoperative treatment naive WGS Healthy 100 9334067400 6314830460
2.51 CGPLH469 Preoperative treatment naive WGS Healthy 100
7376691000 4545246600 1.80 CGPLH47 Preoperative treatment naive WGS
Healthy 100 38485647600 3534883600 9.35 CGPLH470 Preoperative
treatment naive WGS Healthy 100 7899727600 5221650600 2.07 CGPLH471
Preoperative treatment naive WGS Healthy 100 9200430600 6102371000
2.42 CGPLH472 Preoperative treatment naive WGS Healthy 100
8143742400 5399946600 2.14 CGPLH473 Preoperative treatment naive
WGS Healthy 100 8123924600 5419825400 2.15 CGPLH474 Preoperative
treatment naive WGS Healthy 100 3853071400 6084059400 2.41 CGPLH475
Preoperative treatment naive WGS Healthy 100 8115374000 5291718000
2.10 CGPLH476 Preoperative treatment naive WGS Healthy 100
8163162000 5096869660 2.02 CGPLH477 Preoperative treatment naive
WGS Healthy 100 8350093206 5465468600 2.17 CGPLH478 Preoperative
treatment naive WGS Healthy 100 8259642200 5406516200 2.15 CGPLH479
Preoperative treatment naive WGS Healthy 100 8027598600 5417376800
2.15 CGPLH48 Preoperative treatment naive WGS Healthy 100
42232410000 4165893400 11.02 CGPLH480 Preoperative treatment naive
WGS Healthy 100 7832983200 5020127000 1.99 CGPLH481 Preoperative
treatment naive WGS Healthy 100 7578518800 4883280800 1.94 CGPLH482
Preoperative treatment naive WGS Healthy 100 8279364800 5652263600
2.24 CGPLH483 Preoperative treatment naive WGS Healthy 100
8660338800 5823859200 2.31 CGPLH484 Preoperative treatment naive
WGS Healthy 100 8445420000 5794328000 2.30 CGPLH485 Preoperative
treatment naive WGS Healthy 100 8371255406 5490207800 2.18 CGPLH486
Preoperative treatment naive WGS Healthy 100 8216712200 5506871000
2.19 CGPLH487 Preoperative treatment naive WGS Healthy 100
7936294200 5309250200 2.11 CGPLH488 Preoperative treatment naive
WGS Healthy 100 8355603600 545316000 2.16 CGPLH49 Preoperative
treatment naive WGS Healthy 100 33912191800 3310056000 8.76
CGPLH490 Preoperative treatment naive WGS Healthy 100 7768712400
5175567800 2.05 CGPLH491 Preoperative treatment naive WGS Healthy
100 9070904000 6011275000 2.39 CGPLH492 Preoperative treatment
naive WGS Healthy 100 7208727200 4753213800 1.89 CGPLH493
Preoperative treatment naive WGS Healthy 100 10542882600 7225870800
2.87 CGPLH494 Preoperative treatment naive WGS Healthy 100
10908197600 7046645000 2.80 CGPLH495 Preoperative treatment naive
WGS Healthy 100 8945040400 5891697800 2.34 CGPLH496 Preoperative
treatment naive WGS Healthy 100 10859729400 7549608000 3.00
CGPLH497 Preoperative treatment naive WGS Healthy 100 9630507400
6473162800 2.57 CGPLH498 Preoperative treatment naive WGS Healthy
100 10060232600 6744622800 2.68 CGPLH499 Preoperative treatment
naive WGS Healthy 100 10221293600 6951282800 2.76 CGPLH50
Preoperative treatment naive WGS Healthy 100 41248860600 4073272890
10.78 CGPLH500 Preoperative treatment naive WGS Healthy 100
9703168209 6239893800 2.48 CGPLH501 Preoperative treatment naive
WGS Healthy 100 9104779800 6161602800 2.45 CGPLH502 Preoperative
treatment naive WGS Healthy 100 8514467400 5290881400 2.10 CGPLH503
Preoperative treatment naive WGS Healthy 100 9019992209 6100383400
2.42 CGPLH504 Preoperative treatment naive WGS Healthy 100
9320330200 6109750200 2.46 CGPLH505 Preoperative treatment naive
WGS Healthy 100 7499497400 4914559000 1.95 CGPLH506 Preoperative
treatment naive WGS Healthy 100 10526142000 6963312600 2.76
CGPLH507 Preoperative treatment naive WGS Healthy 100 9091018400
6146678600 2.44 CGPLH508 Preoperative treatment naive WGS Healthy
100 10989315600 7360201400 2.92 CGPLH509 Preoperative treatment
naive WGS Healthy 100 9729084600 6702691600 2.66 CGPLH51
Preoperative treatment naive WGS Healthy 100 35967451400 3492833200
9.24 CGPLH510 Preoperative treatment naive WGS Healthy 100
11162691600 7626795400 3.03 CGPLH511 Preoperative treatment naive
WGS Healthy 100 11888619600 8110427600 3.22 CGPLH512 Preoperative
treatment naive WGS Healthy 100 10726438400 7110078000 2.82
CGPLH513 Preoperative treatment naive WGS Healthy 100 10701564200
7105271400 2.84 CGPLH514 Preoperative treatment naive WGS Healthy
100 8822067000 5958773800 2.36 CGPLH515 Preoperative treatment
naive WGS Healthy 100 7792074800 5317464600 2.11 CGPLH516
Preoperative treatment naive WGS Healthy 100 8642620000 5846439400
2.32 CGPLH517 Preoperative treatment naive WGS Healthy 100
11915929600 0013937000 3.18 CGPLH518 Preoperative treatment naive
WGS Healthy 100 12804517400 3606661600 3.42 CGPLH519 Preoperative
treatment naive WGS Healthy 100 11513222200 7922798400 3.14 CGPLH52
Preoperative treatment naive WGS Healthy 100 49247304200 4849531400
12.83 CGPLH520 Preoperative treatment naive WGS Healthy 100
8942102400 6030683400 2.39 CGPLH54 Preoperative treatment naive WGS
Healthy 100 45399346400 4466164600 11.82 CGPLH55 Preoperative
treatment naive WGS Healthy 100 42547725000 4283337600 11.33
CGPLH56 Preoperative treatment naive WGS Healthy 100 33460308000
3226338000 8.53 CGPLH51 Preoperative treatment naive WGS Healthy
100 36504735200 3509125000 9.28 CGPLH59 Preoperative treatment
naive WGS Healthy 100 39642810600 3820011000 10.11 CGPLH625
Preoperative treatment naive WGS Healthy 100 6408225000 4115487600
1.63 CGPLH626 Preoperative treatment naive WGS Healthy 100
9915193600 6391657000 2.54 CGPLH63 Preoperative treatment naive WGS
Healthy 100 37447047600 3506737000 9.26 CGPLH639 Preoperative
treatment naive WGS Healthy 100 8158965890 5216049600 2.07 CGPLH64
Preoperative treatment naive WGS Healthy 100 34275506800 3264503000
8.63 CGPLH640 Preoperative treatment naive WGS Healthy 100
8058876800 5333551800 2.12 CGPLH642 Preoperative treatment naive
WGS Healthy 100 7545555600 4909732800 1.95 CGPLH643 Preoperative
treatment naive WGS Healthy 100 7865776800 5254772000 2.09 CGPLH644
Preoperative treatment naive WGS Healthy 100 6890139000 4599387400
1.83 CGPLH646 Preoperative treatment naive WGS Healthy 100
7757219400 5077408200 2.01 CGPLH75 Preoperative treatment naive WGS
Healthy 100 23882926000 2250344400 5.95 CGPLH76 Preoperative
treatment naive WGS Healthy 100 30631483600 3086042200 8.16 CGPLH77
Preoperative treatment naive WGS Healthy 100 31651741400 3041290200
8.04 CGPLH78 Preoperative treatment naive WGS Healthy 100
31165831200 3130079800 8.28 CGPLH79 Preoperative treatment naive
WGS Healthy 100 31935043000 3128488200 8.27 CGPLH80 Preoperative
treatment naive WGS Healthy 100 32965093000 3311371800 8.76 CGPLH81
Preoperative treatment naive WGS Healthy 100 27035311200 2455084400
6.49 CGPLH82 Preoperative treatment naive WGS Healthy 100
28447051200 2893358200 7.65 CGPLH83 Preoperative treatment naive
WGS Healthy 100 26702240200 2459494000 6.50 CGPLH84 Preoperative
treatment naive WGS Healthy 100 251713861400 2524467400 6.68
CGPLLU13 Pre-treatment, Day-2 WGS Lung Cancer 100 9126585600
5915061800 2.35 CGPLLU13 Post-treatment, Day 5 WGS Lung Cancer 100
7739120200 5071745800 2.01 CGPLLU13 Post-treatment, Day 28 WGS Lung
Cancer 100 9081585400 5764371600 2.29 CGPLLU13 Post-treatment, Day
91 WGS Lung Cancer 100 9576557000 6160760200 2.44 CGPLLU14
Pre-treatment, Day-38 WGS Lung Cancer 100 13659198400 9033455800
3.58 CGPLLU14 Pre-treatment, Day-16 WGS Lung Cancer 100 7178855800
4856643600 1.93 CGPLLU14 Pre-treatment, Day-3 WGS Lung Cancer 100
7653473000 4816193600 1.91 CGPLLU14 Pre-treatment, Day 0 WGS Lung
Cancer 100 7351997400 5193256600 2.06 CGPLLU14 Post-treatment, Day
0.33 WGS Lung Cancer 100 7193040800 4869701600 1.93 CGPLLU14
Post-treatment, Day 7 WGS Lung Cancer 100 7102000000 4741432600
1.88 CGPLLU144 Preoperative treatment naive WGS Lung Cancer 100
4934813600 3415936400 1.36 CGPLLU147 Preoperative treatment naive
WGS Lung Cancer 100 24409561000 2118672800 5.61 CGPLLU161
Preoperative treatment naive WGS Lung Cancer 100 8998813400
6016145000 2.39 CGPLLU162 Preoperative treatment naive WGS Lung
Cancer 100 9709792400 6407866400 2.54 CGPLLU163 Preoperative
treatment naive WGS Lung Cancer 100 9150620200 6063569800 2.41
CGPLLU165 Preoperative treatment naive WGS Lung Cancer 100
28374436400 2651138600 7.01 CGPLLU168 Preoperative treatment naive
WGS Lung Cancer 100 5692739400 3695191000 1.47 CGPLLU169
Preoperative treatment naive WGS Lung Cancer 100 9093975600
5805320800 2.30 CGPLLU175 Preoperative treatment naive WGS Lung
Cancer 100 33794816800 3418750400 9.04 CGPLLU176 Preoperative
treatment naive WGS Lung Cancer 100 8778553800 5794950200 2.30
CGPLLU177 Preoperative treatment naive WGS Lung Cancer 100
3734614800 2578696200 1.02 CGPLLU180 Preoperative treatment naive
WGS Lung Cancer 100 28305936600 2756034200 7.29 CGPLLU198
Preoperative treatment naive WGS Lung Cancer 100 32344959200
2218577200 5.86 CGPLLU202 Preoperative treatment naive WGS Lung
Cancer 100 21110128200 1831279400 4.84 CGPLLU203 Preoperative
treatment naive WGS Lung Cancer 100 4304235600 2806429000 1.15
CGPLLU205 Preoperative treatment naive WGS Lung Cancer 100
10502467000 7386984800 2.93 CGPLLU206 Preoperative treatment naive
WGS Lung Cancer 100 21888248200 2026666000 5.36 CGPLLU207
Preoperative treatment naive WGS Lung Cancer 100 10806230600
7363049000 2.92
CGPLLU208 Preoperative treatment naive WGS Lung Cancer 100
7795426800 5199545800 2.06 CGPLLU209 Preoperative treatment naive
WGS Lung Cancer 100 26174542000 2621961800 6.93 CGPLLU244
Pre-treatment, Day-7 WGS Lung Cancer 100 9967531400 6704365800 2.66
CGPLLU244 Pre-treatment, Day-1 WGS Lung Cancer 100 9547119200
5785172600 2.30 CGPLLU944 Post-treatment, Day 6 WGS Lung Cancer 100
9535898600 6452174000 2.56 CGPLLU244 Post-treatment, Day 62 WGS
Lung Cancer 100 6783628000 5914149000 2.35 CGPLLU245 Pre-treatment,
Day-32 WGS Lung Cancer 100 10025823200 6313303800 2.51 CGPLLU245
Pre-treatment, Day 0 WGS Lung Cancer 100 9462480400 6612867800 2.62
CGPLLU245 Post-treatment, Day 7 WGS Lung Cancer 100 9143025000
6431013200 2.55 CGPLLU245 Post-treatment, Day 21 WGS Lung Cancer
100 9072713800 6368533000 2.53 CGPLLU946 Pre-treatment, Day-21 WGS
Lung Cancer 100 9579787000 6458003400 2.56 CGPLLU246 Pre-treatment,
Day 0 WGS Lung Cancer 100 9512703600 6440535600 2.56 CGPLLU246
Post-treatment, Day 9 WGS Lung Cancer 100 9012645000 6300939200
2.50 CGPLLU246 Post-treatment, Day 42 WGS Lung Cancer 100
11136103000 7358747400 2.92 CGPLLU264 Pre-treatment, Day-1 WGS Lung
Cancer 100 9196305000 6239803600 2.49 CGPLLU264 Post-treatment, Day
6 WGS Lung Cancer 100 8247416600 5600454200 2.22 CGPLLU264
Post-treatment, Day 27 WGS Lung Cancer 100 8681022200 5856109000
2.32 CGPLLU264 Post-treatment, Day 69 WGS Lung Cancer 100
3931976400 5974246000 2.37 CGPLLU265 Pre-treatment, Day 0 WGS Lung
Cancer 100 9460534000 6111185200 2.43 CGPLLU265 Post-treatment, Day
3 WGS Lung Cancer 100 8051601200 4984166600 1.98 CGPLLU265
Post-treatment, Day 7 WGS Lung Cancer 100 8082224600 5110092600
2.03 CGPLLU265 Post-treatment, Day 84 WGS Lung Cancer 100
8368637400 5369526400 2.13 CGPLLU266 Pre-treatment, Day 0 WGS Lung
Cancer 100 8583766400 5846473600 2.32 CGPLLU266 Post-treatment, Day
16 WGS Lung Cancer 100 8795793600 5984531400 2.37 CGPLLU266
Post-treatment, Day 83 WGS Lung Cancer 100 9157947600 6227735060
2.47 CGPLLU266 Post-treatment, Day 328 WGS Lung Cancer 100
7299455400 5049379000 2.00 CGPLLU267 Pre-treatment, Day-1 WGS Lung
Cancer 100 10658657800 6892067000 2.73 CGPLLU267 Post-treatment,
Day 34 WGS Lung Cancer 100 8492833400 5101097800 2.02 CGPLLU267
Post-treatment, Day 90 WGS Lung Cancer 100 12030314800 7757930400
3.09 CGPLLU269 Pre-treatment, Day 0 WGS Lung Cancer 100 9170168000
5830454400 2.31 CGPLLU269 Post-treatment, Day 9 WGS Lung Cancer 100
8905640400 5290461400 2.10 CGPLLU269 Post-treatment, Day 28 WGS
Lung Cancer 100 8455306600 5387927400 2.14 CGPLLU271
Post-treatment, Day 259 WGS Lung Cancer 100 8112060400 5404979000
2.14 CGPLLU271 Pre-treatment, Day 0 WGS Lung Cancer 100 13150818200
8570453400 3.40 CGPLLU271 Post-treatment, Day 6 WGS Lung Cancer 100
9008880600 5854051400 2.32 CGPLLU271 Post-treatment, Day 20 WGS
Lung Cancer 100 8670913000 5461577000 2.17 CGPLLU271
Post-treatment, Day 104 WGS Lung Cancer 100 8887441400 5609039000
2.23 CGPLLU43 Pre-treatment, Day-1 WGS Lung Cancer 100 6407811200
5203486400 2.06 CGPLLU43 Post-treatment, Day 6 WGS Lung Cancer 100
9964335200 5626714400 2.23 CGPLLU43 Post-treatment, Day 27 WGS Lung
Cancer 100 8902283000 5485656200 2.18 CGPLLU43 Post-treatment, Day
83 WGS Lung Cancer 100 9201509200 5875064200 2.33 CGPLLU86
Pre-treatment, Day 0 WGS Lung Cancer 100 9152729200 6248173200 2.48
CGPLLU86 Post-treatment, Day 0.5 WGS Lung Cancer 100 6703253000
4663026800 1.85 CGPLLU86 Post-treatment, Day 7 WGS Lung Cancer 100
6590121400 4559562400 1.81 CGPLLU86 Post-treatment, Day 17 WGS Lung
Cancer 100 8653551800 5900136000 2.34 CGPLLU88 Pre-treatment, Day 0
WGS Lung Cancer 100 8096528000 8505475400 2.18 CGPLLU88
Post-treatment, Day 7 WGS Lung Cancer 100 0283192200 5784217600
2.30 CGPLLU88 Post-treatment, Day 297 WGS Lung Cancer 100
9297110800 6407258000 2.54 CGPLLU89 Pre-treatment, Day 0 WGS Lung
Cancer 100 7042145200 5356095400 2.13 CGPLLU89 Post-treatment, Day
7 WGS Lung Cancer 100 7234220200 4930375200 1.96 CGPLLU89
Post-treatment, Day 22 WGS Lung Cancer 100 6242889800 4057361000
1.61 CGPLOV11 Preoperative treatment naive WGS Ovarian Cancer 100
8985130400 5871959600 2.33 CGPLOV12 Preoperative treatment naive
WGS Ovarian Cancer 100 9705820000 6430505400 2.55 CGPLOV13
Preoperative treatment naive WGS Ovarian Cancer 100 10307949400
7029712000 2.79 CCPLOV15 Preoperative treatment naive WGS Ovarian
Cancer 100 8472829400 8562142400 2.21 CGPLOV16 Preoperative
treatment naive WGS Ovarian Cancer 100 10977781000 7538581600 2.99
CGPLOV19 Preoperative treatment naive WGS Ovarian Cancer 100
8800876200 5855304000 2.32 CGPLOV20 Preoperative treatment naive
WGS Ovarian Cancer 100 8714443600 5605165800 2.26 CGPLOV21
Preoperative treatment naive WGS Ovarian Cancer 100 10180394800
7120260400 2.83 CGPLOV22 Preoperative treatment naive WGS Ovarian
Cancer 100 10107760000 6821916800 2.71 CGPLOV23 Preoperative
treatment naive WGS Ovarian Cancer 100 10643399800 7206330800 2.86
CGPLOV24 Preoperative treatment naive WGS Ovarian Cancer 100
6780929000 4623300400 1.83 CGPLOV25 Preoperative treatment naive
WGS Ovarian Cancer 100 7817548600 5359975200 2.13 CGPLOV26
Preoperative treatment naive WGS Ovarian Cancer 100 11763101400
8178024400 3.25 CGPLOV28 Preoperative treatment naive WGS Ovarian
Cancer 100 9522546400 6259423400 2.48 CGPLOV31 Preoperative
treatment naive WGS Ovarian Cancer 100 9104831200 6109358400 2.42
CGPLOV32 Preoperative treatment naive WGS Ovarian Cancer 100
9222073600 6035150000 2.39 CGPLOV37 Preoperative treatment naive
WGS Ovarian Cancer 100 8898328600 5971018200 2.37 CGPLOV38
Preoperative treatment naive WGS Ovarian Cancer 100 8756825200
5861536600 2.33 CGPLOV40 Preoperative treatment naive WGS Ovarian
Cancer 100 9709391600 6654707200 2.64 CGPLOV41 Preoperative
treatment naive WGS Ovarian Cancer 100 8923625000 5973070400 2.37
CGPLOV42 Preoperative treatment naive WGS Ovarian Cancer 100
10719380400 7353214200 2.92 CGPLOV43 Preoperative treatment naive
WGS Ovarian Cancer 100 10272189000 6423288600 2.55 CGPLOV44
Preoperative treatment naive WGS Ovarian Cancer 100 9861862600
6769185800 2.69 CGPLOV46 Preoperative treatment naive WGS Ovarian
Cancer 100 8788956400 5789863400 2.30 CGPLOV47 Preoperative
treatment naive WGS Ovarian Cancer 100 9380561800 6480763600 2.57
CCPLOV48 Preoperative treatment naive WGS Ovarian Cancer 100
9258552600 6380106400 2.53 CCPLOV49 Preoperative treatment naive
WGS Ovarian Cancer 100 8787025400 6134503600 2.43 CGFLOV50
Preoperative treatment naive WGS Ovarian Cancer 100 10144154400
6984721400 2.77 CGPLPA2 Preoperative treatment naive WGS Pancreatic
Cancer 100 12740651400 9045622000 3.59 CGPLPA113 Preoperative
treatment naive WGS Duodenal Canner 100 8802479000 5909030800 2.34
CGPLPA114 Preoperative treatment naive WGS Bile Duct Cancer 100
8792313600 6019061000 2.39 CGPLPA115 Preoperative treatment naive
WGS Bile Duct Cancer 100 8636551400 5958809000 2.36 CGPLPA117
Preoperative treatment naive WGS Bile Duct Cancer 100 9128885200
6288833200 2.50 CGPLPA118 Preoperative treatment naive WGS Bile
Duct Cancer 100 7931485800 5407532800 2.15 CGPLPA122 Preoperative
treatment naive WGS Bile Duct Cancer 100 10888985000 7530118800
2.99 CGPLPA124 Preoperative treatment naive WGS Bile Duct Cancer
100 8062012400 5860171000 2.33 CGPLPA125 Preoperative treatment
naive WGS Bile Duct Cancer 100 9715576600 6390321000 2.54 CGPLPA126
Preoperative treatment naive WGS Bile Duct Cancer 100 8056768800
5651600800 2.24 CGPLPA127 Preoperative treatment naive WGS Bile
Duct Cancer 100 8000301000 5382987600 2.14 CGPLPAI28 Preoperative
treatment naive WGS Bile Duct Cancer 100 6165751600 4256521400 1.69
CGPLPA129 Preoperative treatment naive WGS Bile Duct Cancer 100
7143147400 4917370400 1.95 CGPLPA130 Preoperative treatment naive
WGS Bile Duct Cancer 100 5664335000 3603919400 1.43 CGPLPA131
Preoperative treatment naive WGS Bile Duct Cancer 100 8292982000
5844942000 2.32 CGPLPA134 Preoperative treatment naive WGS Bile
Duct Cancer 100 7088917000 5048887600 2.00 CGPLPA135 Preoperative
treatment naive WGS Bile Duct Cancer 100 8750665600 5800613200 2.30
CGPLPA136 Preoperative treatment naive WGS Bile Duct Cancer 100
7539715800 5248227600 2.08 CGPLPA137 Preoperative treatment naive
WGS Bile Duct Cancer 100 8391815400 5901273800 2.34 CGPLPA139
Preoperative treatment naive WGS Bile Duct Cancer 100 8992280200
6328314400 2.51 CGPLPA14 Preoperative treatment naive WGS
Pancreatic Cancer 100 8787706200 5731317600 2.27 CGPLPA140
Preoperative treatment naive WGS Bile Duct Cancer 100 16365641800
11216732000 4.45 CGPLPA141 Preoperative treatment naive WGS Bile
Duct Cancer 100 15086298000 10114790200 4.01 CGPLPA15 Preoperative
treatment naive WGS Pancreatic Cancer 100 8255566800 5531677600 2
20 CGPLPA155 Preoperative treatment naive WGS Bile Duct Cancer 100
9457155800 6621881800 2.63 CGPLPA156 Preoperative treatment naive
WGS Pancreatic Cancer 100 9345385800 6728653000 2.67 CGPLPA165
Preoperative treatment naive WGS Bile Duct Cancer 100 8356604600
0829895800 2.31 CGPLPA168 Preoperative treatment naive WGS Bile
Duct Cancer 100 10365661600 7048115600 2.80 CGPLPA17 Preoperative
treatment naive WGS Pancreatic Cancer 100 8073547400 4687803000
1.86 CGPLPA184 Preoperative treatment naive WGS Bile Duct Cancer
100 9014218400 6230922200 2.47 CGPLPA187 Preoperative treatment
naive WGS Bile Duct Cancer 100 8883536200 6140874400 2.44 CGPLPA23
Preoperative treatment naive WGS Pancreatic Cancer 100 9835452000
6246525400 2.48 CGPLPA25 Preoperative treatment naive WGS
Pancreatic Cancer 100 10077515400 6103322200 2.42 CGPLPA26
Preoperative treatment naive WGS Pancreatic Cancer 100 8354272400
5725781000 2.21 CGPLPA28 Preoperative treatment naive WGS
Pancreatic Cancer 100 8477461600 5688846800 2.26 CGPLPA33
Preoperative treatment naive WGS Pancreatic Cancer 100 7287615600
4506723800 1.82 CGPLPA34 Preoperative treatment naive WGS
Pancreatic Cancer 100 6122902400 4094828000 1.62 CGPLPA37
Preoperative treatment naive WGS Pancreatic Cancer 100 12714888200
8527779200 3.38 CGPLPA38 Preoperative treatment naive WGS
Pancreatic Cancer 100 8525500600 5501341400 2.18 CGPLPA39
Preoperative treatment naive WGS Pancreatic Cancer 100 10502663600
6812333000 2.70 CGPLPA40 Preoperative treatment naive WGS
Pancreatic Cancer 100 9083670000 0394717800 2.14 CGPLPA42
Preoperative treatment naive WGS Pancreatic Cancer 100 5072126600
3800395200 1.54 CGPLPA46 Preoperative treatment naive WGS
Pancreatic Cancer 100 4720090200 2626298800 1.04 CGPLPA47
Preoperative treatment naive WGS Pancreatic Cancer 100 7317385800
4543833000 1.80 CGPLPA48 Preoperative treatment naive WGS
Pancreatic Cancer 100 7553856200 5022695600 1.90 CGPLPA52
Preoperative treatment naive WGS Pancreatic Cancer 100 5655875000
3551861600 1.41 COPLPA53 Preoperative treatment naive WGS
Pancreatic Cancer 100 9504749000
6323344800 2.51 CGPLPA58 Preoperative treatment naive WGS
Pancreatic Cancer 100 8088090200 5118138200 2.03 CGPLPA59
Preoperative treatment naive WGS Pancreatic Cancer 100 14547364600
9617773600 3.82 CGPLPA67 Preoperative treatment naive WGS
Pancreatic Cancer 100 8222177400 5351172000 2.12 CGPLPA69
Preoperative treatment naive WGS Pancreatic Cancer 100 7899181400
5006114800 1.90 CGPLPA71 Preoperative treatment naive WGS
Pancreatic Cancer 100 7340620400 4955417400 1.97 CGPLPA74
Preoperative treatment naive WGS Pancreatic Cancer 100 6666371400
4571394200 1.81 CGPLPA76 Preoperative treatment naive WGS
Pancreatic Cancer 100 9755658600 6412606800 2.54 CGPLPA85
Preoperative treatment naive WGS Pancreatic Cancer 100 10853223000
7309498600 2.90 CGPLPA86 Preoperative treatment naive WGS
Pancreatic Cancer 100 8744365400 5514523200 2.19 CGPLPA92
Preoperative treatment naive WGS Pancreatic Cancer 100 8073791200
5390492800 2.14 CGPLPA93 Preoperative treatment naive WGS
Pancreatic Cancer 100 10390273000 7186589400 2.85 CGPLPA94
Preoperative treatment naive WGS Pancreatic Cancer 100 11060347600
7641336400 3.03 CGPLPA95 Preoperative treatment naive WGS
Pancreatic Cancer 100 12416627200 7206503800 2.86 CGST102
Preoperative treatment naive WGS Pancreatic Cancer 100 6637004600
4545072600 1.80 CGST11 Preoperative treatment naive WGS Pancreatic
Cancer 100 9718427800 6259679600 2.48 CGST110 Preoperative
treatment naive WGS Pancreatic Cancer 100 9319661600 6359317400
2.52 CGST114 Preoperative treatment naive WGS Pancreatic Cancer 100
6865213000 4841171600 1.92 CGST13 Preoperative treatment naive WGS
Pancreatic Cancer 100 9284554800 6360843800 2.52 CGST131
Preoperative treatment naive WGS Gastric cancer 100 5924382000
3860677200 1.53 CGST141 Preoperative treatment naive WGS Gastric
cancer 100 8486380800 5860491000 2.33 CGST16 Preoperative treatment
naive WGS Gastric cancer 100 13820725800 9377828000 3.72 CGST18
Preoperative treatment naive WGS Gastric cancer 100 7781288000
5278862400 2.09 CGST21 Preoperative treatment naive WGS Gastric
cancer 100 7171165400 4103970800 1.63 CGST26 Preoperative treatment
naive WGS Gastric cancer 100 8983961800 6053405600 2.40 CGST28
Preoperative treatment naive WGS Gastric cancer 100 9683035400
6745116400 2.68 CGST30 Preoperative treatment naive WGS Gastric
cancer 100 8684086600 5741416000 2.28 CGST32 Preoperative treatment
naive WGS Gastric cancer 100 8568194600 5783369200 2.29 CGST33
Preoperative treatment naive WGS Gastric cancer 100 9351699600
6448718400 2.56 CGST38 Preoperative treatment naive WGS Gastric
cancer 100 8409876400 5770989200 2.29 CGST39 Preoperative treatment
naive WGS Gastric cancer 100 10573763000 7597016000 3.01 CGST41
Preoperative treatment naive WGS Gastric cancer 100 9434854200
6609415400 2.62 CGST45 Preoperative treatment naive WGS Gastric
cancer 100 8203868600 5625223000 2.23 CGST47 Preoperative treatment
naive WGS Gastric cancer 100 8938597600 6178990600 2.45 CGST48
Preoperative treatment naive WGS Gastric cancer 100 9106628800
6517085200 2.59 CGST53 Preoperative treatment naive WGS Gastric
cancer 100 9005374200 5854996200 2.32 CGST58 Preoperative treatment
naive WGS Gastric cancer 100 10020368600 6133458400 2.43 CGST67
Preoperative treatment naive WGS Gastric cancer 100 9198135600
5911071000 2.35 CGST77 Preoperative treatment naive WGS Gastric
cancer 100 8228789400 5119116800 2.03 CGST80 Preoperative treatment
naive WGS Gastric cancer 100 10596963400 7283152800 2.89 CGST81
Preoperative treatment naive WGS Gastric cancer 100 5494881200
5038064000 2.32
TABLE-US-00007 APPENDIX E Table 5. High coverage whole genome cfDNA
analyses of healthy individuals and lung cancer patients
Correlation Correlation of GC of Corrected Correlation Fragment
Fragment of Ratio Ratio Fragment Correlation Profile Profile Ratio
of to Median to Median Profile Fragment Median Fragment Fragment to
Median Ratio cfDNA Ratio Ratio Fragment Profile to Fragment Profile
of Profile of Ratio Lymphocyte Analysis Stage at Size Healthy
Healthy Profile of Nucleosome Patient Patient Type Type Timepoint
Diagnosis (bp) Individuals Individuals Lymphocytes Distances
CGPLH75 Healthy WGS Preoperative treatment naive NA 168 0.977 0.952
0.920 -0.886 CGPLH77 Healthy WGS Preoperative treatment naive NA
166 0.970 0.960 0.904 -0.912 CGPLH80 Healthy WGS Preoperative
treatment naive NA 168 0.955 0.949 0.960 -0.917 CGPLH81 Healthy WGS
Preoperative treatment naive NA 167 0.949 0.953 0.869 -0.883
CGPLH82 Healthy WGS Preoperative treatment naive NA 166 0 969 0.949
0.954 -0.917 CGPLH83 Healthy WGS Preoperative treatment naive NA
167 0.949 0.939 0.919 -0.904 CGPLH84 Healthy WGS Preoperative
treatment naive NA 168 0 967 0.948 0.951 -0.913 CGPLH52 Healthy WGS
Preoperative treatment naive NA 167 0.946 0.968 0.952 -0.924
CGPLH35 Healthy WGS Preoperative treatment naive NA 166 0.981 0.973
0.945 -0.921 CGPLH37 Healthy WGS Preoperative treatment naive NA
168 0.968 0.970 0.951 -0.922 CGPLH51 Healthy WGS Preoperative
treatment naive NA 167 0.968 0.976 0.948 -0.925 CGPLH55 Healthy WGS
Preoperative treatment naive NA 166 0.947 0.964 0.948 -0.917
CGPLH48 Healthy WGS Preoperative treatment naive NA 168 0.959 0.965
0.960 -9.923 CGPLH50 Healthy WGS Preoperative treatment naive NA
167 0.960 0.968 0.952 -0.921 CGPLH36 Healthy WGS Preoperative
treatment naive NA 168 0.955 0.954 0.955 -0.919 CGPLH42 Healthy WGS
Preoperative treatment naive NA 167 0.973 0.963 0.948 -0.918
CGPLH43 Healthy WGS Preoperative treatment naive NA 166 0.952 0.958
0.953 -0.928 CGPLH59 Healthy WGS Preoperative treatment naive NA
168 0.970 0.965 0.951 -0.925 CGPLH45 Healthy WGS Preoperative
treatment naive NA 168 0.965 0.950 0.949 -0.911 CGPLH47 Healthy WGS
Preoperative treatment naive NA 167 0.952 0.944 0.954 -0.921
CGPLH46 Healthy WGS Preoperative treatment naive NA 168 0.966 0.985
0.953 -0.923 CGPLH63 Healthy WGS Preoperative treatment naive NA
168 0.977 0.968 0.939 -0.920 CAPLH51 Healthy WGS Preoperative
treatment naive NA 168 0.935 0.955 0.957 -0.914 CAPLH57 Healthy WGS
Preoperative treatment naive NA 169 0.965 0.954 0.955 -0.917
CGPLH49 Healthy WGS Preoperative treatment naive NA 168 0.958 0.951
0.950 -0.924 CGPLH56 Healthy WGS Preoperative treatment naive NA
166 0.940 0.957 0.959 -0.911 CGPLH64 Healthy WGS Preoperative
treatment naive NA 169 0.960 0.940 0.949 -0.918 CGPLH78 Healthy WGS
Preoperative treatment naive NA 166 0.956 0.936 0.958 -0.911
CGPLH79 Healthy WGS Preoperative treatment naive NA 168 0.960 0.957
0.953 -0.917 CGPLH76 Healthy WGS Preoperative treatment naive NA
167 0.969 0.965 0.953 -0.917 CGPLLU175 Lung Cancer WGS Preoperative
treatment naive I 165 0.316 0.284 0.244 -0.262 CGPLLU180 Lung
Cancer WGS Preoperative treatment naive I 166 0.907 0.846 0.826
-0.819 CGPLLU198 Lung Cancer WGS Preoperative treatment naive I 166
0.972 0.946 0.928 -0.911 CGPLLU202 Lung Cancer WGS Preoperative
treatment naive I 160 0.821 0.605 0.905 -0.843 CGPLLU165 Lung
Cancer WGS Preoperative treatment naive II 163 0.924 0.961 0.815
-0.851 CGPLLU209 Lung Cancer WGS Preoperative treatment naive II
163 0.578 0.526 0.513 -0.534 CGPLLU147 Lung Cancer WGS Preoperative
treatment naive III 166 0.953 0.919 0.939 -0.912 CGPLLU206 Lung
Cancer WGS Preoperative treatment naive III 158 0.488 0.343 0.460
-0.481
TABLE-US-00008 APPENDIX F Table 6. Monitoring response to therapy
using whole genome analyses of cfDNA fragmentation profiles and
targeted mutations analyses Progression- free Survival Patient
Patient Type Analysis Type Timepoint Stage (months) CGPLLU14 Lung
Cancer Targeted Mutation Analysis and WGS Pre-treatment, Day-38 IV
15.4 CGPLLU14 Lung Cancer Targeted Mutation Analysis and WGS
Pre-treatment, Day-16 IV 15.4 CGPLLU14 Lung Cancer Targeted
Mutation Analysis and WGS Pre-treatment, Day-3 IV 15.4 CGPLLU14
Lung Cancer Targeted Mutation Analysis and WGS Pre-treatment, Day 0
IV 15.4 CGPLLU14 Lung Cancer Targeted Mutation Analysis and WGS
Post-treatment, Day 0.33 IV 15.4 CGPLLU14 Lung Cancer Targeted
Mutation Analysis and WGS Post-treatment, Day 7 IV 15.4 CGPLLU88
Lung Cancer Targeted Mutation Analysis and WGS Pre-treatment, Day 0
IV 18.0 CGPLLU88 Lung Cancer Targeted Mutation Analysis and WGS
Post-treatment, Day 7 IV 18.0 CGPLLU88 Lung Cancer Targeted
Mutation Analysis and WGS Post-treatment, Day 297 IV 18.0 CGPLLU244
Lung Cancer Targeted Mutation Analysis and WGS Pre-treatment, Day-7
IV 1.2 CGPLLU244 Lung Cancer Targeted Mutation Analysis and WGS
Pre-treatment, Day-1 IV 1.2 CGPLLU244 Lung Cancer Targeted Mutation
Analysis and WGS Post-treatment, Day 6 IV 1.2 CGPLLU244 Lung Cancer
Targeted Mutation Analysis and WGS Post-treatment, Day 62 IV 1.2
CGPLLU245 Lung Cancer Targeted Mutation Analysis and WGS
Pre-treatment, Day-32 IV 1.7 CGPLLU245 Lung Cancer Targeted
Mutation Analysis and WGS Pre-treatment, Day 0 IV 1.7 CGPLLU245
Lung Cancer Targeted Mutation Analysis and WGS Post-treatment, Day
7 IV 1.7 CGPLLU245 Lung Cancer Targeted Mutation Analysis and WGS
Post-treatment, Day 21 IV 1.7 CGPLLU246 Lung Cancer Targeted
Mutation Analysis and WGS Pre-treatment, Day-21 IV 1.3 CGPLLU246
Lung Cancer Targeted Mutation Analysis and WGS Pre-treatment, Day 0
IV 1.3 CGPLLU246 Lung Cancer Targeted Mutation Analysis and WGS
Post-treatment, Day 9 IV 1.3 CGPLLU246 Lung Cancer Targeted
Mutation Analysis and WGS Post-treatment, Day 42 IV 1.1 CGPLLU86
Lung Cancer Targeted Mutation Analysis and WGS Pre-treatment, Day 0
IV 12.4 CGPLLU86 Lung Cancer Targeted Mutation Analysis and WGS
Post-treatment, Day 0.5 IV 12.4 CGPLLU86 Lung Cancer Targeted
Mutation Analysis and WGS Post-treatment, Day 7 IV 12.4 CGPLLU86
Lung Cancer Targeted Mutation Analysis and WGS Post-treatment, Day
17 IV 12.4 CGPLLU89 Lung Cancer Targeted Mutation Analysis and WGS
Pre-treatment, Day 0 IV 6.7 CGPLLU89 Lung Cancer Targeted Mutation
Analysis and WGS Post-treatment, Day 7 IV 6.7 CGPLLU89 Lung Cancer
Targeted Mutation Analysis and WGS Post-treatment, Day 22 IV 6.7
CGLU316 Lung Cancer Targeted Mutation Analysis and WGS
Pre-treatment, Day-53 IV 1.4 CGLU316 Lung Cancer Targeted Mutation
Analysis and WGS Pre-treatment, Day-4 IV 1.4 CGLU316 Lung Cancer
Targeted Mutation Analysis and WGS Post-treatment, Day 18 IV 1.4
CGLU316 Lung Cancer Targeted Mutation Analysis and WGS
Post-treatment, Day 87 IV 1.4 CGLU344 Lung Cancer Targeted Mutation
Analysis and WGS Pre-treatment, Day-21 IV Ongoing CGLU344 Lung
Cancer Targeted Mutation Analysis and WGS Pre-treatment, Day 0 IV
Ongoing CGLU344 Lung Cancer Targeted Mutation Analysis and WGS
Post-treatment, Day 0.1675 IV Ongoing CGLU344 Lung Cancer Targeted
Mutation Analysis and WGS Post-treatment, Day 59 IV Ongoing CGLU369
Lung Cancer Targeted Mutation Analysis and WGS Pre-treatment, Day-2
IV 7.5 CGLU369 Lung Cancer Targeted Mutation Analysis and WGS
Post-treatment, Day 12 IV 7.5 CGLU369 Lung Cancer Targeted Mutation
Analysis and WGS Post-treatment, Day 68 IV 7.5 CGLU369 Lung Cancer
Targeted Mutation Analysis and WGS Post-treatment, Day 110 IV 7.5
CGLU373 Lung Cancer Targeted Mutation Analysis and WGS
Pre-treatment, Day-2 IV Ongoing CGLU373 Lung Cancer Targeted
Mutation Analysis and WGS Post-treatment, Day 0.125 IV Ongoing
CGLU373 Lung Cancer Targeted Mutation Analysis and WGS
Post-treatment, Day 7 IV Ongoing CGLU373 Lung Cancer Targeted
Mutation Analysis and WGS Post-treatment, Day 47 IV Ongoing
CGPLLU13 Lung Cancer Targeted Mutation Analysis and WGS
Pre-treatment, Day-2 IV 1.5 CGPLLU13 Lung Cancer Targeted Mutation
Analysis and WGS Post-treatment, Day 5 IV 1.5 CGPLLU13 Lung Cancer
Targeted Mutation Analysis and WGS Post-treatment, Day 28 IV 1.5
CGPLLU13 Lung Cancer Targeted Mutation Analysis and WGS
Post-treatment, Day 91 IV 1.5 CGPLLU264 Lung Cancer Targeted
Mutation Analysis and WGS Pre-treatment, Day-1 IV Ongoing CGPLLU264
Lung Cancer Targeted Mutation Analysis and WGS Post-treatment, Day
6 IV Ongoing CGPLLU264 Lung Cancer Targeted Mutation Analysis and
WGS Post-treatment, Day 27 IV Ongoing CGPLLU264 Lung Cancer
Targeted Mutation Analysis and WGS Post-treatment, Day 69 IV
Ongoing CGPLLU265 Lung Cancer Targeted Mutation Analysis and WGS
Pre-treatment, Day 0 IV Ongoing CGPLLU265 Lung Cancer Targeted
Mutation Analysis and WGS Post-treatment, Day 3 IV Ongoing
CGPLLU265 Lung Cancer Targeted Mutation Analysis and WGS
Post-treatment, Day 7 IV Ongoing CGPLLU265 Lung Cancer Targeted
Mutation Analysis and WGS Post-treatment, Day 84 IV Ongoing
CGPLLU266 Lung Cancer Targeted Mutation Analysis and WGS
Pre-treatment, Day 0 IV 9.6 CGPLLU266 Lung Cancer Targeted Mutation
Analysis and WGS Post-treatment, Day 16 IV 9.6 CGPLLU266 Lung
Cancer Targeted Mutation Analysis and WGS Post-treatment, Day 83 IV
9.6 CGPLLU266 Lung Cancer Targeted Mutation Analysis and WGS
Post-treatment, Day 328 IV 9.6 CGPLLU267 Lung Cancer Targeted
Mutation Analysis and WGS Pre-treatment, Day-1 IV 3.9 CGPLLU267
Lung Cancer Targeted Mutation Analysis and WGS Post-treatment, Day
34 IV 3.9 CGPLLU267 Lung Cancer Targeted Mutation Analysis and WGS
Post-treatment, Day 90 IV 3.9 CGPLLU269 Lung Cancer Targeted
Mutation Analysis and WGS Pre-treatment, Day 0 IV Ongoing CGPLLU269
Lung Cancer Targeted Mutation Analysis and WGS Post-treatment, Day
9 IV Ongoing CGPLLU269 Lung Cancer Targeted Mutation Analysis and
WGS Post-treatment, Day 28 IV Ongoing CGPLLU271 Lung Cancer
Targeted Mutation Analysis and WGS Pre-treatment, Day 0 IV 8.2
CGPLLU271 Lung Cancer Targeted Mutation Analysis and WGS
Post-treatment, Day 6 IV 8.2 CGPLLU271 Lung Cancer Targeted
Mutation Analysis and WGS Post-treatment, Day 20 IV 8.2 CGPLLU271
Lung Cancer Targeted Mutation Analysis and WGS Post-treatment, Day
104 IV 8.2 CGPLLU271 Lung Cancer Targeted Mutation Analysis and WGS
Post-treatment, Day 259 IV 8.2 CGPLLU43 Lung Cancer Targeted
Mutation Analysis and WGS Pre-treatment, Day-1 IV Ongoing CGPLLU43
Lung Cancer Targeted Mutation Analysis and WGS Post-treatment, Day
6 IV Ongoing CGPLLU43 Lung Cancer Targeted Mutation Analysis and
WGS Post-treatment, Day 27 IV Ongoing CGPLLU43 Lung Cancer Targeted
Mutation Analysis and WGS Post-treatment, Day 83 IV Ongoing
Correlation of Fragment Ratio Correlation Profile to of Median
Fragment Fragment Ratio Ratio Profile to Maximum Profile of
Lymphocyte Mutant Healthy Nucleosome Allele Patient Individuals
Distances Targeted Mutation Fraction CGPLLU14 0.941 -0.841 EGFR
861L > Q 0.89% CGPLLU14 0.933 -0.833 EGFR 861L > Q 0.18%
CGPLLU14 0.908 -0.814 EGFR 719G > S 0.49% CGPLLU14 0.883 -0.752
EGFR 861L > Q 1.39% CGPLLU14 0.820 -0.692 EGFR 719G > S 1.05%
CGPLLU14 0.927 -0.887 EGFR 861L > Q 0.00% CGPLLU88 0.657 -0.584
EGFR 7459ELREA > T 9.06% CGPLLU88 0.939 -0.799 EGFR 790T > M
0.15% CGPLLU88 0.946 -0.869 EGFR 7459ELREA > T 0.93% CGPLLU244
0.850 -0.706 EGFR 858L > R 4.98% CGPLLU244 0.867 -0.764 EGFR 62L
> R 3.41% CGPLLU244 0.703 -0.639 EGFR 858L > R 5.57%
CGPLLU244 0.659 -0.660 EGFR 858L > R 11.80% CGPLLU245 0.871
-0.724 EGFR 745KELREA > K 10.60% CGPLLU245 0.736 -0.608 EGFR
745KELREA > K 14.10% CGPLLU245 0.731 -0.559 EGFR 745KELREA >
K 8.56% CGPLLU245 0.613 -0.426 EGFR 745KELREA > K 10.69%
CGPLLU246 0.897 -0.757 EGFR 790T > M 0.49% CGPLLU246 0.469
-0.376 EGFR 858L > R 6.17% CGPLLU246 0.874 -0.746 EGFR 858L >
R 1.72% CGPLLU246 0.775 -0.665 EGFR 858L > R 5.29% CGPLLU86
0.817 -0.630 EGFR 746ELREATS > D 0.00% CGPLLU86 0.916 -0.811
EGFR 746ELREATS > D 0.19% CGPLLU86 0.859 -0.694 EGFR 746ELREATS
> D 0.00% CGPLLU86 0.932 -0.848 EGFR 746ELREATS > D 0.00%
CGPLLU89 0.864 -0.729 EGFR 747LREATS > - 0.42% CGPLLU89 0.908
-0.803 EGFR 747LREATS > - 0.20% CGPLLU89 0.853 -0.881 EGFR
747LREATS > - 0.00% CGLU316 0.331 -0.351 EGFR L861Q 15.72%
CGLU316 0.225 -0.253 EGFR L861Q 45.67% CGLU316 0.336 -0.364 EGFR
G719A 33.38% CGLU316 0.340 -0.364 EGFR L861Q 66.01% CGLU344 0.935
-0.818 EGFR E746_A75Cdel 0.00% CGLU344 0.919 -0.774 EGFR
E746_A75Cdel 0.22% CGLU344 0.953 -0.860 EGFR E746_A75Cdel 0.40%
CGLU344 0.944 -0.832 EGFR E746_A75Cdel 0.00% CGLU369 0.825 -0.826
EGFR L858R 20.61% CGLU369 0.950 -0.903 EGFR L858R 0.22% CGLU369
0.945 -0.889 EGFR L858R 0.16% CGLU369 0.886 -0.883 EGFR L858R 0.10%
CGLU373 0.922 -0.804 EGFR E746_A75Cdel 0.82% CGLU373 0.959 -0.853
EGFR E746_A75Cdel 0.00% CGLU373 0.967 -0.886 EGFR E746_A75Cdel
0.15% CGLU373 0.951 -0.890 EGFR E746_A75Cdel 0.00% CGPLLU13 0.425
-0.400 EGFR E746_A75Cdel 7.66% CGPLLU13 0.272 -0.257 EGFR
E746_A75Cdel 13.10% CGPLLU13 0.584 -0.536 EGFR E746_A75Cdel 6.09%
CGPLLU13 0.530 -0.513 EGFR E746_A75Cdel 9.28% CGPLLU264 0.946
-0.824 EGFR D761N 0.00% CGPLLU264 0.927 -0.788 EGFR D761N 0.16%
CGPLLU264 0.962 -0.856 EGFR D761N 0.00% CGPLLU264 0.960 -0.894 EGFR
D761N 0.00% CGPLLU265 0.953 -0.859 EGFR L858R 0.21% CGPLLU265 0.949
-0.842 EGFR L858R 0.21% CGPLLU265 0.955 -0.844 EGFR T790M 0.21%
CGPLLU265 0.946 -0.825 EGFR L858R 0.00% CGPLLU266 0.951 -0.904 NA
0.00% CGPLLU266 0.959 -0.886 NA 0.00% CGPLLU266 0.961 -0.880 NA
0.00% CGPLLU266 0.958 -0.855 NA 0.00% CGPLLU267 0.919 -0.863 EGFR
L858R 1.93% CGPLLU267 0.863 -0.889 EGFR L858R 0.14% CGPLLU267 0.962
-0.876 EGFR L858R 0.38% CGPLLU269 0.951 -0.864 EGFR L858R 0.10%
CGPLLU269 0.941 -0.694 EGFR L858R 0.00% CGPLLU269 0.957 -0.676 EGFR
L858R 0.00% CGPLLU271 0.871 -0.284 EGFR E746_A75Cdel 3.36%
CGPLLU271 0.947 -0.826 EGFR E746_A75Cdel 0.17% CGPLLU271 0.952
-0.839 EGFR E746_A75Cdel 0.00% CGPLLU271 0.944 -0.810 EGFR
E746_A75Cdel 0.00% CGPLLU271 0.950 -0.831 EGFR E746_A75Cdel 0.44%
CGPLLU43 0.944 -0.903 NA 0.00% CGPLLU43 0.956 -0.899 NA 0.00%
CGPLLU43 0.959 -0.901 NA 0.00% CGPLLU43 0.965 -0.896 NA 0.00%
TABLE-US-00009 APPENDIX-G Table 7 Whole genome cfDNA analyses in
healthy individuals and cancer patients Correlation of Fragment
Ratio Profile to Median Median Fragment cfDNA Ratio Size Profile
Stage at Fragment of Healthy Patient Patient Type Analysis Type
Timepoint Diagnosis (bp) Individuals CGCRC291 Colorectal Cancer
Targeted Mutation Analysis and WGS Preoperative treatment naive V
163 0.1972 CGCRC292 Colorectal Cancer Targeted Mutation Analysis
and WGS Preoperative treatment naive V 166 0.7604 CGCRC293
Colorectal Cancer Targeted Mutation Analysis and WGS Preoperative
treatment naive V 166 0.9335 CGCRC294 Colorectal Cancer Targeted
Mutation Analysis and WGS Preoperative treatment naive II 166
0.6531 CGCRC296 Colorectal Cancer Targeted Mutation Analysis and
WGS Preoperative treatment naive II 166 0.8161 CGCRC299 Colorectal
Cancer Targeted Mutation Analysis and WGS Preoperative treatment
naive I 162 0.7325 CGCRC300 Colorectal Cancer Targeted Mutation
Analysis and WGS Preoperative treatment naive I 167 0.9382 CGCRC301
Colorectal Cancer Targeted Mutation Analysis and WGS Preoperative
treatment naive I 165 0.8252 CGCRC302 Colorectal Cancer Targeted
Mutation Analysis and WGS Preoperative treatment naive II 163
0.7499 CGCRC304 Colorectal Cancer Targeted Mutation Analysis and
WGS Preoperative treatment naive II 162 0.4642 CGCRC305 Colorectal
Cancer Targeted Mutation Analysis and WGS Preoperative treatment
naive II 165 0.8909 CGCRC306 Colorectal Cancer Targeted Mutation
Analysis and WGS Preoperative treatment naive II 165 0.8523
CGCRC307 Colorectal Cancer Targeted Mutation Analysis and WGS
Preoperative treatment naive II 165 0.9140 CGCRC308 Colorectal
Cancer Targeted Mutation Analysis and WGS Preoperative treatment
naive III 165 0.8734 CGCRC311 Colorectal Cancer Targeted Mutation
Analysis and WGS Preoperative treatment naive I 166 0.8535 CGCRC315
Colorectal Cancer Targeted Mutation Analysis and WGS Preoperative
treatment naive III 167 0.6083 CGCRC316 Colorectal Cancer Targeted
Mutation Analysis and WGS Preoperative treatment naive III 161
0.1546 CGCRC317 Colorectal Cancer Targeted Mutation Analysis and
WGS Preoperative treatment naive III 163 0.6242 CGCRC318 Colorectal
Cancer Targeted Mutation Analysis and WGS Preoperative treatment
naive I 166 0.8824 CGCRC319 Colorectal Cancer Targeted Mutation
Analysis and WGS Preoperative treatment naive III 160 0.5979
CGCRC320 Colorectal Cancer Targeted Mutation Analysis and WGS
Preoperative treatment naive I 167 0.7949 CGCRC321 Colorectal
Cancer Targeted Mutation Analysis and WGS Preoperative treatment
naive I 164 0.7804 CGCRC333 Colorectal Cancer Targeted Mutation
Analysis and WGS Preoperative treatment naive V 163 0.4263 CGCRC335
Colorectal Cancer Targeted Mutation Analysis and WGS Preoperative
treatment naive V 162 0.6466 CGCRC338 Colorectal Cancer Targeted
Mutation Analysis and WGS Preoperative treatment naive V 162 0.7740
CGCRC341 Colorectal Cancer Targeted Mutation Analysis and WGS
Preoperative treatment naive V 164 0.8995 CGCRC342 Colorectal
Cancer Targeted Mutation Analysis and WGS Preoperative treatment
naive V 158 0.2524 CGPLBR100 Breast Cancer Targeted Mutation
Analysis and WGS Preoperative treatment naive III 166 0.9440
CGPLBR101 Breast Cancer Targeted Mutation Analysis and WGS
Preoperative treatment naive II 169 0.8864 CGPLBR102 Breast Cancer
Targeted Mutation Analysis and WGS Preoperative treatment naive II
168 0.9617 CGPLBR103 Breast Cancer Targeted Mutation Analysis and
WGS Preoperative treatment naive II 167 0.9498 CGPLBR104 Breast
Cancer Targeted Mutation Analysis and WGS Preoperative treatment
naive III 164 0.8490 CGPLBR12 Breast Cancer WGS Preoperative
treatment naive III 163 0.8350 CGPLBR18 Breast Cancer WGS
Preoperative treatment naive II 166 0.8411 CGPLBR23 Breast Cancer
WGS Preoperative treatment naive II 156 0.9714 CGPLBR24 Breast
Cancer WGS Preoperative treatment naive III 166 0.8402 CGPLBR28
Breast Cancer WGS Preoperative treatment naive II 161 0.9584
CGPLBR30 Breast Cancer WGS Preoperative treatment naive II 167
0.6951 CGPLBR31 Breast Cancer WGS Preoperative treatment naive II
166 0.9719 CGPLBR32 Breast Cancer WGS Preoperative treatment naive
II 166 0.9590 CGPLBR33 Breast Cancer WGS Preoperative treatment
naive II 163 0.9706 CGPLBR34 Breast Cancer WGS Preoperative
treatment naive II 168 0.8735 CGPLBR35 Breast Cancer WGS
Preoperative treatment naive II 169 0.9655 CGPLBR36 Breast Cancer
WGS Preoperative treatment naive II 167 0.9394 CGPLBR37 Breast
Cancer WGS Preoperative treatment naive I 165 0.9691 CGPLBR38
Breast Cancer Targeted Mutation Analysis and WGS Preoperative
treatment naive III 167 0.9105 CGPLBR40 Breast Cancer Targeted
Mutation Analysis and WGS Preoperative treatment naive III 168
0.9273 CGPLBR41 Breast Cancer Targeted Mutation Analysis and WGS
Preoperative treatment naive II 164 0.9626 CGPLBR45 Breast Cancer
WGS Preoperative treatment naive III 168 0.9615 CGPLBR46 Breast
Cancer WGS Preoperative treatment naive I 166 0.9322 CGPLBR47
Breast Cancer WGS Preoperative treatment naive II 169 0.9461
CGPLBR48 Breast Cancer Targeted Mutation Analysis and WGS
Preoperative treatment naive II 171 0.7686 CGPLBR49 Breast Cancer
Targeted Mutation Analysis and WGS Preoperative treatment naive I
160 0.8867 CGPLBR50 Breast Cancer WGS Preoperative treatment naive
II 165 0.8593 CGPLBR51 Breast Cancer WGS Preoperative treatment
naive III 164 0.9359 CGPLBR52 Breast Cancer WGS Preoperative
treatment naive III 165 0.8688 CGPLBR55 Breast Cancer Targeted
Mutation Analysis and WGS Preoperative treatment naive II 163
0.9634 CGPLBR56 Breast Cancer WGS Preoperative treatment naive III
166 0.9459 CGPLBR57 Breast Cancer Targeted Mutation Analysis and
WGS Preoperative treatment naive I 168 0.9672 CGPLBR59 Breast
Cancer Targeted Mutation Analysis and WGS Preoperative treatment
naive II 167 0.9438 CGPLBR60 Breast Cancer WGS Preoperative
treatment naive II 163 0.9479 CGPLBR61 Breast Cancer Targeted
Mutation Analysis and WGS Preoperative treatment naive II 165
0.9611 CGPLBR63 Breast Cancer Targeted Mutation Analysis and WGS
Preoperative treatment naive II 168 0.9555 CGPLBR65 Breast Cancer
WGS Preoperative treatment naive II 167 0.9506 CGPLBR68 Breast
Cancer Targeted Mutation Analysis and WGS Preoperative treatment
naive III 163 0.9154 CGPLBR69 Breast Cancer Targeted Mutation
Analysis and WGS Preoperative treatment naive II 165 0.9460
CGPLBR70 Breast Cancer Targeted Mutation Analysis and WGS
Preoperative treatment naive II 168 0.9651 CGPLBR71 Breast Cancer
Targeted Mutation Analysis and WGS Preoperative treatment naive II
165 0.9577 CGPLBR72 Breast Cancer Targeted Mutation Analysis and
WGS Preoperative treatment naive II 167 0.9786 CGPLBR73 Breast
Cancer Targeted Mutation Analysis and WGS Preoperative treatment
naive II 167 0.9576 CGPLBR76 Breast Cancer Targeted Mutation
Analysis and WGS Preoperative treatment naive II 170 0.9410
CGPLBR81 Breast Cancer Targeted Mutation Analysis and WGS
Preoperative treatment naive II 170 0.9643 CGPLBR82 Breast Cancer
Targeted Mutation Analysis and WGS Preoperative treatment naive I
166 0.9254 CGPLBR83 Breast Cancer Targeted Mutation Analysis and
WGS Preoperative treatment naive II 169 0.9451 CGPLBR84 Breast
Cancer Targeted Mutation Analysis and WGS Preoperative treatment
naive III 169 0.9315 CGPLBR87 Breast Cancer Targeted Mutation
Analysis and WGS Preoperative treatment naive II 166 0.9154
CGPLBR88 Breast Cancer Targeted Mutation Analysis and WGS
Preoperative treatment naive II 169 0.9370 CGPLBR90 Breast Cancer
Targeted Mutation Analysis and WGS Preoperative treatment naive II
169 0.9002 CGPLBR91 Breast Cancer Targeted Mutation Analysis and
WGS Preoperative treatment naive III 164 0.7955 CGPLBR92 Breast
Cancer Targeted Mutation Analysis and WGS Preoperative treatment
naive II 162 0.6774 CGPLBR93 Breast Cancer Targeted Mutation
Analysis and WGS Preoperative treatment naive II 164 0.8773
CGPLH189 Healthy WGS Preoperative treatment naive NA 168 0.9325
CGPLH190 Healthy WGS Preoperative treatment naive NA 167 0.9403
CGPLH192 Healthy WGS Preoperative treatment naive NA 167 0.9646
CGPLH193 Healthy WGS Preoperative treatment naive NA 167 0.9423
CGPLH194 Healthy WGS Preoperative treatment naive NA 168 0.9567
CGPLH196 Healthy WGS Preoperative treatment naive NA 167 0.9709
CGPLH197 Healthy WGS Preoperative treatment naive NA 166 0.9605
CGPLH198 Healthy WGS Preoperative treatment naive NA 167 0.9238
CGPLH199 Healthy WGS Preoperative treatment naive NA 165 0.9618
CGPLH200 Healthy WGS Preoperative treatment naive NA 167 0.9183
CGPLH201 Healthy WGS Preoperative treatment naive NA 168 0.9548
CGPLH202 Healthy WGS Preoperative treatment naive NA 168 0.9471
CGPLH203 Healthy WGS Preoperative treatment naive NA 167 0.9534
CGPLH205 Healthy WGS Preoperative treatment naive NA 168 0.9075
CGPLH208 Healthy WGS Preoperative treatment naive NA 168 0.9422
CGPLH209 Healthy WGS Preoperative treatment naive NA 169 0.9556
CGPLH210 Healthy WGS Preoperative treatment naive NA 169 0.9447
CGPLH211 Healthy WGS Preoperative treatment naive NA 169 0.9538
CGPLH300 Healthy WGS Preoperative treatment naive NA 168 0.9019
CGPLH307 Healthy WGS Preoperative treatment naive NA 168 0.9576
CGPLH308 Healthy WGS Preoperative treatment naive NA 168 0.9481
CGPLH309 Healthy WGS Preoperative treatment naive NA 168 0.9672
CGPLH310 Healthy WGS Preoperative treatment naive NA 165 0.9547
CGPLH311 Healthy WGS Preoperative treatment naive NA 167 0.9302
CGPLH314 Healthy WGS Preoperative treatment naive NA 167 0.9482
CGPLH315 Healthy WGS Preoperative treatment naive NA 167 0.8659
CGPLH316 Healthy WGS Preoperative treatment naive NA 165 0.9374
CGPLH317 Healthy WGS Preoperative treatment naive NA 169 0.9542
CGPLH319 Healthy WGS Preoperative treatment naive NA 167 0.9578
CGPLH320 Healthy WGS Preoperative treatment naive NA 164 0.8913
CGPLH322 Healthy WGS Preoperative treatment naive NA 167 0.8751
CGPLH324 Healthy WGS Preoperative treatment naive NA 169 0.9519
CGPLH325 Healthy WGS Preoperative treatment naive NA 167 0.9124
CGPLH326 Healthy WGS Preoperative treatment naive NA 166 0.9574
CGPLH327 Healthy WGS Preoperative treatment naive NA 168 0.9533
CGPLH328 Healthy WGS Preoperative treatment naive NA 166 0.9643
CGPLH329 Healthy WGS Preoperative treatment naive NA 167 0.9609
CGPLH330 Healthy WGS Preoperative treatment naive NA 167 0.9118
CGPLH331 Healthy WGS Preoperative treatment naive NA 166 0.9679
CGPLH333 Healthy WGS Preoperative treatment naive NA 169 0.9474
CGPLH335 Healthy WGS Preoperative treatment naive NA 167 0.8909
CGPLH336 Healthy WGS Preoperative treatment naive NA 169 0.9248
CGPLH337 Healthy WGS Preoperative treatment naive NA 167 0.9533
CGPLH338 Healthy WGS Preoperative treatment naive NA 165 0.9388
CGPLH339 Healthy WGS Preoperative treatment naive NA 167 0.9396
CGPLH340 Healthy WGS Preoperative treatment naive NA 167 0.9488
CGPLH341 Healthy WGS Preoperative treatment naive NA 166 0.9533
CGPLH342 Healthy WGS Preoperative treatment naive NA 166 0.7858
CGPLH343 Healthy WGS Preoperative treatment naive NA 167 0.9421
CGPLH344 Healthy WGS Preoperative treatment naive NA 169 0.9192
CGPLH345 Healthy WGS Preoperative treatment naive NA 169 0.9345
CGPLH346 Healthy WGS Preoperative treatment naive NA 169 0.9475
CGPLH350 Healthy WGS Preoperative treatment naive NA 171 0.9570
CGPLH351 Healthy WGS Preoperative treatment naive NA 168 0.8176
CGPLH352 Healthy WGS Preoperative treatment naive NA 168 0.9521
CGPLH353 Healthy WGS Preoperative treatment naive NA 167 0.9435
CGPLH354 Healthy WGS Preoperative treatment naive NA 168 0.9481
CGPLH355 Healthy WGS Preoperative treatment naive NA 167 0.9613
CGPLH356 Healthy WGS Preoperative treatment naive NA 168 0.9474
CGPLH357 Healthy WGS Preoperative treatment naive NA 167 0.9255
CGPLH358 Healthy WGS Preoperative treatment naive NA 167 0.7777
CGPLH360 Healthy WGS Preoperative treatment naive NA 168 0.8500
CGPLH361 Healthy WGS Preoperative treatment naive NA 167 0.9261
CGPLH362 Healthy WGS Preoperative treatment naive NA 167 0.9236
CGPLH363 Healthy WGS Preoperative treatment naive NA 167 0.9488
CGPLH364 Healthy WGS Preoperative treatment naive NA 168 0.9311
CGPLH365 Healthy WGS Preoperative treatment naive NA 165 0.9371
CGPLH366 Healthy WGS Preoperative treatment naive NA 167 0.9536
CGPLH367 Healthy WGS Preoperative treatment naive NA 166 0.8748
CGPLH368 Healthy WGS Preoperative treatment naive NA 169 0.9490
CGPLH369 Healthy WGS Preoperative treatment naive NA 167 0.9428
CGPLH370 Healthy WGS Preoperative treatment naive NA 167 0.9642
CGPLH371 Healthy WGS Preoperative treatment naive NA 168 0.9621
CGPLH380 Healthy WGS Preoperative treatment naive NA 170 0.9652
CGPLH381 Healthy WGS Preoperative treatment naive NA 169 0.9541
CGPLH382 Healthy WGS Preoperative treatment naive NA 167 0.9380
CGPLH383 Healthy WGS Preoperative treatment naive NA 168 0.9700
CGPLH384 Healthy WGS Preoperative treatment naive NA 169 0.8061
CGPLH385 Healthy WGS Preoperative treatment naive NA 167 0.8856
CGPLH386 Healthy WGS Preoperative treatment naive NA 167 0.6920
CGPLH387 Healthy WGS Preoperative treatment naive NA 169 0.9583
CGPLH388 Healthy WGS Preoperative treatment naive NA 167 0.9348
CGPLH389 Healthy WGS Preoperative treatment naive NA 168 0.9409
CGPLH390 Healthy WGS Preoperative treatment naive NA 167 0.9216
CGPLH391 Healthy WGS Preoperative treatment naive NA 166 0.9334
CGPLH392 Healthy WGS Preoperative treatment naive NA 167 0.9165
CGPLH393 Healthy WGS Preoperative treatment naive NA 169 0.9256
CGPLH394 Healthy WGS Preoperative treatment naive NA 167 0.9257
CGPLH395 Healthy WGS Preoperative treatment naive NA 166 0.8611
CGPLH396 Healthy WGS Preoperative treatment naive NA 167 0.7884
CGPLH398 Healthy WGS Preoperative treatment naive NA 167 0.9463
CGPLH399 Healthy WGS Preoperative treatment naive NA 169 0.8780
CGPLH400 Healthy WGS Preoperative treatment naive NA 168 0.6662
CGPLH401 Healthy WGS Preoperative treatment naive NA 167 0.9428
CGPLH402 Healthy WGS Preoperative treatment naive NA 167 0.9353
CGPLH403 Healthy WGS Preoperative treatment naive NA 168 0.9329
CGPLH404 Healthy WGS Preoperative treatment naive NA 169 0.9402
CGPLH405 Healthy WGS Preoperative treatment naive NA 166 0.9579
CGPLH406 Healthy WGS Preoperative treatment naive NA 167 0.8188
CGPLH407 Healthy WGS Preoperative treatment naive NA 169 0.9527
CGPLH408 Healthy WGS Preoperative treatment naive NA 167 0.9584
CGPLH049 Healthy WGS Preoperative treatment naive NA 168 0.9220
CGPLH410 Healthy WGS Preoperative treatment naive NA 168 0.9102
CGPLH411 Healthy WGS Preoperative treatment naive NA 167 0.9392
CGPLH412 Healthy WGS Preoperative treatment naive NA 167 0.9561
CGPLH413 Healthy WGS Preoperative treatment naive NA 167 0.9451
CGPLH414 Healthy WGS Preoperative treatment naive NA 168 0.9258
CGPLH415 Healthy WGS Preoperative treatment naive NA 169 0.9217
CGPLH416 Healthy WGS Preoperative treatment naive NA 167 0.9672
CGPLH417 Healthy WGS Preoperative treatment naive NA 168 0.9578
CGPLH418 Healthy WGS Preoperative treatment naive NA 169 0.9376
CGPLH419 Healthy WGS Preoperative treatment naive NA 167 0.9228
CGPLH420 Healthy WGS Preoperative treatment naive NA 169 0.9164
CGPLH422 Healthy WGS Preoperative treatment naive NA 166 0.9069
CGPLH423 Healthy WGS Preoperative treatment naive NA 169 0.9606
CGPLH424 Healthy WGS Preoperative treatment naive NA 167 0.9553
CGPLH425 Healthy WGS Preoperative treatment naive NA 168 0.9722
CGPLH426 Healthy WGS Preoperative treatment naive NA 168 0.9560
CGPLH427 Healthy WGS Preoperative treatment naive NA 167 0.9594
CGPLH428 Healthy WGS Preoperative treatment naive NA 167 0.9591
CGPLH429 Healthy WGS Preoperative treatment naive NA 168 0.9358
CGPLH430 Healthy WGS Preoperative treatment naive NA 167 0.9639
CGPLH431 Healthy WGS Preoperative treatment naive NA 167 0.9570
CGPLH432 Healthy WGS Preoperative treatment naive NA 168 0.9485
CGPLH434 Healthy WGS Preoperative treatment naive NA 168 0.9671
CGPLH435 Healthy WGS Preoperative treatment naive NA 170 0.9133
CGPLH436 Healthy WGS Preoperative treatment naive NA 168 0.9360
CGPLH437 Healthy WGS Preoperative treatment naive NA 170 0.9445
CGPLH438 Healthy WGS Preoperative treatment naive NA 170 0.9537
CGPLH439 Healthy WGS Preoperative treatment naive NA 171 0.9547
CGPLH440 Healthy WGS Preoperative treatment naive NA 169 0.9562
CGPLH441 Healthy WGS Preoperative treatment naive NA 167 0.9660
CGPLH442 Healthy WGS Preoperative treatment naive NA 167 0.9569
CGPLH443 Healthy WGS Preoperative treatment naive NA 170 0.9431
CGPLH444 Healthy WGS Preoperative treatment naive NA 171 0.9429
CGPLH445 Healthy WGS Preoperative treatment naive NA 171 0.9446
CGPLH446 Healthy WGS Preoperative treatment naive NA 167 0.9502
CGPLH447 Healthy WGS Preoperative treatment naive NA 169 0.9421
CGPLH448 Healthy WGS Preoperative treatment naive NA 167 0.9553
CGPLH449 Healthy WGS Preoperative treatment naive NA 167 0.9550
CGPLH450 Healthy WGS Preoperative treatment naive NA 167 0.9572
CGPLH451 Healthy WGS Preoperative treatment naive NA 169 0.9548
CGPLH452 Healthy WGS Preoperative treatment naive NA 167 0.9498
CGPLH453 Healthy WGS Preoperative treatment naive NA 166 0.9572
CGPLH455 Healthy WGS Preoperative treatment naive NA 166 0.9626
CGPLH456 Healthy WGS Preoperative treatment naive NA 168 0.9537
CGPLH457 Healthy WGS Preoperative treatment naive NA 167 0.9429
CGPLH458 Healthy WGS Preoperative treatment naive NA 167 0.9511
CGPLH459 Healthy WGS Preoperative treatment naive NA 168 0.9609
CGPLH460 Healthy WGS Preoperative treatment naive NA 168 0.9331
CGPLH463 Healthy WGS Preoperative treatment naive NA 167 0.9506
CGPLH464 Healthy WGS Preoperative treatment naive NA 170 0.9133
CGPLH465 Healthy WGS Preoperative treatment naive NA 167 0.9251
CGPLH466 Healthy WGS Preoperative treatment naive NA 167 0.9679
CGPLH467 Healthy WGS Preoperative treatment naive NA 168 0.9273
CGPLH468 Healthy WGS Preoperative treatment naive NA 167 0.8353
CGPLH469 Healthy WGS Preoperative treatment naive NA 169 0.8225
CGPLH470 Healthy WGS Preoperative treatment naive NA 168 0.9073
CGPLH471 Healthy WGS Preoperative treatment naive NA 167 0.9354
CGPLH472 Healthy WGS Preoperative treatment naive NA 166 0.8509
CGPLH473 Healthy WGS Preoperative treatment naive NA 167 0.9206
CGPLH474 Healthy WGS Preoperative treatment naive NA 168 0.8474
CGPLH475 Healthy WGS Preoperative treatment naive NA 167 0.9155
CGPLH476 Healthy WGS Preoperative treatment naive NA 169 0.8807
CGPLH477 Healthy WGS Preoperative treatment naive NA 169 0.9129
CGPLH478 Healthy WGS Preoperative treatment naive NA 167 0.9588
CGPLH479 Healthy WGS Preoperative treatment naive NA 167 0.9303
CGPLH480 Healthy WGS Preoperative treatment naive NA 169 0.9522
CGPLH481 Healthy WGS Preoperative treatment naive NA 168 0.9558
CGPLH482 Healthy WGS Preoperative treatment naive NA 168 0.9379
CGPLH483 Healthy WGS Preoperative treatment naive NA 168 0.9518
CGPLH484 Healthy WGS Preoperative treatment naive NA 166 0.9630
CGPLH485 Healthy WGS Preoperative treatment naive NA 168 0.9547
CGPLH486 Healthy WGS Preoperative treatment naive NA 169 0.9199
CGPLH487 Healthy WGS Preoperative treatment naive NA 169 0.9575
CGPLH488 Healthy WGS Preoperative treatment naive NA 167 0.9618
CGPLH490 Healthy WGS Preoperative treatment naive NA 167 0.8950
CGPLH491 Healthy WGS Preoperative treatment naive NA 168 0.9631
CGPLH492 Healthy WGS Preoperative treatment naive NA 170 0.9335
CGPLH493 Healthy WGS Preoperative treatment naive NA 168 0.8718
CGPLH494 Healthy WGS Preoperative treatment naive NA 169 0.9623
CGPLH495 Healthy WGS Preoperative treatment naive NA 166 0.8777
CGPLH496 Healthy WGS Preoperative treatment naive NA 166 0.8788
CGPLH497 Healthy WGS Preoperative treatment naive NA 167 0.9576
CGPLH498 Healthy WGS Preoperative treatment naive NA 167 0.9526
CGPLH499 Healthy WGS Preoperative treatment naive NA 167 0.9733
CGPLH500 Healthy WGS Preoperative treatment naive NA 168 0.9542
CGPLH501 Healthy WGS Preoperative treatment naive NA 169 0.9526
CGPLH052 Healthy WGS Preoperative treatment naive NA 167 0.9512
CGPLH503 Healthy WGS Preoperative treatment naive NA 169 0.8947
CGPLH504 Healthy WGS Preoperative treatment naive NA 167 0.9561
CGPLH505 Healthy WGS Preoperative treatment naive NA 166 0.9554
CGPLH506 Healthy WGS Preoperative treatment naive NA 167 0.9733
CGPLH507 Healthy WGS Preoperative treatment naive NA 168 0.9222
CGPLH508 Healthy WGS Preoperative treatment naive NA 167 0.9674
CGPLH509 Healthy WGS Preoperative treatment naive NA 167 0.9475
CGPLH510 Healthy WGS Preoperative treatment naive NA 167 0.9459
CGPLH511 Healthy WGS Preoperative treatment naive NA 168 0.9714
CGPLH512 Healthy WGS Preoperative treatment naive NA 168 0.9442
CGPLH513 Healthy WGS Preoperative treatment naive NA 166 0.9705
CGPLH514 Healthy WGS Preoperative treatment naive NA 167 0.9690
CGPLH515 Healthy WGS Preoperative treatment naive NA 167 0.9568
CGPLH516 Healthy WGS Preoperative treatment naive NA 168 0.9508
CGPLH517 Healthy WGS Preoperative treatment naive NA 168 0.9635
CGPLH518 Healthy WGS Preoperative treatment naive NA 168 0.9647
CGPLH519 Healthy WGS Preoperative treatment naive NA 166 0.9366
CGPLH520 Healthy WGS Preoperative treatment naive NA 166 0.9649
CGPLH625 Healthy WGS Preoperative treatment naive NA 166 0.8766
CGPLH626 Healthy WGS Preoperative treatment naive NA 170 0.9011
CGPLH639 Healthy WGS Preoperative treatment naive NA 165 0.9482
CGPLH640 Healthy WGS Preoperative treatment naive NA 166 0.9131
CGPLH642 Healthy WGS Preoperative treatment naive NA 167 0.9641
CGPLH643 Healthy WGS Preoperative treatment naive NA 169 0.8450
CGPLH644 Healthy WGS Preoperative treatment naive NA 170 0.9398
CGPLH646 Healthy WGS Preoperative treatment naive NA 172 0.296
CGPLLU141 Lung Cancer Targeted Mutation Analysis and WGS
Preoperative treatment naive II 164 0.8702 CGPLLU161 Lung Cancer
Targeted Mutation Analysis and WGS Preoperative treatment naive II
165 0.9128 CGPLLU162 Lung Cancer Targeted Mutation Analysis and WGS
Preoperative treatment naive II 165 0.7753 CGPLLUl63 Lung Cancer
Targeted Mutation Analysis and WGS Preoperative treatment naive II
166 0.4770 CGPLLU168 Lung Cancer Targeted Mutation Analysis and WGS
Preoperative treatment naive I 163 0.9164 CGPLLU169 Lung Cancer
Targeted Mutation Analysis and WGS Preoperative treatment naive I
163 0.9326 CGPLLU176 Lung Cancer Targeted Mutation Analysis and WGS
Preoperative treatment naive I 168 0.9572 CGPLLU177 Lung Cancer
Targeted Mutation Analysis and WGS Preoperative treatment naive II
166 0.8472 CGPLLU203 Lung Cancer Targeted Mutation Analysis and WGS
Preoperative treatment naive II 164 0.9119 CGPLLU205 Lung Cancer
Targeted Mutation Analysis and WGS Preoperative treatment naive II
163 0.9518 CGPLLU207 Lung Cancer Targeted Mutation Analysis and WGS
Preoperative treatment naive II 166 0.9344 CGPLLU208 Lung Cancer
Targeted Mutation Analysis and WGS Preoperative treatment naive II
164 0.9091 CGPLOV11 Ovarian Cancer Targeted Mutation Analysis and
WGS Preoperative treatment naive V 166 0.8902 CGPLOV12 Ovarian
Cancer Targeted Mutation Analysis and WGS Preoperative treatment
naive I 167 0.8779 CGPLOV13 Ovarian Cancer Targeted Mutation
Analysis and WGS Preoperative treatment naive V 166 0.7560 CGPLOV15
Ovarian Cancer Targeted Mutation Analysis and WGS Preoperative
treatment naive III 165 0.8585 CGPLOV16 Ovarian Cancer Targeted
Mutation Analysis and WGS Preoperative treatment naive III 165
0.9052 CGPLOV19 Ovarian Cancer Targeted Mutation Analysis and WGS
Preoperative treatment naive II 165 0.7854 CGPLOV20 Ovarian Cancer
Targeted Mutation Analysis and WGS Preoperative treatment naive II
165 0.8711 CGPLOV21 Ovarian Cancer Targeted Mutation Analysis and
WGS Preoperative treatment naive V 167 0.8942 CGPLOV22 Ovarian
Cancer Targeted Mutation Analysis and WGS Preoperative treatment
naive III 164 0.8944 CGPLOV23 Ovarian Cancer Targeted Mutation
Analysis and WGS Preoperative treatment naive I 169 0.8510 CGPLOV24
Ovarian Cancer Targeted Mutation Analysis and WGS Preoperative
treatment naive I 166 0.9449 CGPLOV25 Ovarian Cancer Targeted
Mutation Analysis and WGS Preoperative treatment naive I 166 0.9590
CGPLOV26 Ovarian Cancer Targeted Mutation Analysis and WGS
Preoperative treatment naive I 161 0.8148 CGPLOV28 Ovarian Cancer
Targeted Mutation Analysis and WGS Preoperative treatment naive I
167 0.9635 CGPLOV31 Ovarian Cancer Targeted Mutation Analysis and
WGS Preoperative treatment naive III 167 0.9461 CGPLOV32 Ovarian
Cancer Targeted Mutation Analysis and WGS Preoperative treatment
naive I 168 0.9582 CGPLOV37 Ovarian Cancer Targeted Mutation
Analysis and WGS Preoperative treatment naive I 170 0.9397 CGPLOV38
Ovarian Cancer Targeted Mutation Analysis and WGS Preoperative
treatment naive I 166 0.5779 CGPLOV40 Ovarian Cancer Targeted
Mutation Analysis and WGS Preoperative treatment naive V 170 0.6097
CGPLOV41 Ovarian Cancer Targeted Mutation Analysis and WGS
Preoperative treatment naive V 167 0.9403 CGPLOV42 Ovarian Cancer
Targeted Mutation Analysis and WGS Preoperative treatment naive I
166 0.9265 CGPLOV43 Ovarian Cancer Targeted Mutation Analysis and
WGS Preoperative treatment naive I 167 0.9626 CGPLOV44 Ovarian
Cancer Targeted Mutation Analysis and WGS Preoperative treatment
naive I 164 0.9536 CGPLOV46 Ovarian Cancer Targeted Mutation
Analysis and WGS Preoperative treatment naive I 166 0.9622 CGPLOV47
Ovarian Cancer Targeted Mutation Analysis and WGS Preoperative
treatment naive I 165 0.9704 CGPLOV48 Ovarian Cancer Targeted
Mutation Analysis and WGS Preoperative treatment naive I 167 0.9675
CGPLOV49 Ovarian Cancer Targeted Mutation Analysis and WGS
Preoperative treatment naive III 164 0.8998 CGPLOV50 Ovarian Cancer
Targeted Mutation Analysis and WGS Preoperative treatment naive III
165 0.9682 CGPLPA112 Pancreatic Cancer WGS Preoperative treatment
naive II 164 0.8914 CGPLPA113 Doudenal Cancer WGS Preoperative
treatment naive I 170 0.8751 CGPLPA114 Bile Duct Cancer WGS
Preoperative treatment naive II 166 0.9098 CGPLPA115 Bile Duct
Cancer WGS Preoperative treatment naive V 165 0.8053 CGPLPA117 Bile
Duct Cancer WGS Preoperative treatment naive II 165 0.9395
CGPLPA118 Bile Duct Cancer Targeted Mutation Analysis and WGS
Preoperative treatment naive I 167 0.9406 CGPLPA122 Bile Duct
Cancer Targeted Mutation Analysis and WGS Preoperative treatment
naive II 164 0.8231 CGPLPA124 Bile Duct Cancer Targeted Mutation
Analysis and WGS Preoperative treatment naive II 166 0.9108
CGPLPA125 Bile Duct Cancer WGS Preoperative treatment naive II 166
0.9675 CGPLPA126 Bile Duct Cancer Targeted Mutation Analysis and
WGS Preoperative treatment naive II 166 0.9155 CGPLPA127 Bile Duct
Cancer WGS Preoperative treatment naive V 167 0.8916 CGPLPA128 Bile
Duct Cancer Targeted Mutation Analysis and WGS Preoperative
treatment naive II 167 0.9262 CGPLPA129 Bile Duct Cancer Targeted
Mutation Analysis and WGS Preoperative treatment naive II 166
0.9220 CGPLPA130 Bile Duct Cancer Targeted Mutation Analysis and
WGS Preoperative treatment naive II 169 0.8586 CGPLPA131 Bile Duct
Cancer Targeted Mutation Analysis and WGS Preoperative treatment
naive II 165 0.7707 CGPLPA134 Bile Duct Cancer Targeted Mutation
Analysis and WGS Preoperative treatment naive II 160 0.7502
CGPLPA135 Bile Duct Cancer WGS Preoperative treatment naive I 165
0.9495 CGPLPA136 Bile Duct Cancer Targeted Mutation Analysis and
WGS Preoperative treatment naive II 164 0.9289 CGPLPA137 Bile Duct
Cancer WGS Preoperative treatment naive II 166 0.9588 CGPLPA139
Bile Duct Cancer WGS Preoperative treatment naive V 166 0.9511
CGPLPA14 Pancreatic Cancer WGS Preoperative treatment naive II 167
0.8718 CGPLPA140 Bile Duct Cancer Targeted Mutation Analysis and
WGS Preoperative treatment naive II 166 0.9215 CGPLPA141 Bile Duct
Cancer WGS Preoperative treatment naive II 165 0.9172 CGPLPA15
Pancreatic Cancer WGS Preoperative treatment naive II 167 0.9111
CGPLPA155 Bile Duct Cancer WGS Preoperative treatment naive II 165
0.9496 CGPLPA156 Pancreatic Cancer WGS Preoperative treatment naive
II 167 0.9479 CCPLPA165 Bile Duct Cancer WGS Preoperative treatment
naive I 168 0.9596 CGPLPA168 Bile Duct Cancer WGS Preoperative
treatment naive II 162 0.7838 CGPLPA17 Pancreatic Cancer WGS
Preoperative treatment naive II 166 0.8624 CGPLPA184 Bile Duct
Cancer WGS Preoperative treatment naive II 165 0.9100 CGPLPA187
Bile Duct Cancer WGS Preoperative treatment naive II 165 0.8577
CGPLPA23 Pancreatic Cancer WGS Preoperative treatment naive II 165
0.7887 CGPLPA25 Pancreatic Cancer WGS Preoperative treatment naive
II 166 0.9549 CGPLPA26 Pancreatic Cancer WGS Preoperative treatment
naive II 166 0.9598 CGPLPA28 Pancreatic Cancer WGS Preoperative
treatment naive II 165 0.9069 CGPLPA33 Pancreatic Cancer WGS
Preoperative treatment naive II 166 0.8361 CGPLPA34 Pancreatic
Cancer WGS Preoperative treatment naive II 168 0.8946
CGPLPA37 Pancreatic Cancer WGS Preoperative treatment naive II 165
0.8840 CGPLPA38 Pancreatic Cancer WGS Preoperative treatment naive
II 167 0.8746 CGPLPA39 Pancreatic Cancer WGS Preoperative treatment
naive II 167 0.8562 CGPLPA40 Pancreatic Cancer WGS Preoperative
treatment naive II 165 0.8563 CGPLPA42 Pancreatic Cancer WGS
Preoperative treatment naive II 167 0.9126 CGPLPA46 Pancreatic
Cancer WGS Preoperative treatment naive II 169 0.8274 CGPLPA47
Pancreatic Cancer WGS Preoperative treatment naive II 166 0.8376
CGPLPA48 Pancreatic Cancer WGS Preoperative treatment naive I 167
0.9391 CGPLPA52 Pancreatic Cancer WGS Preoperative treatment naive
II 167 0.9452 CGPLPA53 Pancreatic Cancer WGS Preoperative treatment
naive I 163 0.9175 CGPLPA58 Pancreatic Cancer WGS Preoperative
treatment naive II 165 0.9587 CGPLPA59 Pancreatic Cancer WGS
Preoperative treatment naive II 163 0.9230 CGPLPA67 Pancreatic
Cancer WGS Preoperative treatment naive II 166 0.9574 CGPLPA69
Pancreatic Cancer WGS Preoperative treatment naive I 168 0.9172
CGPLPA71 Pancreatic Cancer WGS Preoperative treatment naive II 167
0.9424 CGPLPA74 Pancreatic Cancer WGS Preoperative treatment naive
II 166 0.9688 CGPLPA76 Pancreatic Cancer WGS Preoperative treatment
naive II 163 0.9681 CGPLPA85 Pancreatic Cancer WGS Preoperative
treatment naive II 165 0.9137 CGPLPA86 Pancreatic Cancer WGS
Preoperative treatment naive II 165 0.8875 CGPLPA92 Pancreatic
Cancer WGS Preoperative treatment naive II 167 0.9389 CGPLPA93
Pancreatic Cancer WGS Preoperative treatment naive II 166 0.8585
CGPLPA94 Pancreatic Cancer WGS Preoperative treatment naive II 162
0.9365 CGPLPA95 Pancreatic Cancer WGS Preoperative treatment naive
II 163 0.8542 CGST102 Gastric cancer Targeted Mutation Analysis and
WGS Preoperative treatment naive II 167 0.9496 CGST11 Gastric
cancer WGS Preoperative treatment naive IV 169 0.9419 CGST110
Gastric cancer Targeted Mutation Analysis and WGS Preoperative
treatment naive II 167 0.9626 CGST114 Gastric cancer Targeted
Mutation Analysis and WGS Preoperative treatment naive II 164
0.9535 CGST13 Gastric cancer Targeted Mutation Analysis and WGS
Preoperative treatment naive II 166 0.9369 CGST131 Gastric cancer
WGS Preoperative treatment naive II 171 0.9428 CGST141 Gastric
cancer Targeted Mutation Analysis and WGS Preoperative treatment
naive II 168 0.9621 CGST16 Gastric cancer Targeted Mutation
Analysis and WGS Preoperative treatment naive II 166 0.7804 CGST18
Gastric cancer Targeted Mutation Analysis and WGS Preoperative
treatment naive II 169 0.9523 CGST21 Gastric cancer WGS
Preoperative treatment naive II 165 -0.4778 CGST26 Gastric cancer
WGS Preoperative treatment naive IV 166 0.9554 CGST28 Gastric
cancer Targeted Mutation Analysis and WGS Preoperative treatment
naive X 169 0.9076 CGST30 Gastric cancer Targeted Mutation Analysis
and WGS Preoperative treatment naive II 169 0.9246 CGST32 Gastric
cancer Targeted Mutation Analysis and WGS Preoperative treatment
naive II 169 0.9431 CGST33 Gastric cancer Targeted Mutation
Analysis and WGS Preoperative treatment naive I 168 0.7999 CGST38
Gastric cancer WGS Preoperative treatment naive 0 168 0.9368 CGST39
Gastric cancer Targeted Mutation Analysis and WGS Preoperative
treatment naive IV 164 0.8742 CGST41 Gastric cancer Targeted
Mutation Analysis and WGS Preoperative treatment naive IV 168
0.8194 CGST45 Gastric cancer Targeted Mutation Analysis and WGS
Preoperative treatment naive II 168 0.9576 CGST47 Gastric cancer
Targeted Mutation Analysis and WGS Preoperative treatment naive I
168 0.9641 CGST48 Gastric cancer Targeted Mutation Analysis and WGS
Preoperative treatment naive IV 167 0.7469 CGST53 Gastric cancer
WGS Preoperative treatment naive 0 173 0.0019 CGST58 Gastric cancer
Targeted Mutation Analysis and WGS Preoperative treatment naive II
169 0.9470 CGST67 Gastric cancer WGS Preoperative treatment naive I
170 0.9352 CGST77 Gastric cancer WGS Preoperative treatment naive
IV 170 0.0043 CGST80 Gastric cancer Targeted Mutation Analysis and
WGS Preoperative treatment naive II 168 0.9313 CGST81 Gastric
cancer Targeted Mutation Analysis and WGS Preoperative treatment
naive I 168 0.9480 Correlation of GC Corrected Fragment Ratio
Profile to Mutant Median Alelle Fragment Fraction Detected Detected
Fraction Ratio of Reads using using Detected Profile Mapped to
DELFI DELFI using of Healthy Mitochondrial DELFI (95% (98% Targeted
Patient Individuals Genome Score specificity) specificity)
sequencing* CGCRC291 0.5268 0.0484% 0.9976 Y Y 22.85% CGCRC292
0.8835 0 0270% 0.7299 Y N 1.41% CGCRC293 0.9206 0.0748% 0.5234 N N
3.35% CGCRC294 0.8904 0.0135% 0.8757 Y Y 0.17% CGCRC296 0.8395
0.0369% 0.9951 Y Y ND CGCRC299 0.9268 0.0392% 0.9648 Y Y ND
CGCRC300 0.9303 0.0235% 0.4447 N N ND CGCRC301 0.9151 0.0310%
0.2190 N N 3.21% CGCRC302 0.9243 0.0112% 0.9897 Y Y 3.12% CGCRC304
0.9360 0.0093% 0.9358 Y Y 3.27% CGCRC305 0.9250 0 0120% 0.8988 Y Y
3.19% CGCRC306 0.8186 0.0781% 0.9466 Y Y 8.02% CGCRC307 0.9342
0.0781% 0.7042 Y N 0.56% CGCRC308 0.9324 0.0078% 0.9082 Y Y 0.11%
CGCRC311 0.9156 0.0173% 0.1867 N N ND CGCRC315 0.8846 0.0241%
0.6422 Y N 0.27% CGCRC316 0.5879 0.0315% 0.9971 Y Y 5.52% CGCRC317
0.8944 0.0184% 0.9855 Y Y 0.36% CGCRC318 0.9140 0.0156% 0.5615 N N
ND CGCRC319 0.8230 0.1259% 0.9925 Y Y 0.11% CGCRC320 0.9101 0.0383%
0.8019 Y Y 0.64% CGCRC321 0.9091 0.0829% 0.9759 Y Y 3.20% CGCRC333
0.4355 0.4264% 0.9974 Y Y 43.03% CGCRC335 0.6858 0.1154% 0.9887 Y Y
81.61% CGCRC338 0.7573 0.1436% 0.9976 Y Y 36.00% CGCRC341 0.9181
0.0197% 0.9670 Y Y ND CGCRC342 0.1845 0.1732% 0.9987 Y Y 30.72%
CGPLBR100 0.8946 0.1234% 0.8664 Y Y ND CGPLBR101 0.9304 0.0709%
0.9385 Y Y ND CGPLBR102 0.9345 0.4742% 0.9052 Y Y 0.25% CGPLBR103
0.9251 0.0775% 0.5994 N N ND CGPLBR104 0.9192 0.0532% 0.9950 Y Y
0.13% CGPLBR12 0.7760 0.1407% 0.7598 Y Y -- CGPLBR18 0.9534 0.0267%
0.3886 N N -- CGPLBR23 0.9312 0.0144% 0.1235 N N -- CGPLBR24 0.8766
0.0210% 0.7480 Y Y -- CGPLBR28 0.8120 0.1456% 0.9630 Y Y --
CGPLBR30 0.6611 0.0952% 0.9956 Y Y -- CGPLBR31 0.9556 0.0427%
0.2227 N N -- CGPLBR32 0.9229 0.0308% 0.9815 Y Y -- CGPLBR33 0.9432
0.0617% 0.2863 N N -- CGPLBR34 0.9425 0.0115% 0.1637 N N --
CGPLBR35 0.9348 0.1371% 0.5057 N N -- CGPLBR36 0.8884 0.0813%
0.4017 N N -- CGPLBR37 0.9496 0.0518% 0.0314 N N -- CGPLBR38 0.0349
0.1352% 0.8983 Y Y 0.53% CGPLBR40 0.9244 0.0929% 0.9046 Y Y ND
CGPLBR41 0.9346 0.0544% 0.9416 Y Y 0.32% CGPLBR45 0.9285 0.0296%
0.3860 N N -- CGPLBR46 0.9005 0.0345% 0.7270 Y N -- CGPLBR47 0.9028
0.0591% 0.6247 Y Y -- CGPLBR48 0.8246 0.0504% 0.9973 Y Y 0.18%
CGPLBR49 0.7887 0.0377% 0.9946 Y Y ND CGPLBR50 0.9332 0.0137%
0.6820 Y N -- CGPLBR51 0.9160 0.0863% 0.6915 Y N -- CGPLBR52 0.9196
0.0165% 0.6390 Y N -- CGPLBR55 0.9341 0.0356% 0.9494 Y Y 0.68%
CGPLBR56 0.9428 0.2025% 0.4700 N N -- CGPLBR57 0.9416 0.0902%
0.9090 Y Y ND CGPLBR59 0.9130 0.0761% 0.5828 N N ND CGPLBR60 0.8916
0.0626% 0.8779 Y Y -- CGPLBR61 0.9422 0.0601% 0.4417 N N 0.44%
CGPLBR63 0.9132 0.0514% 0.8788 Y Y ND CGPLBR65 0.8970 0.0264%
0.9048 Y Y -- CGPLBR68 0.9532 0.0164% 0.7883 Y Y ND CGPLBR69 0.9474
0.0279% 0.0600 N N ND CGPLBR70 0.9388 0.0171% 0.6447 Y N 0.36%
CGPLBR71 0.9368 0.0271% 0.6706 Y N 0.10% CGPLBR72 0.9640 0.0263%
0.6129 N N ND CGPLBR73 0.9421 0.0142% 0.0746 N N 0.27% CGPLBR76
0.9254 0.0775% 0.9334 Y Y 0.12% CGPLBR81 0.8193 0.0241% 0.9899 Y Y
-- CGPLBR82 0.9288 0.1640% 0.9834 Y Y 0.12% CGPLBR83 0.9138 0.0419%
0.9810 Y Y 0.28% CGPLBR84 0.8659 0.0274% 0.9901 Y Y -- CGPLBR87
0.8797 0.0294% 0.9968 Y Y 0.45% CGPLBR88 0.8547 0.0181% 0.9958 Y Y
0.38% CGPLBR90 0.8330 0.0417% 0.9667 Y Y -- CGPLBR91 0.9408 0.0799%
0.8710 Y Y ND CGPLBR92 0.8835 0.1042% 0.9856 Y Y 0.20% CGPLBR93
0.9072 0.0352% 0.7253 Y N ND CGPLH189 0.8947 0.0591% 0.1748 N N --
CGPLH190 0.9369 0.1193% 0.5168 N N -- CGPLH192 0.9487 0.0276%
0.0178 N N -- CGPLH193 0.9442 0.0420% 0.5794 N N -- CGPLH194 0.9289
0.0407% 0.1616 N N -- CGPLH196 0.9512 0.0266% 0.0999 N N --
CGPLH197 0.9416 0.0334% 0.4699 N N -- CGPLH198 0.9457 0.0302%
0.6571 Y N -- CGPLH199 0.9439 0.0170% 0.5584 N N -- CGPLH200 0.9391
0.0362% 0.3833 N N -- CGPLH201 0.9180 0.0470% 0.8395 Y Y --
CGPLH202 0.9436 0.0501% 0.1088 N N -- CGPLH203 0.9575 0.0455%
0.2485 N N -- CGPLH205 0.9283 0.0409% 0.4401 N N -- CGPLH208 0.9409
0.0371% 0.2706 N N -- CGPLH209 0.9367 0.0427% 0.2213 N N --
CGPLH210 0.9181 0.0279% 0.3500 N N -- CGPLH211 0.9410 0.0317%
0.1752 N N -- CGPLH300 0.9200 0.0397% 0.0226 N N -- CGPLH307 0.9167
0.0388% 0.1789 N N -- CGPLH308 0.8352 0.0311% 0.0155 N N --
CGPLH309 0.9451 0.0226% 0.0441 N N -- CGPLH310 0.9527 0.0145%
0.7135 Y N -- CGPLH311 0.9348 0.0202% 0.2589 N N -- CGPLH314 0.9491
0.0212% 0.1632 N N -- CGPLH315 0.9427 0.0071% 0.3450 N N --
CGPLH316 0.9552 0.0191% 0.4697 N N -- CGPLH317 0.9352 0 0232%
0.4330 N N -- CGPLH319 0.9189 0.0263% 0.2232 N N -- CGPLH320 0.9165
0.0222% 0.1095 N N -- CGPLH322 0.9411 0.0248% 0.0749 N N --
CGPLH324 0.9133 0.0402% 0.0128 N N -- CGPLH325 0.9202 0.0711%
0.0102 N N -- CGPLH326 0.9408 0.0213% 0.0475 N N -- CGPLH327 0.9071
0.1275% 0.4891 N N -- CGPLH328 0.9332 0.0256% 0.0234 N N --
CGPLH329 0.8396 0.0269% 0.0139 N N -- CGPLH330 0.9403 0.0203%
0.2642 N N -- CGPLH331 0.9377 0.0314% 0.0304 N N -- CGPLH333 0.9132
0.0350% 0.1633 N N -- CGPLH335 0.9333 0.0285% 0.0096 N N --
CGPLH336 0.9159 0.0158% 0.3872 N N -- CGPLH337 0.9262 0.0367%
0.2976 N N -- CGPLH338 0.9303 0.0103% 0.0431 N N -- CGPLH339 0.9338
0.0280% 0.0379 N N -- CGPLH340 0.9321 0.0210% 0.0379 N N --
CGPLH341 0.9187 0.0448% 0.1775 N N -- CGPLH342 0.8986 0.0283%
0.0904 N N -- CGPLH343 0.9067 0.0632% 0.0160 N N -- CGPLH344 0.8998
0.0257% 0.0120 N N -- CGPLH345 0.9107 0.0445% 0.0031 N N --
CGPLH346 0.9074 0.0208% 0.0686 N N -- CGPLH350 0.9388 0.0284%
0.0071 N N -- CGPLH351 0.9294 0.0223% 0.0207 N N -- CGPLH352 0.9190
0.0613% 0.0512 N N -- CGPLH353 0.9130 0.0408% 0.0132 N N --
CGPLH354 0.9121 0.0318% 0.0082 N N -- CGPLH355 0.9308 0.0400%
0.6407 Y N -- CGPLH356 0.8312 0.0427% 0.2437 N N -- CGPLH357 0.9540
0.0217% 0.0070 N N -- CGPLH358 0.9372 0.0174% 0.1451 N N --
CGPLH360 0.8775 0.0395% 0.0048 N N -- CGPLH361 0.9283 0.0268%
0.1524 N N -- CGPLH362 0.9503 0.0309% 0.4832 N N -- CGPLH363 0.9187
0.0620% 0.0199 N N -- CGPLH364 0.9480 0.0282% 0.8719 Y Y --
CGPLH365 0.9051 0.1740% 0.9638 Y Y -- CGPLH366 0.9170 0.0344%
0.0952 N N -- CGPLH367 0.9181 0.0353% 0.1235 N N -- CGPLH368 0.9076
0.1073% 0.1252 N N -- CGPLH369 0.9541 0.0246% 0.2821 N N --
CGPLH370 0.9423 0.0410% 0.0989 N N -- CGPLH371 0.9414 0.0734%
0.2173 N N -- CGPLH380 0.9424 0.0523% 0.0128 N N -- CGPLH381 0.9501
0.0435% 0.0152 N N -- CGPLH382 0.9584 0.0340% 0.0326 N N --
CGPLH383 0.9407 0.0389% 0.0035 N N -- CGPLH384 0.9043 0.0207%
0.0258 N N -- CGPLH385 0.9246 0.0165% 0.0566 N N -- CGPLH386 0.8859
0.0502% 0.2677 N N -- CGPLH387 0.9223 0.0375% 0.0081 N N --
CGPLH388 0.9266 0.0527% 0.0499 N N -- CGPLH389 0.9035 0.0667%
0.6585 Y N -- CGPLH390 0.9182 0.0229% 0.0837 N N -- CGPLH391 0.9162
0.0223% 0.0716 N N -- CGPLH392 0.9014 0.0424% 0.1305 N N --
CGPLH393 0.9045 0.0407% 0.0037 N N --
CGPLH394 0.9292 0.0522% 0.1073 N N -- CGPLH395 0.9254 0.0424%
0.0171 N N -- CGPLH396 0.8928 0.0393% 0.0303 N N -- CGPLH398 0.9578
0.0242% 0.3195 N N -- CGPLH399 0.9195 0.0579% 0.0685 N N --
CGPLH400 0.9047 0.0300% 0.2103 N N -- CGPLH401 0.9339 0.0146%
0.0620 N N -- CGPLH402 0.8800 0.1516% 0.0395 N N -- CGPLH403 0.8829
0.0515% 0.0223 N N -- CGPLH404 0.8948 0.0528% 0.0027 N N --
CGPLH405 0.9204 0.0358% 0.0188 N N -- CGPLH406 0.8592 0.0667%
0.0206 N N -- CGPLH407 0.9099 0.0229% 0.0040 N N -- CGPLH408 0.9192
0.0415% 0.1257 N N -- CGPLH409 0.8950 0.0302% 0.0056 N N --
CGPLH410 0.9006 0.0453% 0.0019 N N -- CGPLH411 0.8857 0.0621%
0.0188 N N -- CGPLH412 0.9191 0.0140% 0.0417 N N -- CGPLH413 0.9145
0.0355% 0.0084 N N -- CGPLH414 0.9127 0.0290% 0.0294 N N --
CGPLH415 0.9025 0.0296% 0.0131 N N -- CGPLH416 0.9388 0.0198%
0.0645 N N -- CGPLH417 0.9192 0.0241% 0.0836 N N -- CGPLH418 0.9234
0.0306% 0.0052 N N -- CGPLH419 0.9295 0.0280% 0.0489 N N --
CGPLH420 0.9109 0.0187% 0.0420 N N -- CGPLH422 0.9006 0.0208%
0.0324 N N -- CGPLH423 0.8288 0.0532% 0.0139 N N -- CGPLH424 0.9265
0.1119% 0.0864 N N -- CGPLH425 0.9488 0.0722% 0.0156 N N --
CGPLH426 0.9080 0.0548% 0.1075 N N -- CGPLH427 0.9257 0.0182%
0.0470 N N -- CGPLH428 0.9272 0.0346% 0.0182 N N -- CGPLH429 0.8757
0.0593% 0.8143 Y Y -- CGPLH430 0.9307 0.0258% 0.0389 N N --
CGPLH431 0.9185 0.0234% 0.0174 N N -- CGPLH432 0.9082 0.0433%
0.0181 N N -- CGPLH434 0.9442 0.0297% 0.0050 N N -- CGPLH435 0.9097
0.0179% 0.0441 N N -- CGPLH436 0.9158 0.0290% 0.0958 N N --
CGPLH437 0.9245 0.0156% 0.0136 N N -- CGPLH438 0.9138 0.0169%
0.1041 N N -- CGPLH439 0.9028 0.0226% 0.0078 N N -- CGPLH440 0.8295
0.0330% 0.0687 N N -- CGPLH441 0.9430 0.0178% 0.0085 N N --
CGPLH442 0.9405 0.0169% 0.0582 N N -- CGPLH443 0.8801 0.0207%
0.0578 N N -- CGPLH444 0.8068 0.0464% 0.0097 N N -- CGPLH445 0.8750
0.0267% 0.1939 N N -- CGPLH446 0.9257 0.0281% 0.0340 N N --
CGPLH447 0.8968 0.0167% 0.0017 N N -- CGPLH448 0.9191 0.0401%
0.0389 N N -- CGPLH449 0.9254 0.0236% 0.0116 N N -- CGPLH450 0.9195
0.0331% 0.0597 N N -- CGPLH451 0.9167 0.0262% 0.0104 N N --
CGPLH452 0.8948 0.0480% 0.4722 N N -- CGPLH453 0.9339 0.0186%
0.3419 N N -- CGPLH455 0.9322 0.0455% 0.4536 N N -- CGPLH456 0.9098
0.0207% 0.0385 N N -- CGPLH457 0.9022 0.0298% 0.0384 N N --
CGPLH458 0.9275 0.0298% 0.1891 N N -- CGPLH459 0.9209 0.0281%
0.0371 N N -- CGPLH460 0.8863 0.0227% 0.1157 N N -- CGPLH463 0.9372
0.0130% 0.0865 N N -- CGPLH464 0.8511 0.0659% 0.2040 N N --
CGPLH465 0.9164 0.0325% 0.0124 N N -- CGPLH466 0.9408 0.0155%
0.1733 N N -- CGPLH467 0.9024 0.0229% 0.2303 N N -- CGPLH468 0.9345
0.0247% 0.5427 N N -- CGPLH469 0.8799 0.0201% 0.5351 N N --
CGPLH470 0.9228 0.0715% 0.0327 N N -- CGPLH471 0.9333 0.0150%
0.0406 N N -- CGPLH472 0.8915 0.0481% 0.6152 N N -- CGPLH473 0.9128
0.0443% 0.2995 N N -- CGPLH474 0.9245 0.0316% 0.8246 Y N --
CGPLH475 0.9233 0.0269% 0.0736 N N -- CGPLH476 0.9059 0.0236%
0.0143 N N -- CGPLH477 0.9376 0.0382% 0.1111 N N -- CGPLH478 0.9344
0.0256% 0.0628 N N -- CGPLH479 0.9207 0.0221% 0.0648 N N --
CGPLH480 0.9046 0.0672% 0.7473 Y N -- CGPLH481 0.9113 0.0311%
0.0282 N N -- CGPLH482 0.9336 0.0162% 0.0058 N N -- CGPLH483 0.9275
0.0251% 0.0495 N N -- CGPLH484 0.9366 0.0261% 0.0048 N N --
CGPLH485 0.9128 0.0291% 0.1084 N N -- CGPLH486 0.9042 0.0220%
0.0820 N N -- CGPLH487 0.9098 0.0594% 0.2154 N N -- CGPLH488 0.8299
0.0409% 0.0903 N N -- CGPLH490 0.8794 0.0432% 0.0424 N N --
CGPLH491 0.8332 0.0144% 0.0223 N N -- CGPLH492 0.8799 0.0322%
0.0311 N N -- CGPLH493 0.9330 0.0065% 0.0280 N N -- CGPLH494 0.9303
0.0232% 0.0824 N N -- CGPLH495 0.8908 0.0513% 0.0465 N N --
CGPLH496 0.8398 0.0208% 0.0572 N N -- CGPLH497 0.9330 0.0335%
0.0404 N N -- CGPLH498 0.9315 0.0403% 0.0752 N N -- CGPLH499 0.9442
0.0198% 0.0149 N N -- CGPLH500 0.9240 0.0433% 0.0754 N N --
CGPLH501 0.9308 0.0300% 0.0159 N N -- CGPLH052 0.9200 0.0351%
0.0841 N N -- CGPLH503 0.8939 0.0398% 0.0649 N N -- CGPLH504 0.9324
0.0440% 0.1231 N N -- CGPLH505 0.9243 0.0605% 0.1869 N N --
CGPLH506 0.9498 0.0284% 0.0180 N N -- CGPLH507 0.9192 0.0186%
0.0848 N N -- CGPLH508 0.9410 0.0150% 0.1077 N N -- CGPLH509 0.9323
0.0163% 0.0828 N N -- CGPLH510 0.9548 0.0128% 0.0376 N N --
CGPLH511 0.9493 0.0224% 0.1779 N N -- CGPLH512 0.9244 0.0094%
0.0076 N N -- CGPLH513 0.9595 0.0441% 0.5250 N N -- CGPLH514 0.9369
0.0114% 0.3131 N N -- CGPLH515 0.9283 0.0352% 0.4936 N N --
CGPLH516 0.8298 0.0175% 0.0916 N N -- CGPLH517 0.9494 0.0161%
0.0059 N N -- CGPLH518 0.9432 0.0274% 0.0130 N N -- CGPLH519 0.9351
0.0171% 0.0949 N N -- CGPLH520 0.9476 0.0241% 0.0844 N N --
CGPLH625 0.9231 0.0697% 0.4977 N N -- CGPLH626 0.9269 0.0231%
0.3100 N N -- CGPLH639 0.9410 0.0549% 0.0773 N N -- CGPLH640 0.9264
0.0232% 0.0327 N N -- CGPLH642 0.8376 0.0768% 0.0555 N N --
CGPLH643 0.9271 0.0579% 0.1325 N N -- CGPLH644 0.8948 0.0621%
0.3819 N N -- CGPLH646 0.8691 0.0462% 0.2423 N N -- CGPLLU144
0.6861 0.0423% 0.9892 Y Y 5.10% CGPLLU161 0.9187 0.0273% 0.9955 Y Y
0.20% CGPLLU162 0.0836 0.1410% 0.9966 Y Y 0.22% CGPLLUl63 0.3033
0.0724% 0.9940 Y Y 0.21% CGPLLU168 0.6842 0.0712% 0.9861 Y Y 0.07%
CGPLLU169 0.9189 0.0846% 0.9856 Y Y 0.13% CGPLLU176 0.9081 0.0626%
0.8769 Y Y ND CGPLLU177 0.6790 0.0564% 0.9924 Y Y 3.22% CGPLLU203
0.8741 0.0568% 0.9178 Y Y 0.11% CGPLLU205 0.9476 0.0495% 0.9877 Y Y
ND CGPLLU207 0.9379 0.0421% 0.9908 Y Y 0.32% CGPLLU208 0.8942
0.0815% 0.9273 Y Y 1.33% CGPLOV11 0.8872 0.0469% 0.9343 Y Y 0.87%
CGPLOV12 0.8973 0.2767% 0.9764 Y Y ND CGPLOV13 0.9146 0.1017%
0.9690 Y Y 0.35% CGPLOV15 0.8552 0.0876% 0.9945 Y Y 3.54% CGPLOV16
0.9046 0.0400% 0.9683 Y Y 1.12% CGPLOV19 0.7578 0.1089% 0.9989 Y Y
46.35% CGPLOV20 0.9154 0.0581% 0.9749 Y Y 0.21% CGPLOV21 0.8889
0.0677% 0.9961 Y Y 14.36% CGPLOV22 0.9355 0.0251% 0.9775 Y Y 0.49%
CGPLOV23 0.8850 0.1520% 0.9910 Y Y 1.39% CGPLOV24 0.8995 0.0303%
0.9856 Y Y ND CGPLOV25 0.9228 0.0141% 0.8544 Y Y ND CGPLOV26 0.9351
0.0646% 0.9946 Y Y ND CGPLOV28 0.9378 0.0547% 0.8160 Y Y ND
CGPLOV31 0.9283 0.1605% 0.9795 Y Y ND CGPLOV32 0.9338 0.1351%
0.8609 Y Y ND CGPLOV37 0.8831 0.0985% 0.9849 Y Y 0.29% CGPLOV38
0.6502 0.0490% 0.9990 Y Y 4.89% CGPLOV40 0.8127 0.6145% 0.9963 Y Y
6.73% CGPLOV41 0.8929 0.1110% 0.9484 Y Y 0.60% CGPLOV42 0.9086
0.0489% 0.9979 Y Y 1.24% CGPLOV43 0.9342 0.0432% 0.6042 N N ND
CGPLOV44 0.9173 0.1946% 0.9962 Y Y 0.37% CGPLOV46 0.9291 0.0801%
0.9128 Y Y ND CGPLOV47 0.9461 0.0270% 0.3410 N N 3.20% CGPLOV48
0.9429 0.0422% 0.4874 N N 10.70% CGPLOV49 0.8083 0.1527% 0.9897 Y Y
2.03% CGPLOV50 0.9382 0.0907% 0.9955 Y Y ND CGPLPA112 0.9429
0.0268% 0.0856 N N -- CGPLPA113 0.7674 1.0116% 0.9935 Y Y --
CGPLPA114 0.9246 0.0836% 0.7598 Y Y -- CGPLPA115 0.8810 0.0763%
0.9974 Y Y -- CGPLPA117 0.8767 0.1084% 0.9049 Y Y -- CGPLPA118
0.9001 0.1842% 0.9859 Y Y 0.14% CGPLPA122 0.8058 0.2047% 0.9983 Y Y
37.22% CGPLPA124 0.9238 0.1542% 0.8791 Y Y 0.62% CGPLPA125 0.9373
0.0273% 0.0228 N N -- CGPLPA126 0.9139 0.4349% 0.9908 Y Y ND
CGPLPA127 0.8117 0.4371% 0.9789 Y Y -- CGPLPA128 0.9003 0.1317%
0.9812 Y Y ND CGPLPA129 0.9155 0.0642% 0.9839 Y Y ND CGPLPA130
0.8499 0.1055% 0.9895 Y Y ND CGPLPA131 0.9195 0.0760% 0.9685 Y Y
0.21% CGPLPA134 0.8847 0.0260% 0.9896 Y Y 0.93% CGPLPA135 0.9184
0.0558% 0.6594 Y N -- CGPLPA136 0.9050 0.0769% 0.9596 Y Y 0.10%
CGPLPA137 0.9320 0.0499% 0.7282 Y N -- CGPLPA139 0.9374 0.0465%
0.0743 N N -- CGPLPA14 0.9069 0.0515% 0.9824 Y Y -- CGPLPA140
0.9548 0.0330% 0.9751 Y Y 3.21% CGPLPA141 0.9381 0.0920% 0.9388 Y Y
-- CGPLPA15 0.8927 0.0160% 0.8737 Y Y -- CGPLPA155 0.9313 0.0260%
0.8013 Y Y -- CGPLPA156 0.9432 0.0290% 0.0159 N N -- CCPLPA165
0.9309 0.0558% 0.2158 N N -- CGPLPA168 0.7757 0.3123% 0.9878 Y Y --
CGPLPA17 0.6771 1.2600% 0.9956 Y Y -- CGPLPA184 0.9203 0.0897%
0.9926 Y Y -- CGPLPA187 0.8968 0.0658% 0.9875 Y Y -- CGPLPA23
0.6938 0.5785% 0.9984 Y Y -- CGPLPA25 0.9239 0.0380% 0.8103 Y Y --
CGPLPA26 0.9356 0.0247% 0.8231 Y Y -- CGPLPA28 0.8930 0.0546%
0.9036 Y Y -- CGPLPA33 0.8553 0.0894% 0.9967 Y Y -- CGPLPA34 0.8885
0.0438% 0.7977 Y Y -- CGPLPA37 0.9294 0.0410% 0.9924 Y Y --
CGPLPA38 0.8941 0.0372% 0.9851 Y Y -- CGPLPA39 0.7972 0.5058%
0.9951 Y Y -- CGPLPA40 0.8865 0.2268% 0.9920 Y Y -- CGPLPA42 0.8863
0.0283% 0.3544 N N -- CGPLPA46 0.7525 1.0982% 0.9952 Y Y --
CGPLPA47 0.8439 0.1598% 0.9946 Y Y -- CGPLPA48 0.9207 1.0232%
0.2251 N N -- CGPLPA52 0.8863 0.0154% 0.0963 N N -- CGPLPA53 0.8776
0.1824% 0.8946 Y Y -- CGPLPA58 0.9224 0.0803% 0.9056 Y Y --
CGPLPA59 0.9193 0.1479% 0.9759 Y Y -- CGPLPA67 0.9248 0.0329%
0.6716 Y N -- CGPLPA69 0.8592 0.0458% 0.1245 Y Y -- CGPLPA71 0.8888
0.0479% 0.0524 Y Y -- CGPLPA74 0.9372 0.0292% 0.0108 Y Y --
CGPLPA76 0.9441 0.0345% 0.0897 Y Y -- CGPLPA85 0.9337 0.0363%
0.0508 Y Y -- CGPLPA86 0.8042 0.7564% 0.9864 Y Y -- CGPLPA92 0.9003
0.1458% 0.7061 N N -- CGPLPA93 0.8023 0.6250% 0.9978 Y Y --
CGPLPA94 0.9433 0.0180% 0.9025 Y Y -- CGPLPA95 0.8571 0.0815%
0.9941 Y Y -- CGST102 0.9057 0.0704% 0.8581 Y Y 0.43% CGST11 0.9161
0.0651% 0.1435 N N -- CGST110 0.9232 0.0817% 0.8900 Y Y ND CGST114
0.9038 0.0317% 0.5893 N N ND CGST13 0.9156 0.0321% 0.9754 Y Y ND
CGST131 0.8886 0.2752% 0.9409 Y Y -- CGST141 0.9205 0.0388% 0.2008
N N ND CGST16 0.8355 0.1744% 0.9974 Y Y 0.93% CGST18 0.9111 0.0298%
0.3842 N N 0.14% CGST21 0.2687 0.2295% 0.9910 Y Y -- CGST26 0.9140
0.0399% 0.5009 N N -- CGST28 0.7832 0.1295% 0.9955 Y Y 1.62% CGST30
0.9121 0.0338% 0.9183 Y Y 0.42% CGST32 0.8639 0.0247% 0.9512 Y Y
2.99% CGST33 0.7770 0.0798% 0.9805 Y Y 2.32% CGST38 0.8758 0.0540%
0.9416 Y Y -- CGST39 0.9401 0.0287% 0.8480 Y Y ND CGST41 0.9284
0.0398% 0.9253 Y Y ND CGST45 0.9036 0.0220% 0.9713 Y Y ND CGST47
0.9096 0.0157% 0.9687 Y Y 0.45% CGST48 0.5445 0.0220% 0.9975 Y Y
4.21% CGST53 0.7888 0.1140% 0.9914 Y Y -- CGST58 0.9094 0.0696%
0.9705 Y Y ND
CGST67 0.8853 0.3245% 0.9002 Y Y -- CGST77 0.8295 0.1851% 0.9981 Y
Y -- CGST80 0.8845 0.0490% 0.9513 Y Y 1.04% CGST81 0.8851 0.0138%
0.9748 Y Y 0.21% *NO indicates not detected. please see reference
10 for additional information on targeted sequencing analyes. DELFI
cancer detection at 95% and 98% specificity is based on scores
greater than 0.6200 and 0.7500 respectively.
* * * * *