U.S. patent application number 16/285819 was filed with the patent office on 2019-08-29 for compositions and methods for genetic markers to identify risk of oral mucositis.
The applicant listed for this patent is The Charlotte-Mecklenburg Hospital Authority d/b/a/ Atrium Health, The Charlotte-Mecklenburg Hospital Authority d/b/a/ Atrium Health. Invention is credited to Farah K. B. Mougeot, Jean-Luc C. Mougeot.
Application Number | 20190264265 16/285819 |
Document ID | / |
Family ID | 67685037 |
Filed Date | 2019-08-29 |
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United States Patent
Application |
20190264265 |
Kind Code |
A1 |
Mougeot; Jean-Luc C. ; et
al. |
August 29, 2019 |
COMPOSITIONS AND METHODS FOR GENETIC MARKERS TO IDENTIFY RISK OF
ORAL MUCOSITIS
Abstract
The present invention provides methods and compositions
involving genetic markers and their association with oral mucositis
occurring in patients who are treated with cancer therapy and/or
conditioning therapy for hematopoietic stein cell
transplantation.
Inventors: |
Mougeot; Jean-Luc C.;
(Charlotte, NC) ; Mougeot; Farah K. B.;
(Charlotte, NC) |
|
Applicant: |
Name |
City |
State |
Country |
Type |
The Charlotte-Mecklenburg Hospital Authority d/b/a/ Atrium
Health |
Charlotte |
NC |
US |
|
|
Family ID: |
67685037 |
Appl. No.: |
16/285819 |
Filed: |
February 26, 2019 |
Related U.S. Patent Documents
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Application
Number |
Filing Date |
Patent Number |
|
|
62635235 |
Feb 26, 2018 |
|
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Current U.S.
Class: |
1/1 |
Current CPC
Class: |
G16H 20/40 20180101;
C12Q 1/6858 20130101; C12Q 1/6876 20130101; C12Q 2600/158 20130101;
G16H 10/40 20180101; C12Q 1/6883 20130101; C12Q 2600/118 20130101;
C12Q 2600/156 20130101; G16H 50/30 20180101; G16H 20/10 20180101;
G16H 50/20 20180101; C12Q 1/6827 20130101 |
International
Class: |
C12Q 1/6827 20060101
C12Q001/6827; C12Q 1/6858 20060101 C12Q001/6858; C12Q 1/6876
20060101 C12Q001/6876; G16H 50/20 20060101 G16H050/20; G16H 50/30
20060101 G16H050/30 |
Claims
1. A method of identifying a subject who has undergone and/or will
undergo hematopoietic stem cell transplantation (HSCT) and/or a
subject who has undergone and/or will undergo chemotherapy and/or
radiation therapy as having an increased risk of developing oral
mucositis, comprising: a. obtaining a DNA sample from the subject;
b. contacting the DNA sample from the subject with reagents to
determine the presence or absence of the following risk alleles: 1.
GG at single nucleotide polymorphism (SNP) site rs4847278; 2. GG at
SNP site rs10797854 and GG at SNP site rs20560 and CC at SNP site
rs944970 and CC at SNP site rs1062044 and AA at SNP site rs944971
and GG at SNP site rs6424888 and CC at SNP site rs20563 and CC at
SNP site rs2333620 (combined SNP genotype); 3. AA at SNP site
rs7373116; 4. GA at SNP site rs61742149; 5. AA at SNP site
rs10935321; and 6. TT at SNP site rs111482845 and TT at SNP site
rs11728441 (combined SNP genotype); and c. detecting one or more
of: the single risk alleles of (1), (3), (4), or (5) or the
multiple risk alleles of (2) or (6) in the DNA sample, thereby
identifying the subject as having an increased risk of developing
oral mucositis.
2. The method of claim 1, further comprising the steps of: d.
contacting the DNA sample with reagents to determine the presence
of absence of the following risk alleles: 7. GG at SNP site
rs147960186; 8. GG at SNP site rs11787880; 9. AA at SNP site
rs10973387; and 10. AA at SNP site rs4030473 and GG at SNP site
rs5915052 (combined SNP genotype); and e. detecting one or more of
the single risk alleles of (7), (8) or (9) or the multiple risk
alleles of (10) in the DNA sample, thereby identifying the subject
as having an increased risk of developing oral mucositis.
3. The method of claim 1, further comprising the steps of
administering to the subject a treatment to optimize wound healing,
a probiotic diet to reduce levels of proinflammatory hydrogen
sulfide and/or methylmercaptan produced by oral bacteria, an oral
hygiene protocol, amifostine, palifermin, benzidamine, calcium
phosphate, cryotherapy, iseganan, a cryoprotective (e.g.,
sucralfate, oral glutamine, hyaluronic acid), a growth factor,
topical polyvinylpyrrolidone, low power laser irradiation, gene
therapy treatment, and any combination thereof.
4. A method of guiding clinical decision making for a subject in
need of radiation therapy and/or chemotherapy and/or in need of
conditioning therapy for HSCT, comprising: a. obtaining a DNA
sample from the subject; b, contacting the DNA sample from the
subject with reagents to determine the presence or absence of the
following risk alleles: 1. GG at single nucleotide polymorphism
(SNP) site rs4847278; 2. GG at SNP site rs10797854 and GG at SNP
site rs20560 and CC at SNP site rs944970 and CC at SNP site
rs1062044 and AA at SNP site rs944971 and GG at SNP site rs6424888
and CC at SNP site rs20563 and CC at SNP site rs2333620 (combined
SNP genotype); 3. AA at SNP site rs7373116; 4. GA at SNP site
rs61742149; 5. AA at SNP site rs10935321; and 6. TT at SNP site
rs111482845 and TT at SNP site rs11728441 (combined SNP genotype),
b. detecting one or more of: the single risk alleles of (1), (3),
(4), or (5) or the multiple risk alleles of (2) or (6) in the DNA
sample, thereby identifying the subject as having an increased risk
of developing oral mucositis; and c. administering a therapy to
prevent, ameliorate and/or reduce the symptoms of oral mucositis to
the subject before, during and/or after the radiation therapy
and/or chemotherapy and/or conditioning therapy.
5. The method of claim 4, wherein the therapy to prevent,
ameliorate or reduce the symptoms of oral mucositis is a treatment
to optimize wound healing, a probiotic diet to reduce levels of
proinflammatory hydrogen sulfide or methylmercaptan produced by
oral bacteria, an oral hygiene protocol, amifostine, palifermin,
benzidamine, calcium phosphate, cryotherapy, iseganan, a
cryoprotective (e.g., sucralfate, oral glutamine, hyaluronic acid),
a growth factor, topical polyvinylpyrrolidone, low power laser
irradiation, gene therapy treatment, and any combination
thereof.
6. A method of correlating a genetic marker profile of a subject
with oral mucositis associated with radiation therapy and/or
chemotherapy and/or conditioning therapy for HSCT, comprising: a)
identifying a subject or population of subjects having oral
mucositis associated with radiation and/or chemotherapy and/or
conditioning therapy for HSCT; b) determining the genetic marker
profile of the subject or of each of the subjects of the population
of (a); and c) correlating the presence of the genetic marker
profile of step (b) with oral mucositis in the subject or
population of subjects.
Description
STATEMENT OF PRIORITY
[0001] This application claims the benefit, under 35 U.S.C. .sctn.
119(e), of U.S. Provisional Application No. 62/635,235, filed Feb.
26, 2018, the entire contents of which are incorporated by
reference herein.
FIELD OF THE INVENTION
[0002] The present invention relates to genetic polymorphisms
signatures and their association with oral mucositis in patients
with hematologic cancer receiving radiation and/or chemotherapy or
patients receiving conditioning regimen in preparation for
hematopoietic stem cell transplant (HSCT) (e.g., cancer patients,
patients with immunodeficiency condition, patients with other
blood-related disorder, or other condition requiring HSCT).
BACKGROUND OF THE INVENTION
[0003] Oral mucositis (OM) is a common dose-limiting side effect of
conditioning therapy used in cancer or immunodeficiency treatment
of hematopoietic stem cell transplant (HSCT) patients. There is a
need to identify genetic markers predictive of risk and severity of
OM following radiation and/or chemotherapy.
[0004] The present invention overcomes previous shortcomings in the
art by providing methods and compositions employing genetic
biomarkers for prediction of risk for oral mucositis associated
with cancer therapy and conditioning for HSCT.
DETAILED DESCRIPTION OF THE INVENTION
[0005] For the purposes of promoting an understanding of the
principles of the present invention, reference will now be made to
particular embodiments and specific language will be used to
describe the same. It will nevertheless be understood that no
limitation of the scope of the disclosure is thereby intended, such
alteration and further modifications of the disclosure as
illustrated herein, being contemplated as would normally occur to
one skilled in the art to which the invention relates.
[0006] The present invention is based on the unexpected discovery
that a subject's genetic markers can be used to predict the
subject's risk of having or developing oral mucositis associated
with radiation therapy and/or chemotherapy and/or conditioning
therapy for HSCT. Accordingly, in one embodiment, the present
invention provides a method of identifying a subject (e.g., a
subject who has undergone and/or will undergo hematopoietic stem
cell transplantation (HSCT) and/or a subject who has undergone
and/or will undergo chemotherapy and/or radiation therapy) as
having an increased risk of developing oral mucositis, comprising:
a. obtaining a DNA sample from the subject; b. contacting the DNA
sample from the subject with reagents to determine the presence or
absence of the following risk alleles: 1. GG at single nucleotide
polymorphism (SNP) site rs4847278; 2. GG at SNP site rs10797854 and
GG at SNP site rs20560 and CC at SNP site rs944970 and CC at SNP
site rs1062044 and AA at SNP site rs944971 and GG at SNP site
rs6424888 and CC at SNP site rs20563 and CC at SNP site rs2333620
(combined SNP genotype); 3. AA at SNP site rs7373116; 4. GA at SNP
site rs61742149; 5. AA at SNP site rs10935321; and 6. TT at SNP
site rs111482845 and TT at SNP site rs11728441 (combined SNP
genotype); and c. detecting one or more of: the single risk alleles
of (1), (3), (4), or (5) or the multiple risk alleles of (2) or (6)
in the DNA sample, thereby identifying the subject as having an
increased risk of developing oral mucositis.
[0007] The method described above, can further comprise the steps
of: d. contacting the DNA sample with reagents to determine the
presence of absence of the following risk alleles: 7. GG at SNP
site rs147960186; 8. GG at SNP site rs11787880; 9. AA at SNP site
rs10973387; and 10. AA at SNP site rs4030473 and GG at SNP site
rs5915052 (combined SNP genotype); and e. detecting one or more of
the single risk alleles of (7), (8) or (9) or the multiple risk
alleles of (10) in the DNA sample, thereby identifying the subject
as having an increased risk of developing oral mucositis.
[0008] In some embodiments, the methods of this invention can
further comprise administering to the subject a treatment to
optimize wound healing, based on the initial knowledge of a risk
genotype, a probiotic diet to reduce levels of proinflammatory
hydrogen sulfide or methylmercaptan produced by oral bacteria, an
oral hygiene protocol, amifostine, palifermin, benzidamine, calcium
phosphate, cryotherapy, iseganan, a cryoprotective (e.g.,
sucralfate, oral glutamine, hyaluronic acid), a growth factor,
topical polyvinylpyrrolidone, low power laser irradiation, gene
therapy treatment (e.g., AG013, Oragenics), and any combination
thereof.
[0009] In some embodiments, a wound healing treatment would be a
mouth rinse-based gene therapy such as AG013 (Lactococcus lactis
delivering human trefoil factor protein [hTFF1], which is not a
growth factor. hTFF1 protects the mucosa from insults, stabilizes
the mucus layer and affects healing of the epithelium. Proteins
and/or nucleic acids (such as small inhibitory siRNAs) may be
delivered as an oral rinse (e.g., to minimize systemic side
effects).
[0010] The present invention further provides a method of guiding
clinical decision making for a subject in need of radiation therapy
and/or chemotherapy and/or in need of conditioning therapy for
HSCT, comprising: a. obtaining a DNA sample from the subject; b.
contacting the DNA sample from the subject with reagents to
determine the presence or absence of the following risk alleles: 1.
GG at single nucleotide polymorphism (SNP) site rs4847278; 2. GG at
SNP site rs10797854 and GG at SNP site rs20560 and CC at SNP site
rs944970 and CC at SNP site rs1062044 and AA at SNP site rs944971
and GG at SNP site rs6424888 and CC at SNP site rs20563 and CC at
SNP site rs2333620 (combined SNP genotype); 3. AA at SNP site
rs7373116; 4. GA at SNP site rs61742149; 5. AA at SNP site
rs10935321; and 6. TT at SNP site rs111482845 and TT at SNP site
rs11728441 (combined SNP genotype); c. detecting one or more of:
the single risk alleles of (1), (3), (4), or (5) or the multiple
risk alleles of (2) or (6) in the DNA sample, thereby identifying
the subject as having an increased risk of developing oral
mucositis; and d. administering a therapy to prevent, ameliorate
and/or reduce the symptoms of oral mucositis to the subject before,
during and/or after the radiation therapy and/or chemotherapy
and/or conditioning therapy for HSCT.
[0011] In some embodiments of the method above, the therapy to
prevent, ameliorate or reduce the symptoms of oral mucositis can be
a treatment to optimize wound healing, a probiotic diet to reduce
levels of proinflammatory hydrogen sulfide or methylmercaptan
produced by oral bacteria, an oral hygiene protocol, amifostine,
palifermin, benzidamine, calcium phosphate, cryotherapy, iseganan,
a cryoprotective (e.g., sucralfate, oral glutamine, hyaluronic
acid), a growth factor, topical polyvinylpyrrolidone, low power
laser irradiation, and any combination thereof.
[0012] In further embodiments, the present invention provides a
method of correlating a genetic marker profile of a subject with
oral mucositis associated with radiation therapy and/or
chemotherapy and/or conditioning therapy for HSCT, comprising: a)
identifying a subject or population of subjects having oral
mucositis associated with radiation and/or chemotherapy and/or
conditioning therapy for HSCT; b) determining the genetic marker
profile of the subject or of each of the subjects of the population
of (a); and c) correlating the presence of the genetic marker
profile of step (b) with oral mucositis in the subject or
population of subjects.
[0013] The methods of this invention can be used to identify and/or
monitor a subject for oral mucositis who may benefit from
treatment, which can be prior to, during and/or following radiation
therapy and/or chemotherapy and/or conditioning therapy for HSCT.
The treatment of such subjects can also be monitored and/or
modified according to the methods described herein.
[0014] It is understood that although the methods of this invention
can be used in isolation, they can also form a part of a
multimarker approach for diagnosing and/or identifying risk of oral
mucositis associated with radiation therapy and/or chemotherapy
and/or conditioning therapy for HSCT. Thus, the methods of the
present invention might not only be used in place of a measurement
of other biomarkers, but might also be used in combination, or in
addition to the measurement or analysis of one or more other
markers or biomarkers known to be associated with oral mucositis
associated with radiation therapy and/or chemotherapy and/or
conditioning therapy for HSCT.
[0015] Techniques that can be used to identify single nucleotide
polymorphisms (SNPs) of this invention can include, but are not
limited to, whole genome exome sequencing (using next generation
sequencing technology, i.e., NGS), targeted allelic sequencing,
which focuses on the target genes instead of the whole genome, by
generating amplicons by PCR, and/or techniques based on Taqman
Sanger sequencing, which is equivalent to the targeted allelic
sequencing, but does not use NGS. All techniques are valid to
determine the SNPs of this invention.
Definitions
[0016] The terms "a," "an" and "the" are used herein to refer to
one or to more than one (i.e., at least one) of the grammatical
object of the article. By way of example, "an element" means at
least one element and can include more than one element (e.g., a
multiplicity or plurality of elements).
[0017] As used herein, the term "and/or" refers to and encompasses
any and all possible combinations of one or more of the associated
listed items, as well as the lack of combinations when interpreted
in the alternative ("or").
[0018] As used herein, the term "about," when used in reference to
a measurable value such as an amount of mass, dose, time,
temperature, and the like, is meant to encompass variations of 20%,
10%, 5%, 1%, 0.5%, or even 0.1% of the specified amount.
[0019] As used herein, "one or more" can mean one, two, three,
four, five, six, seven, eight, nine, ten or more, up to any
number.
[0020] As used herein, the transitional phrase "consisting
essentially of" means that the scope of a claim is to be
interpreted to encompass the specified materials or steps recited
in the claim, "and those that do not materially affect the basic
and novel characteristic(s)" of the claimed invention. See, In re
Herz, 537 F.2d 549, 551-52, 190 USPQ 461, 463 (CCPA 1976) (emphasis
in the original); see also MPEP .sctn. 2111.03. Thus, the term
"consisting essentially of" when used in a claim of this invention
is not intended to be interpreted to be equivalent to
"comprising."
[0021] Unless otherwise defined, all technical terms used herein
have the same meaning as commonly understood by one of ordinary
skill in the art to which this disclosure belongs.
[0022] As used herein, the term "subject" and "patient" are used
interchangeably herein and refer to both human and nonhuman
animals. A subject of this invention can be any subject that is
susceptible to oral mucositis associated with radiation therapy
and/or chemotherapy and/or conditioning therapy for HSCT, and in
particular embodiments, the subject of this invention is a human
subject.
[0023] A "subject in need thereof" or "a subject in need of" is a
subject known to have, or is suspected of having or developing oral
mucositis associated with radiation therapy and/or chemotherapy
and/or conditioning therapy for HSCT. In particular embodiments,
the subject is in need of, is scheduled for and/or is planning to
undergo radiation and/or chemotherapy and/or conditioning therapy
for HSCT, and/or other cancer treatment.
[0024] The term "administering" or "administered" as used herein is
meant to include topical, parenteral and/or oral administration,
all of which are described herein. Parenteral administration
includes, without limitation, intravenous, subcutaneous and/or
intramuscular administration (e.g., skeletal muscle or cardiac
muscle administration). It will be appreciated that the actual
method and order of administration will vary according to, inter
alia, the particular preparation of compound(s) being utilized, and
the particular formulation(s) of the one or more other compounds
being utilized. The optimal method and order of administration of
the compounds of the invention for a given set of conditions can be
ascertained by those skilled in the art using conventional
techniques and in view of the information set out herein.
[0025] The term "administering" or "administered" also refers,
without limitation, to oral, sublingual, buccal, transnasal,
transdermal, rectal, intramuscular, intravenous, intraarterial
(intracoronary), intraventricular, intrathecal, and subcutaneous
routes. In accordance with good clinical practice, the instant
compounds can be administered at a dose that will produce effective
beneficial effects without causing undue harmful or untoward side
effects, i.e., the benefits associated with administration outweigh
the detrimental effects.
[0026] Also as used herein, the terms "treat," "treating" or
"treatment" refer to any type of action that imparts a modulating
effect, which, for example, can be a beneficial and/or therapeutic
effect, to a subject afflicted with a condition, disorder, disease
or illness, including, for example, improvement in the condition of
the subject (e.g., in one or more symptoms), delay in the
progression of the disorder, disease or illness, and/or change in
clinical parameters of the condition, disorder, disease or illness,
etc., as would be well known in the art.
[0027] Additionally, as used herein, the terms "prevent,"
preventing" or "prevention" refer to any type of action that
results in the absence, avoidance and/or delay of the onset and/or
progression of a disease, disorder and/or a clinical symptom(s) in
a subject and/or a reduction in the severity of the onset of the
disease, disorder and/or clinical symptom(s) relative to what would
occur in the absence of the methods of the invention. The
prevention can be complete, e.g., the total absence of the disease,
disorder and/or clinical symptom(s). The prevention can also be
partial, such that the occurrence of the disease, disorder and/or
clinical symptom(s) in the subject and/or the severity of onset is
less than what would occur in the absence of the present
invention.
[0028] As used herein, the term "ameliorate" refers to the ability
to make better or more tolerable, a condition such as oral
mucositis associated with radiation therapy and/or chemotherapy
and/or conditioning therapy for HSCT. In some embodiments, the term
"prevent" refers to the ability to keep a condition such as oral
mucositis associated with radiation therapy and/or chemotherapy
and/or conditioning therapy for HSCT from happening or existing as
well as to diminish or delay onset. In some embodiments, the term
"treating" refers to the caring for, or dealing with, a condition
such as oral mucositis associated with radiation therapy and/or
chemotherapy and/or conditioning therapy for HSCT.
[0029] Oral mucositis is inflammation of the mucous membrane in the
mouth. For those suffering from oral mucositis, it is very
important to have a good oral hygiene routine. Other self-care
treatments include avoiding certain foods and drinks, sucking on
ice cubes or ice chips, taking painkillers in the form of a mouth
rinse, gel or spray, or taking palifermin.
[0030] Infection treatments may include antibiotics, antifungal,
and/or antiviral medications. Oral cryotherapy (e.g. ice in the
mouth) can also be employed prior to, during and/or following
radiation therapy and/or chemotherapy and/or conditioning therapy
for HSCT.
[0031] Patients receiving aggressive cancer therapies typically
need aggressive nutrition management to help with nutritional
compromise.
[0032] An "effective amount" or "therapeutically effective amount"
refers to an amount of a compound or composition of this invention
that is sufficient to produce a desired effect, which can be a
therapeutic and/or beneficial effect. The effective amount will
vary with the age, general condition of the subject, the severity
of the condition being treated, the particular agent administered,
the duration of the treatment, the nature of any concurrent
treatment, the pharmaceutically acceptable carrier used, and like
factors within the knowledge and expertise of those skilled in the
art. As appropriate, an effective amount or therapeutically
effective amount in any individual case can be determined by one of
ordinary skill in the art by reference to the pertinent texts and
literature and/or by using routine experimentation. (See, for
example, Remington, The Science and Practice of Pharmacy (latest
edition)).
[0033] Pharmaceutical compositions may be prepared as medicaments
to be administered in any method suitable for the subject's
condition, for example, orally, parenterally (including
subcutaneous, intramuscular, and intravenous), rectally,
transdermally, buccally, or nasally, or may be delivered directly
to the heart by injection and/or catheter, or may be delivered to
the eye as a liquid solution.
[0034] "Pharmaceutically acceptable," as used herein, means a
material that is not biologically or otherwise undesirable, i.e.,
the material may be administered to a subject along with the
compositions of this invention, without causing substantial
deleterious biological effects or interacting in a deleterious
manner with any of the other components of the composition in which
it is contained. The material would naturally be selected to
minimize any degradation of the active ingredient and to minimize
any adverse side effects in the subject, as would be well known to
one of skill in the art (see, e.g., Remington's Pharmaceutical
Science; latest edition). Exemplary pharmaceutically acceptable
carriers for the compositions of this invention include, but are
not limited to, sterile pyrogen-free water and sterile pyrogen-free
physiological saline solution, as well as other carriers suitable
for injection into and/or delivery to a subject of this invention,
particularly a human subject, as would be well known in the
art.
[0035] Suitable forms for oral administration include, but are not
limited to, tablets, powders, compressed or coated pills, dragees,
sachets, hard or gelatin capsules, sub-lingual tablets, syrups, and
suspensions. Suitable forms of parenteral administration include,
but are not limited to, an aqueous or non-aqueous solution or
emulsion. Suitable forms for rectal administration, include, but
are not limited to, suppositories with hydrophilic or hydrophobic
vehicles. For topical administration, suitable forms include, but
are not limited to, suitable transdermal delivery systems known in
the art, such as patches, and for nasal delivery, suitable forms
include, but are not limited to, aerosol and nebulized delivery
systems known in the art.
[0036] A composition of the present invention (e.g., a
pharmaceutical composition) may contain one or more excipients or
adjuvants. Selection of excipients and/or adjuvants and the amounts
to use may be readily determined by the formulation scientist upon
experience and consideration of standard procedures and reference
works in the field.
[0037] By "parenteral" is meant intravenous, subcutaneous or
intramuscular administration. In the methods of the present
invention, the composition or compound may be administered alone,
simultaneously with one or more other compounds, or the composition
and/or compounds may be administered sequentially, in either order.
It will be appreciated that the actual method and order of
administration will vary according to, inter alia, the particular
preparation of compound(s) being utilized, the particular
formulation(s) of the one or more other compounds being utilized,
and the conditions to be treated. The optimal method and order of
administration of the compounds of the disclosure for a given set
of conditions can be ascertained by those skilled in the art using
conventional techniques and in view of the information set out
herein.
[0038] In prophylactic applications, pharmaceutical compositions or
medicaments are administered to a subject susceptible to, or
otherwise at risk of, occlusion or narrowing of an artery and/or
its branches and/or a disease, disturbance and/or pathological
condition of an artery and/or its branches in an amount sufficient
to eliminate or reduce the risk, lessen the severity, or delay the
onset, including biochemical, histologic and/or physiologic
symptoms. In therapeutic applications, compositions or medicants
are administered to a subject suspected of, or already having,
occlusion or narrowing of an artery and/or its branches and/or has
had or is having a disease, disturbance and/or pathological
condition of an artery and/or its branches in an amount sufficient
to treat, or at least partially reduce or arrest, the symptoms
(biochemical, histologic and/or physiological). An amount adequate
to accomplish therapeutic or prophylactic treatment is defined as
an effective amount or a therapeutically or prophylactically
effective dose. In either prophylactic or therapeutic regimens,
compounds and/or compositions of the present invention can be
administered in several doses until a desired effect has been
achieved.
[0039] An effective dose or effective doses of the compositions of
the present invention, for the treatment of the conditions
described herein can vary depending upon many different factors,
including means of administration, target site, physiological state
of the subject, whether the subject is human or an animal, other
medications administered, and/or whether treatment is prophylactic
or therapeutic. In some embodiments, the subject is a human but
nonhuman mammals including transgenic mammals can also be treated.
Treatment dosages can be titrated to optimize safety and efficacy.
Generally, an effective amount of the compositions of this
invention will be determined by the age, weight and condition or
severity of disease or disorder of the subject.
[0040] Generally, dosing (e.g., an administration) can be one or
more times daily, or less frequently, such as once a day, once a
week, once a month, once a year, to once in a decade, etc. and may
be in conjunction with other compositions as described herein.
[0041] The dosage and frequency of administration can vary
depending on whether the treatment is prophylactic or therapeutic.
In prophylactic applications, a relatively low dosage can be
administered at relatively infrequent intervals over a long period
of time. In therapeutic applications, a relatively high dosage at
relatively short intervals is sometimes appropriate until severity
of the injury is reduced or terminated, and typically until the
subject shows partial or complete amelioration of symptoms of
injury. Thereafter, the subject can be administered a prophylactic
regimen.
[0042] The terms "increased risk" and "decreased risk" as used
herein define the level of risk that a subject has of having or
developing oral mucositis as described herein, as compared to a
control subject.
[0043] A sample of this invention can be cells, tissue and/or fluid
(e.g., saliva, buccal swab, salivary gland tissue, etc.) from the
oral cavity of a subject, as well as any other biological material
from the subject that can be used to identify the genetic marker
profile of the subject.
[0044] The present invention further provides a kit of reagents
that can be used in the methods of this invention to determine the
presence or absence of an allele of this invention in a DNA
sample.
[0045] As will be understood by one skilled in the art, there are
several embodiments and elements for each aspect of the claimed
invention, and all combinations of different elements are hereby
anticipated, so the specific combinations exemplified herein are
not to be construed as limitations in the scope of the invention as
claimed. If specific elements are removed or added to the group of
elements available in a combination, then the group of elements is
to be construed as having incorporated such a change.
[0046] The present invention is more particularly described in the
following examples that are intended as illustrative only since
numerous modifications and variations therein will be apparent to
those skilled in the art.
EXAMPLES
Example 1. Conditioning Therapy-Induced Oral Mucositis Associated
Single Nucleotide Polymorphisms (SNPs) Identified by Exome Sequence
Analysis: A Pilot Study
[0047] Using exome-sequencing, our objective was to identify
candidate SNPs associated with oral mucositis (OM) in hematopoietic
stem cell transplantation (HSCT) patients.
[0048] Saliva DNA was extracted from HSCT patients (n=63) with
WHO-OM scores 2-4 (Group-2-4; n=24), or 0-1 (Group-0-1; n=39).
Illumina HiSeq2000-paired-end platform was used for
exome-sequencing. SNP calling was determined with GATK pipeline.
Using a simplified log it model, ruling out that severity of OM
would be solely associated with the intensity of conditioning
treatment, a list of 309 SNPs/209 genes was obtained (uncorrected
p-value<0.01). Assuming a "toxic gain in function", homozygous
variant alleles overrepresented by more than 20% in Group-2-4
(possibly representing true positives independent from diagnosis)
were determined. Proportions differences were evaluated by
two-tailed 2-sample z-test.
[0049] Ten genes with SNP(s) were identified, including LAMC1 and
ABCA4. LAMC1, essential for basal cell adhesion, had 8 SNPs that
encompass 28 kbp. All SNPs combined were either heterozygous or
homozygous for reference or variant genotype. Ten patients, eight
in Group-2-4 and one with WHO-OM score 1, had variant homozygous
genotype in LAMC1. Also, an overrepresented intronic homozygous SNP
variant (100% penetrance) was found in ABCA4, a gene adjacent to
ARHGAP29 gene. In a previous cleft lip/palate association study, a
different intronic SNP in ABCA4 was found within a long distance
regulatory element of ARHGAP29. ARHGAP29 is critical for
craniofacial development and involved in oral epithelial cell
adhesion.
[0050] Exome sequencing has potential to uncover SNPs relevant to
oral mucositis.
Example 2. Conditioning Therapy-Induced Oral Mucositis-Associated
Single Nucleotide Polymorphisms (SNPs) Identified by Exome
Sequencing Analysis
[0051] We have identified a set of ten candidate genes containing
single nucleotide polymorphisms associated with a high incidence
and moderate to high severity of oral mucositis (OM) following
conditioning therapy of hematologic cancer patients prior to
hematopoietic stem cell transplant (HSCT).
[0052] The idea of the study was to determine candidate genes that
will demonstrate an increased risk for the development of severe
mucositis in hematologic cancer and immunodeficient patients
following conditioning therapy and prior to stem cell transplant.
In our lab, we have received saliva samples from CMC, Sweden and
Canada and have designed genomic studies to sequence the exome
regions of the genomes using next generation sequencing.
[0053] Briefly, for analysis of the sequencing data, we have used a
data analysis method that has not been described in the
multi-center protocol. We ranked the results according to severity
and looked for the significant single nucleotide polymorphisms
(SNPs), and looked for their penetrance in the "2 to 4" WHO score
"moderate to severe group" compared to the "0-1" score "none to low
group."
[0054] We found SNPs in 10 genes out of list of 209 candidate genes
(uncorrected p value<0.01) coming from the raw exome SNP data
for 63 patients.
[0055] For these SNPs, we determined that if one patient had one of
these mutations on the two parental chromosomes, there was a
70-100% chance for this patient to get moderate to severe oral
mucositis. We are still working on getting data for a larger sample
size to see how these odds would change, especially for the six
genes that were 100% predictive. Also, there was no evidence of a
correlation with the type of hematologic cancer, since these
mutations hit all the cancer types we analysed (except one type for
which we only had one patient). The biomarkers we identified appear
to be independent of the type of cancer and conditioning regime
(chemotherapy with or without radiation), based on the preliminary
data we have for 63 patients.
[0056] Upon confirmation of these results for a larger population,
we could develop a diagnostic test to let the patient know about
the risks and determine preventive treatment approaches that are
more aggressive before the cancer conditioning therapy is started
and/or during such therapy.
Statistical Model for Mucositis Genetic Association
[0057] Instead of using the marginal or classical "log it" logistic
regression model, a conditional log it model was used (conditioned
on myeloablative chemotherapy group c=1 versus non-myeloablative
group c=0)
Log it[P(M=1|c=1)]=.alpha.+.beta.g
Variables in the model are:
[0058] M: Mucositis grade (M=0, 1) (M=0: Low mucositis group OM
score Group 0-1; M=1:
Moderate to severe mucositis OM score Group 2-4) g: genotype or SNV
at a specific locus, i.e., dose of the minor allele (g=0, 1, 2)
(ref/ref, alt/ref, alt/alt) c: chemotherapy group (c=0, 1)
[0059] The model was fitted to estimate the coefficients .alpha.
and .beta., with .beta. indicating the effect (direction and
magnitude) of the genotype or SNV (single nucleotide variant
corresponding to single nucleotide polymorphisms or indels
[insertions/deletions]) on mucositis. From the fitted model, we
also determined whether .beta. is significantly different from 0
(null hypothesis HO: .beta.=0), or whether the SNV is associated
with mucositis. We obtained about 200,000 SNVs called in the Exome
Sequencing data of the 63 patients. Most of these SNV are
non-informative since these do not present much variability between
different patients. Therefore, only .about.73,000 informative SNVs
were included in the model, thereby reducing the number of false
positives. A total of 309 intragenic SNVs corresponding to 209
genes, potentially associated with mucositis (uncorrected p-value
<0.01), were identified.
Secondary Analysis to Identify Potentialpotential True
Positives.
[0060] Assuming a "toxic gain in function," homozygous variant
alleles overrepresented by more than 20% in Group-2-4 (possibly
representing true positives independent from diagnosis) were
determined. Proportions differences were evaluated by two-tailed
2-sample z-test and the penetrance was determined for the genes
with significant >20% change in proportion of the homozygous
variant allele. We identified the following ten genes that had SNVs
meeting the criteria. Genes with most discriminatory SNPs are shown
in bold.
TABLE-US-00001 Gene # Symbol Risk 1 ABCA4 rs4847278 G/G 2 LAMC1
rs10797854 rs20560 rs944970 rs1062044 G/G G/G C/C C/C LAMC1
rs944971 rs6424888 rs20563 rs2333620 A/A G/G C/C C/C 3 ORM1
rs147960186 G/G 4 COPB2 rs7373116 A/A 5 ACTL7B rs11787880 G/G 6
FBXO10 rs10973387 A/A 7 SF3B6 rs61742149 G/A 8 MRPS22 rs10935321
A/A 9 FAAH2 rs4030473 rs5915052 A/A G/G 10 MIR548I2 rs111482845
rs11728441 T/T T/T
Saliva Samples for Functional Genomic Studies.
[0061] DNA saliva samples are obtained from patients prior to a
conditioning regimen for autologous or allogeneic stem cell
transplantation. These patients are followed prospectively to
document the incidence and severity of mucositis. Genomic
approaches are used to determine candidate genes (e.g., determine a
genetic marker profile for a subject and/or population of subjects)
that will demonstrate an increased risk for the development of
severe mucositis (WHO grade 3 or 4) and determine the genes'
function in developing OM. Genomic approaches may include the use
of sequence analysis methods (e.g., SNP Arrays, Exome sequencing
and/or other Next Generation Sequencing methods) for the
determination of mutations (SNPs, indels [insertions/deletions],
copy number variations [CNVs]), and/or the use of DNA methylation
analytical methods (e.g., Infinium HumanMethylation450 Illumina
BeadChip). This will provide preliminary data to achieve a power of
80%. In some embodiments, at least 2000 samples may be obtained to
identify mutations associated with susceptibility to OM considering
an effect size between 1.3 and 1.6. DNA libraries which will guide
future functional genomic studies may also be developed.
Example 3. Targeted Allelic Sequencing Validation of Conditioning
Therapy-Induced Oral Mucositis-Associated Single Nucleotide
Polymorphisms (SNPs) Identified by Exome Sequencing
[0062] Introduction. Oral mucositis (OM) is a common dose-limiting
side effect of conditioning therapy for patients with hematologic
cancer undergoing hematopoietic stem cell transplant (HSCT). Using
exome sequencing in a pilot study, we have previously identified
nine genes with SNPs associated with OM in HSCT patients. Our
objective was to validate the candidate SNPs using targeted allelic
sequencing.
[0063] Methods. Saliva DNA from HSCT patients (n=63), which was
previously analyzed by whole genome exome sequencing, was subjected
to targeted allelic sequencing for nine candidate genes. Sequencing
was performed by Illumina HiSeq TruSeq paired-end sequencing of PCR
amplicons of the targeted regions. SNPs/INDELS were identified
using basic variant detection model within CLC Genomics Server
software v9.0.1.
[0064] Results. Of the nine genes, LAMC1 had eight SNP locations
which were either all heterozygous or homozygous for 56 out of the
63 patients. The full homozygote variant genotype was
overrepresented in patients with OM WHO score 1-4. While targeted
allelic sequencing confirmed the genotypes for the 56 patients, of
the 16 ambiguous SNP locations for remaining seven patients, 11
were corrected per conserved pattern. Indeed, one patient (WHO
score=1), who had five ambiguous SNP locations in LAMC1, was
confirmed having the full homozygote variant genotype. While SNP
correction was related to low DNA concentration, non-correction was
associated with lower DNA quality. Overall accuracy for the nine
genes, including 13 corrections, was 99.3%.
[0065] Conclusions. Targeted allelic sequencing is an effective
approach for confirming select SNPs prior to engaging into large
sample size investigation of SNPs associated with OM in HSCT
patients.
[0066] The foregoing is illustrative of the present invention, and
is not to be construed as limiting thereof. The invention is
defined by the following claims, with equivalents of the claims to
be included therein. All publications, patent applications,
patents, patent publications, sequences identified by GenBank
and/or SNP and/or EntrezID and/or any other accession numbers, and
other references cited herein are incorporated by reference in
their entireties for the teachings relevant to the sentence and/or
paragraph in which the reference is presented.
List of 309 intragenic SNVs and 209 corresponding genes:
TABLE-US-00002 ENTREZID SYMBOL beta p. val CHROM ID REF ALT 4735
SEPT2 -2.5767083 0.0099746 chr2 rs12477089 C A 24 ABCA4 2.9708532
0.0029697 chr1 rs2297634 T C 24 ABCA4 2.8819911 0.0039517 chr1
rs4847278 A G 4363 ABCC1 -2.7692145 0.0056192 chr16 rs246232 C G
125981 ACER1 2.9370196 0.0033138 chr19 rs72981971 T C 10880 ACTL7B
-3.0206808 0.0025221 chr9 rs11787880 A G 10880 ACTL7B 2.8236865
0.0047475 chr9 rs3750469 T C 170689 ADAMTS15 -2.7329452 0.0062771
chr11 rs731446 T C 105 ADARB2 2.8537339 0.0043209 chr10 rs4880498 T
G 84435 ADGRA1 2.5919747 0.0095427 chr10 rs9419103 C T 222611
ADGRF2 2.5979603 0.0093779 chr6 rs10948375 C T 222487 ADGRG3
-2.8196435 0.0048077 chr16 rs12444859 C T 84059 ADGRV1 2.6418998
0.0082442 chr5 rs41308293 A T 3267 AGFG1 3.1755816 0.0014954 chr2
rs4402755 A T 8659 ALDH4A1 -2.7495943 0.0059669 chr1 rs4592275 G A
51321 AMZ2 2.6265541 0.0086254 chr17 rs3213690 A G 286 ANK1
-2.8625479 0.0042025 chr8 rs7826127 T C 286 ANK1 -2.7174232
0.0065792 chr8 rs2304883 G A 286 ANK1 -2.5928753 0.0095177 chr8
rs2304871 G A 80831 APOL5 2.9853959 0.0028321 chr22 rs2076673 C G
80831 APOL5 2.8557877 0.004293 chr22 rs2076671 C T 9411 ARHGAP29
2.6815259 0.0073287 chr1 rs1048854 T C 10620 ARID3B -2.85784
0.0042654 chr15 .cndot. TACAC TAC, T 84239 ATP13A4 -2.6642603
0.0077158 chr3 rs61401139 G A 10079 ATP9A -2.7320009 0.0062951
chr20 rs2255341 C T 8313 AXIN2 2.6609294 0.0077925 chr17 rs28760438
A G 8313 AXIN2 2.6609294 0.0077925 chr17 rs1133683 G A 135152
B3GAT2 2.6167767 0.0088764 chr6 rs1320315 T C 145173 B3GLCT
-2.8012546 0.0050904 chr13 rs9564692 C T 60468 BACH2 2.6617085
0.0077745 chr6 rs10455512 T C 100129094 BTNL10 2.6349379 0.0084153
chr1 rs6665115 T C 64897 C12orf43 -2.5887247 0.0096332 chr12
rs2464195 G A 64897 C12orf43 -2.5887247 0.0096332 chr12 rs2259816 G
T 388381 C1701198 -2.6659294 0.0076776 chr17 rs597234 G A 57545
CC2D2A -2.6665465 0.0076635 chr4 rs28419165 C T 374864 CCDC178
-3.1703586 0.0015225 chr18 rs8087168 A T, * 84960 CCDC183 2.6561146
0.0079047 chr9 rs2784042 T C 79741 CCDC7 2.7106764 0.0067146 chr10
rs1977606 C G, CGG, * 80381 CD276 2.5807237 0.0098593 chr15
rs11574495 G A 8881 CDC16 -2.7495943 0.0059669 chr13 rs8002514 G A
8881 CDC16 -2.7495943 0.0059669 chr13 rs17337828 AT A 8881 CDC16
-2.7495943 0.0059669 chr13 rs373731427 TGCATCTCTTAAATA T TGTGTGA
5218 CDK14 -2.6918616 0.0071054 chr7 rs3814097 G A 1057 CELP
2.6507605 0.0080311 chr9 rs640502 G A 84131 CEP78 -2.8966494
0.0037717 chr9 rs10867166 G C 84131 CEP78 -2.8966494 0.0037717 chr9
rs13292584 G A 84131 CEP78 -2.6329381 0.008465 chr9 rs11137579 C T
9076 CLDN1 -2.5819011 0.0098258 chr3 rs17500920 T A 79745 CLIP4
-2.692565 0.0070905 chr2 rs3213947 A G 80790 CMIP -2.7056145
0.0068178 chr16 rs4889356 A G 26047 CNTNAP2 2.6246144 0.0086747
chr7 rs2074715 A G 150684 COMMD1 -2.6329381 0.008465 chr2
rs67059162 G A 9276 COPB2 2.6856931 0.007238 chr3 rs7373116 G A
1379 CR1L -3.1424532 0.0016754 chr1 rs2296158 A G 51232 CRIM1
-3.2737649 0.0010612 chr2 rs10181664 C T 51232 CRIM1 -3.136271
0.0017111 chr2 rs10180760 T G 51232 CRIM1 -2.9913185 0.0027778 chr2
rs10178965 G A 51232 CRIM1 -2.9366696 0.0033176 chr2 rs1533946 T C
51232 CRIM1 -2.7385584 0.0061709 chr2 rs10194100 T C 23191 CYFIP1
-3.0916991 0.0019901 chr15 rs3217548 AC A 91351 DDX60L -2.6432183
0.0082122 chr4 rs34009039 G GT, GTT 55526 DHTKD1 2.6113789
0.0090178 chr10 rs12416681 G A 27122 DKK3 2.7309057 0.0063161 chr11
rs67506856 C A 27120 DKKL1 2.6837226 0.0072807 chr19 rs11421569 A
AG 1741 DLG3 2.7555526 0.0058593 chrX rs3811371 A G 127602 DNAH14
3.1179197 0.0018213 chr1 rs630120 T C 127602 DNAH14 3.1179197
0.0018213 chr1 rs670255 G T 1793 DOCK1 2.6658964 0.0076783 chr10
rs2296636 C T 9980 DOPEY2 -2.9826662 0.0028575 chr21 rs9977791 C T
9980 DOPEY2 -2.9826662 0.0028575 chr21 rs9978057 G A 9980 DOPEY2
2.7309057 0.0063161 chr21 rs58117793 A AT 23167 EFR3A 2.6744301
0.0074856 chr8 rs2270875 A G 23167 EFR3A 2.6744301 0.0074856 chr8
rs8859 C G 2041 EPHA1 -3.2439307 0.0011789 chr7 rs45497499 A G 2041
EPHA1 -3.085143 0.0020345 chr7 rs1131885 T C 285965 EPHA1-AS1
2.7595525 0.0057881 chr7 rs117188605 G A 2066 ERBB4 -2.8015873
0.0050852 chr2 rs141267844 G GT 220081 ERICH6B -2.7692145 0.0056192
chr13 rs1536207 C A 56605 ERO1B 2.6663347 0.0076683 chr1 rs1269025
C T 2099 ESR1 -3.0029226 0.002674 chr6 rs1801132 G C 2131 EXT1
2.5988812 0.0093528 chr8 rs17439693 G A 2138 EYA1 -2.7204359
0.0065196 chr8 rs7846086 G A 2138 EYA1 -2.7204359 0.0065196 chr8
rs3735935 C A 158584 FAAH2 2.9244829 0.0034503 chrX rs5915052 T G
158584 FAAH2 2.8655162 0.0041633 chrX rs4030473 T A 221061 FAM171A1
2.7991092 0.0051244 chr10 rs6602828 C T 221061 FAM171A1 2.6744301
0.0074856 chr10 rs3814165 G A 23116 FAM179B 2.5919747 0.0095427
chr14 .cndot. AT A, ATT 26267 FBXO10 2.5781364 0.0099335 chr9
rs10973387 G A 654463 FER1L6 2.5781364 0.0099335 chr8 rs7820272 G A
9637 FEZ2 -3.1489465 0.0016386 chr2 rs2072533 A G 9637 FEZ2
-3.136271 0.0017111 chr2 rs2072534 G A 9637 FEZ2 -3.0965273
0.001958 chr2 rs11691767 G T 9637 FEZ2 -3.0561234 0.0022422 chr2
rs848638 C T 9637 FEZ2 -2.8753906 0.0040353 chr2 rs14291 T C 221472
FGD2 2.738796 0.0061665 chr6 rs75479065 C CT 121512 FGD4 2.5930064
0.0095141 chr12 .cndot. CT CTT, C, CTTT 2322 FLT3 2.867619
0.0041357 chr13 rs61944200 C T 2322 FLT3 2.6861202 0.0072287 chr13
rs9581971 C T 79025 FNDC11 -2.8966494 0.0037717 chr20 rs3746348 T C
79025 FNDC11 -2.7976388 0.0051478 chr20 rs734750 T C 202309 GAPT
-2.7811431 0.0054168 chr5 rs7704785 T C 202309 GAPT -2.7811431
0.0054168 chr5 rs1389308 T G 220032 GDPD4 2.5881572 0.0096491 chr11
rs4945161 G A 390637 GDPGP1 3.1318335 0.0017372 chr15 rs8025610 G C
390637 GDPGP1 2.9409025 0.0032726 chr15 rs10153004 C T 2733 GLE1
3.5275981 0.0004193 chr9 rs2275260 A G 59345 GNB4 -2.6317543
0.0084945 chr3 rs3774225 C T 2982 GUCY1A3 2.8970065 0.0037674 chr4
rs3796585 G A 2982 GUCY1A3 2.7516233 0.0059301 chr4 rs2306555 T A
3037 HAS2 -2.7148821 0.0066299 chr8 rs2028506 G C 55355 HJURP
-2.6152191 0.008917 chr2 rs2286430 C T 64342 HS1BP3 -2.7998216
0.0051131 chr2 rs10186292 C A 64342 HS1BP3 -2.729085 0.006351 chr2
rs2305460 G A, T 283284 IGSF22 2.738796 0.0061665 chr11 rs7106673 G
A 283284 IGSF22 2.738796 0.0061665 chr11 rs7125943 T C 283284
1GSF22 2.738796 0.0061665 chr11 rs4424652 C T 283284 IGSF22
2.738796 0.0061665 chr11 rs10766494 C T 22806 IKZF3 -2.7901787
0.0052679 chr17 rs1453559 T C 27178 IL37 3.0531476 0.0022645 chr2
rs3811047 A G 27178 IL37 2.6552232 0.0079256 chr2 rs3811045 T C
27178 IL37 2.6552232 0.0079256 chr2 rs3811046 G T 359948 IRF2BP2
-2.792731 0.0052265 chr1 rs4636 C A
3689 ITGB2 2.735279 0.0062327 chr21 rs7282201 G A 100505746
ITGB2-AS1 2.735279 0.0062327 chr21 rs12483718 C G 23189 KANK1
-2.6730359 0.0075168 chr9 rs10125507 G A 25962 K1AA1429 -2.7831611
0.0053832 chr8 rs1866844 T C 57614 K1AA1468 3.3453216 0.0008219
chr18 .cndot. CT C, CTT 85379 KIAA1671 -2.6702525 0.0075794 chr22
rs763279 G A 85379 KIAA1671 2.6541057 0.0079519 chr22 rs2330986 T G
9585 KIF2OB 3.269783 0.0010763 chr10 rs11185853 G A 9585 KIF2OB
3.2148563 0.0013051 chr10 rs144593231 C CTAAAAG 9585 KIF2OB
3.1613754 0.0015703 chr10 rs10881648 G T 9585 KIF2OB 3.1613754
0.0015703 chr10 rs2026549 A G 9585 KIF2OB 3.1613754 0.0015703 chr10
rs3824609 T C 9585 KIF2OB 3.0474634 0.0023078 chr10 rs7089473 T G
9585 KIF2OB 3.0474634 0.0023078 chr10 rs8181361 G A 9585 KIF2OB
3.0474634 0.0023078 chr10 rs1062465 T A 9585 KIF2OB 3.0474634
0.0023078 chr10 rs1886997 A G 9585 KIF2OB 3.0474634 0.0023078 chr10
rs1126480 A G 9585 KIF2OB 3.0142257 0.0025764 chr10 rs3758389 A T
9585 KIF2OB 2.9111774 0.0036007 chr10 rs1048057 A C 9585 K1F20B
2.591782 0.009548 chr10 rs10881632 A G 55083 KIF26B -2.9279094
0.0034125 chr1 rs12409851 C T 8609 KLF7 -2.9366696 0.0033176 chr2
rs2284934 C T 8609 KLF7 -2.7385584 0.0061709 chr2 rs768090 A T
387264 KRTAP5-1 -2.8643675 0.0041784 chill .cndot. ACCACAGCCACCCTTG
A GATCCCCCACAAGAG 387264 KRTAP5-1 -2.5855687 0.0097219 chill
rs80025267 T G,* 3915 LAMC1 2.9137985 0.0035706 chr1 rs10797854 G A
3915 LAMC1 2.9002164 0.0037291 chr1 rs20560 T C 3915 LAMC1
2.8375629 0.0045459 chr1 rs944970 T C 3915 LAMC1 2.7067296 0.006795
chr1 rs1062044 A G 3915 LAMC1 2.7067296 0.006795 chr1 rs944971 T C
3915 LAMC1 2.645959 0.008146 chr1 rs6424888 A G 3915 LAMC1 2.645959
0.008146 chr1 rs20563 A G 3915 LAMC1 2.6246144 0.0086747 chr1
rs2333620 T C 3937 LCP2 2.6113789 0.0090178 chr5 rs395407 G C 3988
LIPA -2.7038647 0.0068538 chr10 rs1051338 T G 643414 LIPK 3.0490129
0.0022959 chr10 rs415996 T G 643414 LIPK 2.9738969 0.0029404 chr10
rs376036 C T 643414 LIPK 2.9738969 0.0029404 chr10 rs432950 C T
643414 LIPK 2.9738969 0.0029404 chr10 rs390414 A T 643414 LIPK
2.9738969 0.0029404 chr10 rs406102 C A 643414 LIPK 2.9738969
0.0029404 chr10 rs427687 A G 643414 LIPK 2.8292695 0.0046654 chr10
rs11358016 GA G 4005 LMO2 2.6741038 0.0074929 chr11 rs2038602 A G
80856 LNPK 2.8285266 0.0046763 chr2 rs935492 C T 100506639
L0C100506 -2.6347851 0.0084191 chr5 rs11748187 C T 639 120892 LRRK2
2.6418998 0.0082442 chr12 rs7966550 T C 4046 LSP1 2.6837289
0.0072806 chr11 rs2089910 C T 28986 MAGEH1 2.711683 0.0066943 chrX
rs11545211 G A 6885 MAP3K7 2.6418998 0.0082442 chr6 .cndot. G GA
4163 MCC 2.9111647 0.0036008 chr5 rs113825892 GGTCACTGGGCA G 55669
MFN1 -2.6317543 0.0084945 chr3 rs73043490 C T 125170 MIEF2
2.8192567 0.0048135 chr17 rs80026520 CCCT C 100302233 M1R1268A
3.4516155 0.0005572 chr9 rs869455 G T 100302233 M1R1268A 2.9738969
0.0029404 chr9 rs3924786 T A 442905 M1R337 2.5879676 0.0096544
chr14 rs41286558 G A 100302277 M1R54812 2.8915656 0.0038333 chr4
rs111482845 TAGAAGG T 100302277 M1R54812 2.7261648 0.0064075 chr4
rs11728441 T C 389690 MR0H5 2.7018075 0.0068964 chr8 rs2748421 A G
389690 MR0H5 2.7018075 0.0068964 chr8 rs2613648 C T 389690 MR0H5
-2.7018075 0.0068964 chr8 rs11355664 TG T, TGG 56945 MRPS22
2.6856931 0.007238 chr3 rs10935321 G A 84437 MSANTD4 2.7193317
0.0065414 ch411 rs1043144 C T 283463 MUC19 -2.9586724 0.0030897
chr12 rs11564168 T C 283463 MUC19 -2.9586724 0.0030897 chr12
rs60890556 C CA 283463 MUC19 -2.9160475 0.003545 chr12 rs7139187 A
C 283463 MUC19 -2.8978491 0.0037573 chr12 rs7971316 G C 53904 MY03A
2.7235946 0.0064576 chr10 rs16926628 T C 53904 MY03A 2.6805577
0.00735 chr10 rs17739680 T C 4646 MY06 2.6418998 0.0082442 chr6
.cndot. G GA 8736 MYOM1 2.5979603 0.0093779 chr18 rs948298 G T
89795 NAV3 2.7235946 0.0064576 chr12 rs1731740 G C 10725 NFAT5
2.8575121 0.0042698 chr16 rs3826154 A G 4843 NOS2 2.9864431
0.0028224 chr17 rs2297518 G A 64067 NPAS3 2.9409025 0.0032726 chr14
rs3831102 T TC 255743 NPNT 2.6156026 0.008907 chr4 rs6817700 A G
2494 NR5A2 2.7585031 0.0058067 chr1 rs117679244 T G, * 203447 NRK
2.8329271 0.0046124 chrX rs58225635 G A 203447 NRK 2.6090081
0.0090805 chrX rs209373 G A 11164 NUDT5 2.7554841 0.0058605 chr10
rs150891932 GT G, GTT 11164 NUDT5 2.7545414 0.0058774 chr10
rs2272207 C T 128368 OR10Z1 3.1066582 0.0018922 chr1 rs2427808 A T
401666 OR51A4 2.7595525 0.0057881 chr11 rs2605301 A G 401666 OR51A4
2.735279 0.0062327 chr11 rs2595992 G T 5004 ORM1 2.9157173
0.0035487 chr9 rs147960186 G A 29948 OSGIN1 2.5879676 0.0096544
chr16 rs173776 A G 8974 P4HA2 2.9148398 0.0035587 chr5 rs154483 A G
5058 PAK1 2.6849305 0.0072545 chr11 rs51500 C T 53354 PANK1
2.9290917 0.0033995 chr10 rs11185826 C G 5101 PCDH9 2.7067296
0.006795 chr13 rs9571740 G A 5138 PDE2A -2.5773855 0.0099551 chr11
rs1980091 G A 5155 PDGFB -2.7398647 0.0061464 chr22 rs2239769 C T
8863 PER3 2.735279 0.0062327 chr1 rs10462021 A G 8863 PER3
2.6155844 0.0089075 chr1 rs2640909 T C 5208 PFKFB2 3.1154003
0.001837 chr1 rs2075863 G A 55276 PGM2 2.6054259 0.009176 chr4
rs3832307 AT A 23035 PHLPP2 2.6113789 0.0090178 chr16 rs61733127 A
G 118788 PIK3AP1 -2.5773855 0.0099551 chr10 rs3748231 C T 283748
PLA2G4D -2.8978491 0.0037573 chr15 rs12906547 T G 283748 PLA2G4D
-2.8978491 0.0037573 chr15 rs11635685 G C 283748 PLA2G4D -2.6659294
0.0076776 chr15 rs4924618 A T 151056 PLB1 3.1363171 0.0017108 chr2
rs1534478 C T 57475 PLEKHH1 2.7595525 0.0057881 chr14 rs3742873 G A
119548 PNLIPRP3 2.6617085 0.0077745 chr10 rs10749217 A C 55844
PPP2R2D -2.8734909 0.0040596 chr10 rs7894 G C 5558 PRIM2 -2.5919747
0.0095427 chr6 rs73752376 A G 26121 PRPF31 2.5885668 0.0096376
chr19 rs45513391 G A 23198 PSME4 -2.6606836 0.0077982 chr2 .cndot.
G GA 5794 PTPRH 2.6418998 0.0082442 chr19 rs111326663 G C 5794
PTPRH 2.6418998 0.0082442 chr19 rs2288520 G A 65997 RASL11B
2.6609294 0.0077925 chr4 rs11734439 C T 5968 REG1B 2.5942684
0.0094792 chr2 rs2073445 G T 84957 RELT 2.5885668 0.0096376 chr11
rs11826896 C T 8796 SCEL 2.7383078 0.0061756 chr13 rs9574090 T C
55681 SCYL2 2.9566681 0.0031098 chr12 rs11110340 A T 55176 SEC61A2
2.7545414 0.0058774 chr10 rs3780860 T C 26470 SEZ6L2 2.7309057
0.0063161 chr16 rs11649499 C G 51639 SF3B6 2.5919747 0.0095427 chr2
rs61742149 G A 84561 SLC12A8 -2.5859765 0.0097104 chr3 rs1574340 A
G 6570 SLC18A1 -2.5819011 0.0098258 chr8 rs2270637 C G 9389
SLC22A14 2.7098895 0.0067306 chr3 rs753330 T G 5002 SLC22A18
2.9480242 0.0031981 chr11 rs1048047 G A 126969 SLC44A3 3.1626232
0.0015635 chr1 rs17407097 A G 126969 SLC44A3 2.7991092 0.0051244
chr1 rs2640065 T C 9498 SLC4A8 -2.6281702 0.0085846 chr12
rs10783448 G A
113278 SLC52A3 -2.8966494 0.0037717 chr20 rs11273404 A ACAGGTCAAT
9152 SLC6A5 2.9409025 0.0032726 chill rs1443548 T C 9351 SLC9A3R2
-2.6730359 0.0075168 chr16 rs11876 C T 140775 SMCR8 2.8192567
0.0048135 chr17 rs12449313 A G 140775 SMCR8 2.8192567 0.0048135
chr17 rs2273029 G A 23293 SMG6 -2.8184381 0.0048258 chr17 rs216196
T C 26796 SNORD53 2.9347033 0.0033387 chr2 rs9653591 G T 26796
SNORD53 2.6598962 0.0078165 chr2 rs34113296 T G 51429 SNX9
-2.6809798 0.0073407 chr6 rs11324404 GA G 51429 SNX9 -2.668953
0.0076088 chr6 rs3211067 G A 80309 SPHKAP -2.8049331 0.0050327 chr2
rs4585022 G A 80309 SPHKAP -2.6473672 0.0081121 chr2 rs4353646 A G
6726 SRP9 2.6460429 0.0081439 chr1 rs4653433 A G 55808 ST6GALNA
-3.249793 0.0011549 chr17 rs2286595 C T C1 55808 ST6GALNA
-3.0039956 0.0026646 chr17 rs719430 T C C1 6489 ST8SIA1 -2.5819011
0.0098258 chr12 .cndot. G GA 442038 SULT1C3 -2.7495943 0.0059669
chr2 rs9308806 A C 26032 SUSD5 2.735279 0.0062327 chr3 rs4257493 G
A 26032 SUSD5 2.735279 0.0062327 chr3 rs61743511 G A 23345 SYNE1
2.7748317 0.005523 chr6 rs2296254 C T 23345 SYNE1 2.7748317
0.005523 chr6 rs36215566 T TA 143425 SYT9 -2.7028692 0.0068744
chr11 rs2035639 C G 23329 TBC1D30 2.6113789 0.0090178 chr12
rs61730726 A G 6929 TCF3 2.5942684 0.0094792 chr19 rs1140828 G A
8463 TEAD2 2.6837226 0.0072807 chr19 rs2303758 G T 83741 TFAP2D
-2.7377615 0.0061859 chr6 rs3765306 A G 57103 TIGAR -2.6230947
0.0087135 chr12 rs7296163 T C 8914 TIMELESS 2.9971308 0.0027253
chr12 rs66491720 G A 10430 TMEM147 2.8790953 0.0039882 chr19 rs7599
A G 56674 TMEM9B 2.6633559 0.0077366 chr11 .cndot. TAGGAAG GAGGAAG,
* 7156 TOP3A 2.8192567 0.0048135 chr17 rs3817992 C A 7156 TOP3A
2.8192567 0.0048135 chr17 rs2294913 C T 127262 TPRG1L -2.699407
0.0069463 chr1 rs147637374 GTTCTGGGAGCT G CCTCCCCC 162514 TRPV3
2.7437543 0.0060741 chr17 rs322937 T C 441631 TSPAN11 2.6418998
0.0082442 chr12 rs11051187 C T 54970 TTC12 2.7664373 0.0056672
chr11 rs723078 C G 145567 TTC7B -2.761318 0.0057569 chr14
rs10146731 C T 9690 UBE3C -2.5767083 0.0099746 chr7 rs7807 C A
29979 UBQLN1 -2.5767083 0.0099746 chr9 rs7866234 C A 54576 UGT1A8
2.9586092 0.0030903 chr2 rs6738678 C T, * 57663 USP29 2.6805577
0.00735 chr19 rs9973206 C A 7450 VWF 2.9566681 0.0031098 chr12
rs55867239 G A 7450 VWF 2.9566681 0.0031098 chr12 rs1053523 T C
7450 VWF -2.8015873 0.0050852 chr12 rs216902 G A 23160 WDR43
3.0439318 0.0023351 chr2 rs6715296 C G 100131176 WDR86-AS1
2.5899613 0.0095987 chr7 rs12533730 C T 80014 WWC2 -3.2172997
0.001294 chr4 rs3814422 G C 80014 WWC2 -3.0742807 0.0021101 chr4
rs2292414 C G 51741 WWOX 2.6493809 0.0080639 chr16 rs2288034 C G
51741 WWOX 2.6493809 0.0080639 chr16 rs2288033 T C 55432 YOD1
2.9036194 0.0036888 chr1 rs3790619 T G 55432 YOD1 2.8964843
0.0037737 chr1 rs2629665 C A 29799 YPEL1 -2.7524989 0.0059142 chr22
rs2236643 A G 7771 ZNF112 2.6856931 0.007238 chr19 rs2609880 T G
7771 ZNF112 2.6856931 0.007238 chr19 rs2722723 C G 7771 ZNF112
2.6856931 0.007238 chr19 rs2571104 T C 84911 ZNF382 2.6186037
0.008829 chr19 rs3108171 A G 90649 ZNF486 2.6518891 0.0080043 chr19
rs836897 C G 57711 ZNF529 2.8192567 0.0048135 chr19 rs3108598 T C
57711 ZNF529 2.7261648 0.0064075 chr19 rs3096618 C T 124626 ZPBP2
-2.7692145 0.0056192 chr17 rs11557467 G T 54764 ZRANB1 2.6636806
0.0077291 chr10 rs72416239 ACGCGCGCGCG ACG, ACGCG, ACGCGCG, ACGCG,
CGCG, A
z-scores for >20% variant allele predominance in Group 2-4
"HighMuc" versus Group 0-1 "LowMuc" for the ten genes: Example of
non-significant gene LIPK:
[0067] No significant predominance in Group 2-4 vs. Group 0-1 of
the variant allele
[0068] No significant z-score
[0069] No significant penetrance for any genotype
[0070] LIPK had seven SNPs with similar structure as LAMC1, i.e.
altogether homozygote for Ref or Alt alleles or altogether
heterozygous (3 combined genotypes possible)
This supports that LAMC1 is a true positive.
TABLE-US-00003 Non-significant gene LIPK Entrez ID 643414 Role
Lipoprotein Polymorphism rs415996 rs376036 rs432950 Reference REF C
GA C Variant ALT T G T Polymorphism rs390414 rs406102 rs427687
rs11358016 Reference REF A C T A Variant ALT T A G G CC CT TT
LowMUC 5.13% 30.77% 64.10% HighMuc 8.33% 62.50% 29.17% Predominance
No increase of the variant homozygous No significant increase of
the reference Assuming that heterozygous CT genotype would
represent Penetrance Group 2-4 OM 56% (too low) Penetrance OM score
1-4 (CT) 70% (too low)
* * * * *