U.S. patent application number 14/890712 was filed with the patent office on 2016-03-31 for variants of tnfsf15 and dcr3 associated with crohn's disease.
This patent application is currently assigned to CEDARS-SINAI MEDICAL CENTER. The applicant listed for this patent is CEDARS-SINAI MEDICAL CENTER. Invention is credited to Dermot P. McGovern.
Application Number | 20160090629 14/890712 |
Document ID | / |
Family ID | 51899024 |
Filed Date | 2016-03-31 |
United States Patent
Application |
20160090629 |
Kind Code |
A1 |
McGovern; Dermot P. |
March 31, 2016 |
VARIANTS OF TNFSF15 AND DCR3 ASSOCIATED WITH CROHN'S DISEASE
Abstract
Described herein are methods and compositions related to the
discovery of associations in TNFSF15 15 and DcR3 genetic loci
across in Caucasian, Puerto Rican, and Korean Crohn's Disease, as
demonstrated via trans-ethnic fine mapping. The present invention
provides methods of quantifying risk and diagnosing susceptibility
to Crohn's disease in a subject by determining the presence of one
or more risk variants are at the TNFSF15 (or TL1A) and/or DcR3
genetic loci.
Inventors: |
McGovern; Dermot P.; (Los
Angeles, CA) |
|
Applicant: |
Name |
City |
State |
Country |
Type |
CEDARS-SINAI MEDICAL CENTER |
Los Angeles |
CA |
US |
|
|
Assignee: |
CEDARS-SINAI MEDICAL CENTER
Los Angeles
CA
|
Family ID: |
51899024 |
Appl. No.: |
14/890712 |
Filed: |
May 16, 2014 |
PCT Filed: |
May 16, 2014 |
PCT NO: |
PCT/US14/38468 |
371 Date: |
November 12, 2015 |
Related U.S. Patent Documents
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Application
Number |
Filing Date |
Patent Number |
|
|
61824932 |
May 17, 2013 |
|
|
|
Current U.S.
Class: |
514/789 ;
435/6.11; 506/9 |
Current CPC
Class: |
A61P 1/04 20180101; C12Q
1/6883 20130101; C12Q 2600/118 20130101; C12Q 2600/156 20130101;
A61P 43/00 20180101; C12Q 2600/112 20130101; A61P 29/00 20180101;
C12Q 2600/172 20130101; A61P 37/06 20180101 |
International
Class: |
C12Q 1/68 20060101
C12Q001/68 |
Claims
1. An assay for quantifying risk in a subject to Crohn's disease
and/or fibrosis, comprising: obtaining a sample from a subject;
subjecting the sample to a genotyping assay adapted to determine
the presence or absence of one or more variants at the TNFSF15
and/or DcR3 genetic loci; and quantifying risk in a subject to
Crohn's disease and/or fibrosis based on the presence of one or
more variants at the TNFSF15 and/or DcR3genetic loci.
2. The method of claim 1, wherein the variants consist of one or
more variants selected from the group consisting of: SEQ ID NO. 1,
SEQ ID NO. 2, SEQ ID NO. 3, SEQ ID NO. 4, SEQ ID NO. 5, SEQ ID NO.
6, SEQ ID NO. 7, SEQ ID NO. 8, SEQ ID NO. 9, SEQ ID NO. 10, SEQ ID
NO. 11, SEQ ID NO. 12, SEQ ID NO. 13, SEQ ID NO. 14, SEQ ID NO. 15,
SEQ ID NO. 16, SEQ ID NO. 17, SEQ ID NO. 18, SEQ ID NO. 19, SEQ ID
NO. 20, SEQ ID NO. 21, SEQ ID NO. 22, SEQ ID NO. 23, SEQ ID NO. 24,
SEQ ID NO. 25, and SEQ ID NO. 26.
3. The method of claim 1, wherein the variants are SEQ ID NO. 3
and/or SEQ ID NO.13.
4. The method of claim 1, wherein the variant is SEQ ID NO. 22.
5. The method of claim 1, wherein the subject is non-Jewish
Caucasian, Ashkenazi, South Korean and/or Puerto Rican.
6. The method of claim 1, wherein the subject is South Korean and
the variant are SEQ ID NO. 3, SEQ ID NO.13 and/or SEQ ID NO.
22.
7. The method of claim 1, wherein the variant is a risk
variant.
8. The method of claim 1, wherein the variant is a protective
variant.
9. The method of claim 1, wherein the protective variant quantifies
a reduced risk in the subject for stricturing, CD, small bowel
involvement and/or need for surgical intervention.
10. A method of diagnosing susceptibility to Crohn's disease and/or
fibrosis in a subject, comprising: obtaining a sample from a
subject; subjecting the sample to a genotyping assay adapted to
determine the presence or absence of one or more variants at the
TNFSF15 and/or DcR3 genetic loci; and diagnosing susceptibility to
Crohn's disease and/or fibrosis in the subject based on the
presence of one or more variants at the TNFSF15 and/or DcR3 genetic
loci.
11. The method of claim 10, wherein the variants consist of one or
more variants selected from the group consisting of: SEQ ID NO. 1,
SEQ ID NO. 2, SEQ ID NO. 3, SEQ ID NO. 4, SEQ ID NO. 5, SEQ ID NO.
6, SEQ ID NO. 7, SEQ ID NO. 8, SEQ ID NO. 9, SEQ ID NO. 10, SEQ ID
NO. 11, SEQ ID NO. 12, SEQ ID NO. 13, SEQ ID NO. 14, SEQ ID NO. 15,
SEQ ID NO. 16, SEQ ID NO. 17, SEQ ID NO. 18, SEQ ID NO. 19, SEQ ID
NO. 20, SEQ ID NO. 21, SEQ ID NO. 22, SEQ ID NO. 23, SEQ ID NO. 24,
SEQ ID NO. 25, and SEQ ID NO. 26.
12. The method of claim 10, wherein the variants are SEQ ID NO. 3
and/or SEQ ID NO.13.
13. The method of claim 10, wherein the variant is SEQ ID NO.
22.
14. The method of claim 10, wherein the subject is non-Jewish
Caucasian, Ashkenazi, South Korean and/or Puerto Rican.
15. The method of claim 10, wherein the subject is South Korean and
the variant are SEQ ID NO. 3, SEQ ID NO.13 and/or SEQ ID NO.
22.
16. A method of treating Crohn's disease and/or fibrosis in a
subject, comprising: obtaining a sample from the subject;
subjecting the sample to a genotyping assay adapted to determine
the presence of one or more variants at the TNFSF15 and/or DcR3
genetic loci; and treating the Crohn's disease and/or fibrosis.
17. The method of claim 16, wherein the variants consist of one or
more variants selected from the group consisting of: SEQ ID NO. 1,
SEQ ID NO. 2, SEQ ID NO. 3, SEQ ID NO. 4, SEQ ID NO. 5, SEQ ID NO.
6, SEQ ID NO. 7, SEQ ID NO. 8, SEQ ID NO. 9, SEQ ID NO. 10, SEQ ID
NO. 11, SEQ ID NO. 12, SEQ ID NO. 13, SEQ ID NO. 14, SEQ ID NO. 15,
SEQ ID NO. 16, SEQ ID NO. 17, SEQ ID NO. 18, SEQ ID NO. 19, SEQ ID
NO. 20, SEQ ID NO. 21, SEQ ID NO. 22, SEQ ID NO. 23, SEQ ID NO. 24,
SEQ ID NO. 25, and SEQ ID NO. 26.
Description
CROSS-REFERENCE TO OTHER APPLICATIONS
[0001] This application includes a claim of priority under 35
U.S.C. .sctn.119(e) to U.S. provisional patent applications No.
61/824,932, filed May 17, 2013.
FIELD OF THE INVENTION
[0002] The claimed invention relates to prognosis, diagnosis and
treatment of inflammatory bowel disease and related conditions,
including methods and compositions for medical therapies.
BACKGROUND
[0003] All publications herein are incorporated by reference to the
same extent as if each individual publication or patent application
was specifically and individually indicated to be incorporated by
reference. The following description includes information that may
be useful in understanding the present invention. It is not an
admission that any of the information provided herein is prior art
or relevant to the presently claimed invention, or that any
publication specifically or implicitly referenced is prior art.
[0004] Inflammatory bowel disease (IBD) such as Crohn's disease
(CD) are chronic inflammatory conditions with pathological features
such as patchy transmural inflammation and fibrostenosis. Previous
studies show that TL1A may drive intestinal inflammation through
enhancing Th1, Th2 and Th17 effector function, TL1A appears to also
drive fibrogenesis through increased number of fibroblasts and
activated fibroblasts and constitutive TL1A expression in mice has
been found to confer worsened murine ileo-cecal inflammation, and
intestinal fibrostenosis.
[0005] SNPs of TL1A (TNFSF15), a TNF superfamily member, have been
found to be associated with IBD, and certain TNFSF15 haplotypes
have been found to be associated with increased TL1A expression and
have a higher risk of small bowel surgery. Decoy Receptor 3 (DcR3),
a known IBD susceptibility gene, is a decoy receptor that can
neutralize pro-inflammatory ligands including, TL1A (TNFSF15).
BRIEF DESCRIPTION OF THE FIGURES
[0006] Exemplary embodiments are illustrated in referenced figures.
It is intended that the embodiments and figures disclosed herein
are to be considered illustrative rather than restrictive.
[0007] FIG. 1 depicts, in accordance with embodiments herein,
principal component analysis (PC1/PC2).
[0008] FIG. 2 depicts, in accordance with embodiments herein, pACTs
of TNFSF15 region in NJ (Non-Jewish) and AJ (Ashkenazi Jewish)
CD.
[0009] FIG. 3 depicts, in accordance with embodiments herein, pACTs
of DcR3 (TNFRSF6B) region in NJ and AJ CD.
[0010] FIG. 4 depicts, in accordance with embodiments herein,
linkage disequilibrium maps (r.sup.2) of the associated TNFSF15
SNPs in NJ and SK.
SUMMARY OF THE INVENTION
[0011] Described herein is an assay for quantifying risk in a
subject to Crohn's disease and/or fibrosist, including obtaining a
sample from a subject, subjecting the sample to a genotyping assay
adapted to determine the presence or absence of one or more
variants at the TNFSF15 and/or DcR3 genetic loci, and quantifying
risk in a subject to Crohn's disease and/or fibrosis based on the
presence of one or more variants at the TNFSF15 and/or DcR3genetic
loci. In various embodiments, the variants include one or more
variants selected from the group including: SEQ ID NO. 1, SEQ ID
NO. 2, SEQ ID NO. 3, SEQ ID NO. 4, SEQ ID NO. 5, SEQ ID NO. 6, SEQ
ID NO. 7, SEQ ID NO. 8, SEQ ID NO. 9, SEQ ID NO. 10, SEQ ID NO. 11,
SEQ ID NO. 12, SEQ ID NO. 13, SEQ ID NO. 14, SEQ ID NO. 15, SEQ ID
NO. 16, SEQ ID NO. 17, SEQ ID NO. 18, SEQ ID NO. 19, SEQ ID NO. 20,
SEQ ID NO. 21, SEQ ID NO. 22, SEQ ID NO. 23, SEQ ID NO. 24, SEQ ID
NO. 25, and SEQ ID NO. 26. In other embodiments, the variants are
SEQ ID NO. 3 and/or SEQ ID NO.13. In other embodiments, the variant
is SEQ ID NO. 22. In other embodiments, the subject is non-Jewish
Caucasian, Ashkenazi, South Korean and/or Puerto Rican. In other
embodiments, the subject is South Korean and the variant are SEQ ID
NO. 3, SEQ ID NO.13 and/or SEQ ID NO. 22. In other embodiments, the
variant is a risk variant. In other embodiments, the variant is a
protective variant. In other embodiments, the protective variant
quantifies a reduced risk in the subject for structuring, CD, small
bowel involvement and/or need for surgical intervention.
[0012] Also described herein is a method of diagnosing
susceptibility to Crohn's disease and/or fibrosis in a subject,
including obtaining a sample from a subject, subjecting the sample
to a genotyping assay adapted to determine the presence or absence
of one or more variants at the TNFSF15 and/or DcR3 genetic loci,
and diagnosing susceptibility to Crohn's disease and/or fibrosis in
the subject based on the presence of one or more variants at the
TNFSF15 and/or DcR3 genetic loci. In other embodiments, variants
consist of one or more variants selected from the group including:
SEQ ID NO. 1, SEQ ID NO. 2, SEQ ID NO. 3, SEQ ID NO. 4, SEQ ID NO.
5, SEQ ID NO. 6, SEQ ID NO. 7, SEQ ID NO. 8, SEQ ID NO. 9, SEQ ID
NO. 10, SEQ ID NO. 11, SEQ ID NO. 12, SEQ ID NO. 13, SEQ ID NO. 14,
SEQ ID NO. 15, SEQ ID NO. 16, SEQ ID NO. 17, SEQ ID NO. 18, SEQ ID
NO. 19, SEQ ID NO. 20, SEQ ID NO. 21, SEQ ID NO. 22, SEQ ID NO. 23,
SEQ ID NO. 24, SEQ ID NO. 25, and SEQ ID NO. 26. In other
embodiments, variants are SEQ ID NO. 3 and/or SEQ ID NO.13. In
other embodiments, variant is SEQ ID NO. 22. In other embodiments,
subject is non-Jewish Caucasian, Ashkenazi, South Korean and/or
Puerto Rican. In other embodiments, subject is South Korean and the
variant are SEQ ID NO. 3, SEQ ID NO.13 and/or SEQ ID NO. 22.
[0013] Also described herein is a method of treating Crohn's
disease and/or fibrosis in a subject, including obtaining a sample
from the subject, subjecting the sample to a genotyping assay
adapted to determine the presence of one or more variants at the
TNFSF15 and/or DcR3 genetic loci, and treating the Crohn's disease
and/or fibrosis. In one embodiment, the variants consist of one or
more variants selected from the group including: SEQ ID NO. 1, SEQ
ID NO. 2, SEQ ID NO. 3, SEQ ID NO. 4, SEQ ID NO. 5, SEQ ID NO. 6,
SEQ ID NO. 7, SEQ ID NO. 8, SEQ ID NO. 9, SEQ ID NO. 10, SEQ ID NO.
11, SEQ ID NO. 12, SEQ ID NO. 13, SEQ ID NO. 14, SEQ ID NO. 15, SEQ
ID NO. 16, SEQ ID NO. 17, SEQ ID NO. 18, SEQ ID NO. 19, SEQ ID NO.
20, SEQ ID NO. 21, SEQ ID NO. 22, SEQ ID NO. 23, SEQ ID NO. 24, SEQ
ID NO. 25, and SEQ ID NO. 26.
DESCRIPTION OF THE INVENTION
[0014] All references cited herein are incorporated by reference in
their entirety as though fully set forth. Unless defined otherwise,
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 belongs. Allen et al., Remington: The Science and
Practice of Pharmacy 22.sup.nd ed., Pharmaceutical Press (Sep. 15,
2012); Hornyak et al., Introduction to Nanoscience and
Nanotechnology, CRC Press (2008); Singleton and Sainsbury,
Dictionary of Microbiology and Molecular Biology 3.sup.rd ed.,
revised ed., J. Wiley & Sons (New York, NY 2006); Smith,
March's Advanced Organic Chemistry Reactions, Mechanisms and
Structure 7.sup.th ed., J. Wiley & Sons (New York, NY 2013);
Singleton, Dictionary of DNA and Genome Technology 3.sup.rd ed.,
Wiley-Blackwell (Nov. 28, 2012); and Green and Sambrook, Molecular
Cloning: A Laboratory Manual 4th ed., Cold Spring Harbor Laboratory
Press (Cold Spring Harbor, N.Y. 2012), provide one skilled in the
art with a general guide to many of the terms used in the present
application. For references on how to prepare antibodies, see
Greenfield, Antibodies A Laboratory Manual 2.sup.nd ed., Cold
Spring Harbor Press (Cold Spring Harbor N.Y., 2013); Kohler and
Milstein, Derivation of specific antibody-producing tissue culture
and tumor lines by cell fusion, Eur. J. Immunol. 1976 July,
6(7):511-9; Queen and Selick, Humanized immunoglobulins, U.S. Pat.
No. 5,585,089 (1996 Dec); and Riechmann et al., Reshaping human
antibodies for therapy, Nature 1988 Mar. 24, 332(6162):323-7.
[0015] As disclosed herein, the inventors examined the effect of
T-helper pathway on TL1A induced colitis, and the effect of
T-helper pathway on TL1A induced gut fibrosis. A role for TL1A in
gut mucosal inflammation is highlighted by the finding that
neutralizing TL1A antibody prevented and treated chronic colitis in
mice. However, the contribution of either lymphoid or myeloid
derived TL1A to the development of gut inflammation is not fully
known. TL1A is the product of the TNFSF15 gene that is expressed by
both lymphoid and myeloid derived cells. Variants in the TNFSF15
gene have been found to be associated with IBD. The protein product
of TNFSF15, TL1A, is elevated in the intestinal mucosa of IBD
patients. Certain TNFSF15 haplotypes are associated with
susceptibility in non-Jewish Caucasian CD and UC. In addition,
TNFSF15 haplotype B is not only associated with risk, but also with
severity in Jewish CD patients. Moreover, monocytes from Jewish
patients carrying the risk haplotype B express higher levels of
TL1A in response to FcyR stimulation. These results show that CD
associated TNFSF15 genetic variations contribute to enhanced
induction of TL1A, resulting in severe, chronic mucosal
inflammation and that modulation of TL1A may be a potential target
for therapeutic development. TL1A signals via death domain receptor
3 (DR3) and several studies implicate the TL1A/DR3 signaling
pathway in mucosal inflammation. Neutralizing TL1A-antibody
ameliorates inflammation in DSS and G.alpha.i2-/- T cell transfer
chronic colitis models. Constitutive TL1A expression in mice leads
to mild spontaneous ileitis and increased collagen deposition. TL1A
modulates the adaptive immune response in the T-helper (Th)-1
effector arm, as shown by TL1A enhanced interferon (IFN)-.gamma.
production from peripheral and mucosal T-cells. TL1A is a TNF
superfamily member. Thus, in summary TNFSF15 SNPs are associated
with IBD, TNFSF15 haplotype B has increased TL1A expression with a
higher risk of small bowel surgery, and constitutive T11a
expression in mice confers worsened murine ileo-cecal inflammation
and intestinal fibrostenosis. While it is known TL1A can enhance
Th1, Th2, and Th17 effector cell function, it is poorly understood
which TL1A activated T-helper effector pathway induces intestinal
inflammation and fibrosis. Thus, a critical scientific question is
understanding the effect of T-helper pathway on TL1A induced
colitis and effect of T-helper pathway on TL1A induced gut
fibrosis.
[0016] As disclosed herein, the inventors performed trans-ethnic
fine mapping across TNFSF15 and DcR3 in Caucasian, Puerto Rican,
and Korean CD. The inventors identified associations with Non
Jewish Caucasian (NJ) Crohn's disease (CD) and rare TNFSF15
variants. This association is independent of previously reported
common variants. Also, these variants are much more common in the
South Korean (SK) population, and also associated with SK CD. DcR3
is significantly associated with NJ CD, a finding replicated in SK
and variation at this locus modifies stricturing phenotype.
[0017] Described herein is an assay for quantifying risk in a
subject to Crohn's disease and/or fibrosist, including obtaining a
sample from a subject, subjecting the sample to a genotyping assay
adapted to determine the presence or absence of one or more
variants at the TNFSF15 and/or DcR3 genetic loci, and quantifying
risk in a subject to Crohn's disease and/or fibrosis based on the
presence of one or more variants at the TNFSF15 and/or DcR3genetic
loci. In various embodiments, the variants include one or more
variants selected from the group including: SEQ ID NO. 1, SEQ ID
NO. 2, SEQ ID NO. 3, SEQ ID NO. 4, SEQ ID NO. 5, SEQ ID NO. 6, SEQ
ID NO. 7, SEQ ID NO. 8, SEQ ID NO. 9, SEQ ID NO. 10, SEQ ID NO. 11,
SEQ ID NO. 12, SEQ ID NO. 13, SEQ ID NO. 14, SEQ ID NO. 15, SEQ ID
NO. 16, SEQ ID NO. 17, SEQ ID NO. 18, SEQ ID NO. 19, SEQ ID NO. 20,
SEQ ID NO. 21, SEQ ID NO. 22, SEQ ID NO. 23, SEQ ID NO. 24, SEQ ID
NO. 25, and SEQ ID NO. 26. In other embodiments, the variants are
SEQ ID NO. 3 and/or SEQ ID NO.13. In other embodiments, the variant
is SEQ ID NO. 22. In other embodiments, the subject is non-Jewish
Caucasian, Ashkenazi, South Korean and/or Puerto Rican. In other
embodiments, the subject is South Korean and the variant are SEQ ID
NO. 3, SEQ ID NO.13 and/or SEQ ID NO. 22. In other embodiments, the
variant is a risk variant. In other embodiments, the variant is a
protective variant. In other embodiments, the protective variant
quantifies a reduced risk in the subject for structuring, CD, small
bowel involvement and/or need for surgical intervention.
[0018] Also described herein is a method of diagnosing
susceptibility to Crohn's disease and/or fibrosis in a subject,
including obtaining a sample from a subject, subjecting the sample
to a genotyping assay adapted to determine the presence or absence
of one or more variants at the TNFSF15 and/or DcR3 genetic loci,
and diagnosing susceptibility to Crohn's disease and/or fibrosis in
the subject based on the presence of one or more variants at the
TNFSF15 and/or DcR3 genetic loci. In other embodiments, variants
consist of one or more variants selected from the group including:
SEQ ID NO. 1, SEQ ID NO. 2, SEQ ID NO. 3, SEQ ID NO. 4, SEQ ID NO.
5, SEQ ID NO. 6, SEQ ID NO. 7, SEQ ID NO. 8, SEQ ID NO. 9, SEQ ID
NO. 10, SEQ ID NO. 11, SEQ ID NO. 12, SEQ ID NO. 13, SEQ ID NO. 14,
SEQ ID NO. 15, SEQ ID NO. 16, SEQ ID NO. 17, SEQ ID NO. 18, SEQ ID
NO. 19, SEQ ID NO. 20, SEQ ID NO. 21, SEQ ID NO. 22, SEQ ID NO. 23,
SEQ ID NO. 24, SEQ ID NO. 25, and SEQ ID NO. 26. In other
embodiments, variants are SEQ ID NO. 3 and/or SEQ ID NO.13. In
other embodiments, variant is SEQ ID NO. 22. In other embodiments,
subject is non-Jewish Caucasian, Ashkenazi, South Korean and/or
Puerto Rican. In other embodiments, subject is South Korean and the
variant are SEQ ID NO. 3, SEQ ID NO.13 and/or SEQ ID NO. 22.
[0019] Also described herein is a method of treating Crohn's
disease and/or fibrosis in a subject, including obtaining a sample
from the subject, subjecting the sample to a genotyping assay
adapted to determine the presence of one or more variants at the
TNFSF15 and/or DcR3 genetic loci, and treating the Crohn's disease
and/or fibrosis. In one embodiment, the variants consist of one or
more variants selected from the group including: SEQ ID NO. 1, SEQ
ID NO. 2, SEQ ID NO. 3, SEQ ID NO. 4, SEQ ID NO. 5, SEQ ID NO. 6,
SEQ ID NO. 7, SEQ ID NO. 8, SEQ ID NO. 9, SEQ ID NO. 10, SEQ ID NO.
11, SEQ ID NO. 12, SEQ ID NO. 13, SEQ ID NO. 14, SEQ ID NO. 15, SEQ
ID NO. 16, SEQ ID NO. 17, SEQ ID NO. 18, SEQ ID NO. 19, SEQ ID NO.
20, SEQ ID NO. 21, SEQ ID NO. 22, SEQ ID NO. 23, SEQ ID NO. 24, SEQ
ID NO. 25, and SEQ ID NO. 26.
[0020] In one embodiment, the present invention provides a method
of diagnosing susceptibility to Crohn's disease in a subject by
obtaining a sample from the subject, assaying the sample to
determine the presence or absence of one or more risk variants in
the subject, and diagnosing susceptibility to Crohn's disease based
on the presence of one or more risk variants. In another
embodiment, the one or more risk variants are at the TNFSF15 and/or
DcR3 genetic loci. In another embodiment, the one or more risk
variants are described in Tables 2 and 3 herein. In another
embodiment, the subject is Caucasian, Puerto Rican, or South
Korean. In another embodiment, the subject is Non-Caucasian.
[0021] In one embodiment, the present invention provides a method
of diagnosing a Crohn's disease subtype in a subject by obtaining a
sample from the subject, assaying the sample to determine the
presence or absence of one or more risk variants in the subject,
and diagnosing the Crohn's disease subtype based on the presence of
one or more risk variants. In another embodiment, the one or more
risk variants are at the TNFSF15 and/or DcR3 genetic loci. In
another embodiment, the one or more risk variants are described in
Tables 2 and 3 herein. In another embodiment, the subject is
Caucasian, Puerto Rican, or South Korean. In another embodiment,
the subject is Non-Caucasian.
[0022] In one embodiment, the present invention provides a method
of treating Crohn's disease in a subject by determining the
presence of one or more one or more risk variants in the subject,
and treating the subject. In another embodiment, the one or more
risk variants are at the TNFSF15 and/or DcR3 genetic loci. In
another embodiment, the one or more risk variants are described in
Tables 2 and 3 herein. In another embodiment, the subject is
Caucasian, Puerto Rican, or South Korean. In another embodiment,
the subject is Non-Caucasian.
[0023] In one embodiment, the present invention provides a method
of diagnosing susceptibility to fibrosis in a subject by obtaining
a sample from the subject, assaying the sample to determine the
presence or absence of one or more risk variants in the subject,
and diagnosing susceptibility to fibrosis based on the presence of
one or more risk variants. In another embodiment, the one or more
risk variants are at the TNFSF15 and/or DcR3 genetic loci. In
another embodiment, the one or more risk variants are described in
Tables 2 and 3 herein. In another embodiment, the subject is
Caucasian, Puerto Rican, or South Korean. In another embodiment,
the subject is Non-Caucasian.
[0024] In one embodiment, the present invention provides a method
of diagnosing a fibrosis subtype in a subject by obtaining a sample
from the subject, assaying the sample to determine the presence or
absence of one or more risk variants in the subject, and diagnosing
the fibrosis subtype based on the presence of one or more risk
variants. In another embodiment, the one or more risk variants are
at the TNFSF15 and/or DcR3 genetic loci. In another embodiment, the
one or more risk variants are described in Tables 2 and 3 herein.
In another embodiment, the subject is Caucasian, Puerto Rican, or
South Korean. In another embodiment, the subject is
Non-Caucasian.
[0025] In one embodiment, the present invention provides a method
of treating fibrosis in a subject by determining the presence of
one or more one or more risk variants in the subject, and treating
the subject. In another embodiment, the one or more risk variants
are at the TNFSF15 and/or DcR3 genetic loci. In another embodiment,
the one or more risk variants are described in Tables 2 and 3
herein. In another embodiment, the subject is Caucasian, Puerto
Rican, or South Korean. In another embodiment, the subject is
Non-Caucasian.
[0026] The various methods and techniques described above provide a
number of ways to carry out the invention. Of course, it is to be
understood that not necessarily all objectives or advantages
described may be achieved in accordance with any particular
embodiment described herein. Thus, for example, those skilled in
the art will recognize that the methods can be performed in a
manner that achieves or optimizes one advantage or group of
advantages as taught herein without necessarily achieving other
objectives or advantages as may be taught or suggested herein. A
variety of advantageous and disadvantageous alternatives are
mentioned herein. It is to be understood that some preferred
embodiments specifically include one, another, or several
advantageous features, while others specifically exclude one,
another, or several disadvantageous features, while still others
specifically mitigate a present disadvantageous feature by
inclusion of one, another, or several advantageous features.
[0027] Furthermore, the skilled artisan will recognize the
applicability of various features from different embodiments.
Similarly, the various elements, features and steps discussed
above, as well as other known equivalents for each such element,
feature or step, can be mixed and matched by one of ordinary skill
in this art to perform methods in accordance with principles
described herein. Among the various elements, features, and steps
some will be specifically included and others specifically excluded
in diverse embodiments.
[0028] Although the invention has been disclosed in the context of
certain embodiments and examples, it will be understood by those
skilled in the art that the embodiments of the invention extend
beyond the specifically disclosed embodiments to other alternative
embodiments and/or uses and modifications and equivalents
thereof.
[0029] Many variations and alternative elements have been disclosed
in embodiments of the present invention. Still further variations
and alternate elements will be apparent to one of skill in the art.
Among these variations, without limitation, are the selection of
constituent modules for the inventive compositions, and the
diseases and other clinical conditions that may be diagnosed,
prognosed or treated therewith. Various embodiments of the
invention can specifically include or exclude any of these
variations or elements.
[0030] In some embodiments, the numbers expressing quantities of
ingredients, properties such as concentration, reaction conditions,
and so forth, used to describe and claim certain embodiments of the
invention are to be understood as being modified in some instances
by the term "about." Accordingly, in some embodiments, the
numerical parameters set forth in the written description and
attached claims are approximations that can vary depending upon the
desired properties sought to be obtained by a particular
embodiment. In some embodiments, the numerical parameters should be
construed in light of the number of reported significant digits and
by applying ordinary rounding techniques. Notwithstanding that the
numerical ranges and parameters setting forth the broad scope of
some embodiments of the invention are approximations, the numerical
values set forth in the specific examples are reported as precisely
as practicable. The numerical values presented in some embodiments
of the invention may contain certain errors necessarily resulting
from the standard deviation found in their respective testing
measurements.
[0031] In some embodiments, the terms "a" and "an" and "the" and
similar references used in the context of describing a particular
embodiment of the invention (especially in the context of certain
of the following claims) can be construed to cover both the
singular and the plural. The recitation of ranges of values herein
is merely intended to serve as a shorthand method of referring
individually to each separate value falling within the range.
Unless otherwise indicated herein, each individual value is
incorporated into the specification as if it were individually
recited herein. All methods described herein can be performed in
any suitable order unless otherwise indicated herein or otherwise
clearly contradicted by context. The use of any and all examples,
or exemplary language (e.g. "such as") provided with respect to
certain embodiments herein is intended merely to better illuminate
the invention and does not pose a limitation on the scope of the
invention otherwise claimed. No language in the specification
should be construed as indicating any non-claimed element essential
to the practice of the invention.
[0032] Groupings of alternative elements or embodiments of the
invention disclosed herein are not to be construed as limitations.
Each group member can be referred to and claimed individually or in
any combination with other members of the group or other elements
found herein. One or more members of a group can be included in, or
deleted from, a group for reasons of convenience and/or
patentability. When any such inclusion or deletion occurs, the
specification is herein deemed to contain the group as modified
thus fulfilling the written description of all Markush groups used
in the appended claims.
[0033] Preferred embodiments of this invention are described
herein, including the best mode known to the inventors for carrying
out the invention. Variations on those preferred embodiments will
become apparent to those of ordinary skill in the art upon reading
the foregoing description. It is contemplated that skilled artisans
can employ such variations as appropriate, and the invention can be
practiced otherwise than specifically described herein.
Accordingly, many embodiments of this invention include all
modifications and equivalents of the subject matter recited in the
claims appended hereto as permitted by applicable law. Moreover,
any combination of the above-described elements in all possible
variations thereof is encompassed by the invention unless otherwise
indicated herein or otherwise clearly contradicted by context.
[0034] Furthermore, numerous references have been made to patents
and printed publications throughout this specification. Each of the
above cited references and printed publications are herein
individually incorporated by reference in their entirety.
[0035] In closing, it is to be understood that the embodiments of
the invention disclosed herein are illustrative of the principles
of the present invention. Other modifications that can be employed
can be within the scope of the invention. Thus, by way of example,
but not of limitation, alternative configurations of the present
invention can be utilized in accordance with the teachings herein.
Accordingly, embodiments of the present invention are not limited
to that precisely as shown and described.
EXAMPLES
[0036] The following examples are provided to better illustrate the
claimed invention and are not to be interpreted as limiting the
scope of the invention. To the extent that specific materials are
mentioned, it is merely for purposes of illustration and is not
intended to limit the invention. One skilled in the art may develop
equivalent means or reactants without the exercise of inventive
capacity and without departing from the scope of the invention.
Example 1
Methods
[0037] The inventors performed trans-ethnic fine mapping across
TNFSF15 and DcR3 in Caucasian, Puerto Rican (PR) and South Korean
(SK) CD. Immunochip genotyping as performed on the following
populations presented in Table 1.
TABLE-US-00001 TABLE 1 Study subjects by ethnicity Population CD
Control Non-Jewish Caucasian (NJ) 779 4182 Ashkenazi Jewish (AJ)
492 395 Puerto Rican (PR) 300 235 South Korean (SK) 729 469
[0038] To measure association of TNFSF15 (416 SNPs) and DcR3 (13
SNPs),logistic regression was applied after controlling for
population structure using principal component analysis (PCA) (FIG.
1). The result pACTs function corrects for multiple testing. A
value of pACTs <0.05 was considered as statistically
significant. Thereafter, population attributable risk (PAR) of the
associated TNFSF15-DcR3 pathway SNPs was calculated in each
population, the results of which are shown in Tables 2-4.
TABLE-US-00002 TABLE 2 SNPs associated with NJ CD. (pACTs <
0.05) Allele 1 Frequency SNP dbSNP Location A1 A2 CD Control
P-Values pACT Odds Ratio Rare variants TNFSF15-130 rs4979462 INTRON
T C 0.64% 0.11% 4.89E-05 7.76E-03 6.62 [SEQ ID NO. 1] TNFSF15-150
rs55768522 INTERGENIC A G 0.58% 0.07% 4.12E-05 6.63E-03 8.95 [SEQ
ID NO. 2] TNFSF15-160 rs1322057 INTERGENIC G A 0.83% 0.13% 3.02E-06
5.23E-04 6.97 [SEQ ID NO. 3] TNFSF15-271 rs76779588 INTERGENIC T C
0.64% 0.11% 4.48E-05 7.14E-03 6.70 [SEQ ID NO. 4] Common variants
TNFSF15-90 rs4574921 INTERGENIC T C 77.3% 72.3% 5.31E-05 8.38E-03
1.30 [SEQ ID NO. 5] TNFSF15-106 rs10114470 INTERGENIC C T 72.2%
67.0% 7.98E-05 1.24E-02 1.27 [SEQ ID NO. 6] TNFSF15-110 rs3810936
CODING(SYN) C T 72.1% 67.1% 1.42E-04 2.14E-02 1.26 [SEQ ID NO. 7]
TNFSF15-111 rs4246905 INTRON C T 74.9% 69.9% 1.07E-04 1.61E-02 1.28
[SEQ ID NO. 8] TNFSF15-120 rs6478108 INTRON T C 70.2% 65.1%
1.11E-04 1.66E-02 1.26 [SEQ ID NO. 9] TNFSF15-134 rs6478109
INTERGENIC G A 71.0% 66.3% 3.25E-04 4.60E-02 1.24 [SEQ ID NO. 10]
TNFSF15-137 rs7848647 INTERGENIC C T 71.2% 66.3% 1.55E-04 2.33E-02
1.26 [SEQ ID NO. 11] TNFSF15-144 rs59418409 INTERGENIC I D 74.3%
69.2% 1.05E-04 1.61E-02 1.27 [SEQ ID NO. 12] TNFSF15-164 rs7869487
INTERGENIC T C 72.8% 67.6% 7.26E-05 1.12E-02 1.28 [SEQ ID NO.
13]
TABLE-US-00003 TABLE 3 Association results of DcR3 gene in NJ CD
Allele 1 Frequency SNP dbSNP Gene Location A1 A2 CD Control
P-Values pACT Odds Ratio DcR3-1 rs6011033 RTEL1 INTRON G A 79.6%
78.0% 1.27E-01 5.90E-01 1.11 [SEQ ID NO. 14] DcR3-2 rs80132799
RTEL1 INTRON C T 93.6% 93.3% 6.93E-01 6.93E-01 1.05 [SEQ ID NO. 15]
DcR3-3 rs34412639 RTEL1 INTRON C A 99.6% 99.3% 1.43E-01 5.07E-01
1.88 [SEQ ID NO. 16] DcR3-4 rs2236507 RTEL1 INTRON C G 79.4% 77.3%
5.35E-02 3.23E-01 1.14 [SEQ ID NO. 17] DcR3-5 rs74506932 RTEL1
INTRON T C 1.80% 1.58% 5.28E-01 7.76E-01 1.14 [SEQ ID NO. 18]
DcR3-6 rs2738787 TNFRSF6B CODING G A 92.5% 91.7% 3.36E-01 6.54E-01
1.11 [SEQ ID NO. 19] DcR3-7 rs55765053 TNFRSF6B CODING T C 8.09%
7.08% 1.34E-01 5.52E-01 1.17 [SEQ ID NO. 20] DcR3-8 rs1291205
TNFRSF6B CODING C G 78.4% 76.2% 5.02E-02 3.09E-01 1.14 [SEQ ID NO.
21] DcR3-9 rs6062496 TNFRSF6B INTRON A G 59.3% 54.8% 5.83E-04
4.93E-03 1.22 [SEQ ID NO. 22] DcR3-10 rs1291206 TNFRSF6B INTRON G A
78.4% 76.2% 4.88E-02 3.02E-01 1.14 [SEQ ID NO. 23] DcR3-11
rs1291208 ARFRP1 INTRON C T 92.4% 91.7% 3.66E-01 6.87E-01 1.10 [SEQ
ID NO. 24] DcR3-12 rs2738788 ARFRP1 INTRON A G 0.19% 0.07% 1.70E-01
4.87E-01 2.67 [SEQ ID NO. 25] DcR3-13 rs2236508 ARFRP1 INTRON G A
78.6% 76.7% 8.49E-02 4.60E-01 1.12 [SEQ ID NO. 26]
TABLE-US-00004 TABLE 4A Trans-ethnic allele frequences and results
in SNPs associated with NJ-CD NJ AJ PR SK SNP CD Ctrl CD Ctrl CD
Ctrl CD Ctrl Rare Variants of TNFSF15 TNFSF15-130 0.64% 0.11% 2.34%
2.28% 14.0% 11.1% 52.7% 34.5% TNFSF15-150 0.58% 0.07% 2.24% 2.03%
8.50% 5.11% 52.6% 34.4% TNFSF15-160 0.83% 0.13% 2.34% 2.78% 10.2%
6.60% 52.7% 34.6% TNFSF15-271 0.64% 0.11% 2.34% 2.15% 8.00% 4.26%
44.9% 31.8% Common Variants of TNFSF15 TNFSF15-90 77.3% 72.3% 77.7%
79.9% 83.2% 81.1% 79.6% 64.7% TNFSF15-106 72.2% 67.0% 73.9% 77.0%
77.5% 77.4% 68.9% 49.9% TNFSF15-110 72.1% 67.1% 74.1% 77.2% 77.3%
77.7% 68.5% 49.8% TNFSF15-111 74.9% 69.9% 77.3% 79.1% 82.3% 79.8%
80.5% 65.9% TNFSF15-120 70.2% 65.1% 75.2% 77.7% 77.8% 77.0% 71.5%
51.3% TNFSF15-134 71.2% 66.3% 78.7% 80.0% 79.5% 76.6% 71.7% 51.8%
TNFSF15-137 71.0% 66.3% 78.6% 79.2% 79.3% 77.0% 71.7% 51.8%
TNFSF15-144 74.3% 69.2% 81.9% 82.5% 83.3% 79.1% 77.3% 59.1%
TNFSF15-164 72.8% 67.6% 80.3% 81.1% 83.0% 79.1% 77.4% 59.1% DcR3
variant DcR3-9 59.3% 54.8% 67.1% 64.3% 60.5% 57.0% 17.6% 14.3%
TABLE-US-00005 TABLE 4B Trans-ethnic allele frequences and results
in SNPs associated with NJ-CD NJ AJ PR SK SNP CD Ctrl CD Ctrl CD
Ctrl CD Ctrl Rare Variants of TNFSF15 TNFSF15-130 4.89E-05 8.70E-01
1.54E-01 6.92E-17 6.62 1.05 1.31 2.10 TNFSF15-150 4.12E-05 7.23E-01
3.10E-02 5.28E-17 8.95 1.13 1.75 2.12 TNFSF15-160 3.02E-06 5.81E-01
3.19E-02 8.66E-17 6.97 0.84 1.67 2.10 TNFSF15-271 4.48E-05 7.99E-01
1.25E-02 3.15E-10 6.70 1.09 2.02 1.76 Common Variants of TNFSF15
TNFSF15-90 5.31E-05 2.92E-01 3.70E-01 5.70E-16 1.30 0.88 1.15 2.26
TNFSF15-106 7.98E-05 1.34E-01 9.96E-01 2.52E-19 1.27 0.84 1.00 2.26
TNFSF15-110 1.42E-04 1.29E-01 8.91E-01 4.03E-19 1.26 0.84 0.98 2.25
TNFSF15-111 1.07E-04 3.90E-01 3.06E-01 5.83E-16 1.28 0.90 1.17 2.30
TNFSF15-120 1.11E-04 2.49E-01 7.65E-01 4.71E-22 1.26 0.88 1.04 2.46
TNFSF15-134 1.55E-04 5.83E-01 2.74E-01 1.69E-21 1.26 0.94 1.17 2.42
TNFSF15-137 3.25E-04 8.34E-01 3.84E-01 1.69E-21 1.24 0.98 1.14 2.42
TNFSF15-144 1.05E-04 8.59E-01 9.14E-02 3.24E-21 1.27 0.98 1.29 2.55
TNFSF15-164 7.26E-05 7.69E-01 1.24E-01 1.98E-21 1.28 0.96 1.26 2.56
DcR3 variant DcR3-9 5.83E-04 1.51E-01 2.49E-01 2.01E-02 1.22 1.16
1.16 1.32
TABLE-US-00006 TABLE 5 Conditional analysis of the associated
TNFSF15 SNPs in NJ CD and SK CD P-value P-value on SNP 160 P-value
on SNP 164 P-value on SNP 160&164 SNP NJ SK NJ SK NJ SK NJ SK
Rare Variants of TNFSF15 TNFSF15-130 4.89E-05 6.92E-17 8.18E-01
4.82E-01 1.12E-04 9.39E-04 7.83E-01 6.17E-01 TNFSF15-150 4.12E-05
5.28E-17 4.37E-01 2.30E-01 9.92E-05 7.68E-04 4.87E-01 2.73E-01
TNFSF15-160 3.02E-06 8.66E-17 -- -- 7.83E-06 1.07E-03 -- --
TNFSF15-271 4.48E-05 3.15E-10 8.11E-01 4.46E-01 1.04E-04 4.38E-02
8.47E-01 5.84E-01 Common Variants of TNFSF15 TNFSF15-90 5.31E-05
5.70E-16 1.07E-04 3.46E-06 1.10E-01 4.34E-01 1.20E-01 4.63E-01
TNFSF15-106 7.98E-05 2.52E-19 1.75E-04 1.87E-06 1.61E-01 7.18E-04
1.87E-01 2.51E-02 TNFSF15-110 1.42E-04 4.03E-19 3.05E-04 2.95E-06
2.42E-01 1.16E-03 2.77E-01 3.78E-02 TNFSF15-111 1.05E-04 5.83E-16
2.09E-04 4.32E-06 2.69E-01 5.35E-01 2.81E-01 5.65E-01 TNFSF15-120
1.11E-04 4.71E-22 2.54E-04 3.38E-08 6.21E-01 1.94E-03 6.91E-01
6.24E-02 TNFSF15-134 3.25E-04 1.69E-21 5.02E-04 1.18E-07 8.35E-01
6.14E-03 7.55E-01 1.49E-01 TNFSF15-137 1.55E-04 1.69E-21 3.38E-04
1.18E-07 5.28E-01 6.14E-03 5.81E-01 1.49E-01 TNFSF15-144 1.07E-04
3.24E-21 2.09E-04 1.99E-08 8.08E-01 7.98E-01 7.88E-01 5.37E-01
TNFSF15-164 7.26E-05 1.98E-21 1.54E-04 1.12E-08 -- -- -- --
TABLE-US-00007 TABLE 6 Su results of DcR3 gene in NJ CD n CD Risk
Allele Freq SNP Phenotype (+) (-) (+) (-) P-Value Odds Ratio DcR3-9
Surgery 323 248 56.7% 62.9% 3.62E-02 0.77 DcR3-9 Stricturing CD
(B2) 229 293 56.1% 63.3% 2.95E-02 0.75 DcR3-9 SB involvement (L1 +
L3) 460 98 57.6% 66.3% 2.26E-02 0.68
TABLE-US-00008 TABLE 7 G .times. G interaction analysis with
TNFSF15 and DcR3 P-values (SNP .times. SNP) SNP NJ CD SK CD DcR3-9
TNFSF15_160 0.175 0.607 TNFSF15_164 0.523 0.742
TABLE-US-00009 TABLE 8 Population attributable risk of TNFSF15-DcR3
SNPs SNP Gene NJ CD SK CD TNFSF15-160 TNFSF15 1.4% 41.4%
TNFSF15-164 TNFSF15 17.0% 70.8% DcR3-9 DcR3 20.5% 9.0% TNFSF15-DCR3
3 SNPs -- 32.3% 76.4%
Example 3
TNFSF 15 Analysis
[0039] As shown by the above results, 4 rare variants and 9 common
variants were significantly associated with NJ CD (Table 2). All 13
associations were replicated in SK CD (Table 4), but the rare
variants were much more common in the SK population.
[0040] Importantly, the `rare` and `common` variants can each be
tagged by a single SNP (SNP160 & SNP164 respectively) in both
NJ and SK. (Table 5,FIG. 4) The `rare` variants were associated
with CD in PR (at higher allele frequency). No association was seen
in PR with the common variants. (Table 4). No significant SNP
associations were observed in AJ CD. (FIG. 2, Table 4). After
correcting for multiple comparisons there were no significant
associations with rare or common CD-associated SNPs with clinical
subphenotypes in NJ CD.
Example 4
DcR3 Analysis
[0041] The above results further indicated that rs6062496 in intron
6 was significantly associated with NJ CD. (FIG. 3, Table3). The
association was confirmed in SK CD, but not in PR and AJ CD. (Table
4). It was further identified that rs6062496 also associated with
protection against stricturing CD, small bowel involvement and need
for surgery (Table 6).
Example 5
TNFSF1 5-DcR3 Analysis
[0042] The above results further suggest no significant DcR3 and
TNFSF15 gene-gene interactions in NJ and SK. (Table 7). The PAR by
TNFSF15-DcR3 pathway was 32.3% in NJ CD. (Table 8). The PAR by
TNFSF15 variants in SK was the highest seen in either population
explaining the dominant effect of this locus in Asian CD (Table
8)
Example 6
Conclusions
[0043] Based on the described results, the inventors identified
associations with NJ CD and rare TNFSF15 variants. This association
is independent of previously reported common variants. These
variants are much more common in the SK population, and also
associated with SK CD. DcR3 is significantly associated with NJ CD,
a finding replicated in SK and variation at this locus modifies
stricturing phenotype.
[0044] The various methods and techniques described above provide a
number of ways to carry out the invention. Of course, it is to be
understood that not necessarily all objectives or advantages
described may be achieved in accordance with any particular
embodiment described herein. Thus, for example, those skilled in
the art will recognize that the methods can be performed in a
manner that achieves or optimizes one advantage or group of
advantages as taught herein without necessarily achieving other
objectives or advantages as may be taught or suggested herein. A
variety of advantageous and disadvantageous alternatives are
mentioned herein. It is to be understood that some preferred
embodiments specifically include one, another, or several
advantageous features, while others specifically exclude one,
another, or several disadvantageous features, while still others
specifically mitigate a present disadvantageous feature by
inclusion of one, another, or several advantageous features.
[0045] Furthermore, the skilled artisan will recognize the
applicability of various features from different embodiments.
Similarly, the various elements, features and steps discussed
above, as well as other known equivalents for each such element,
feature or step, can be mixed and matched by one of ordinary skill
in this art to perform methods in accordance with principles
described herein. Among the various elements, features, and steps
some will be specifically included and others specifically excluded
in diverse embodiments.
[0046] Although the invention has been disclosed in the context of
certain embodiments and examples, it will be understood by those
skilled in the art that the embodiments of the invention extend
beyond the specifically disclosed embodiments to other alternative
embodiments and/or uses and modifications and equivalents
thereof.
[0047] Many variations and alternative elements have been disclosed
in embodiments of the present invention. Still further variations
and alternate elements will be apparent to one of skill in the art.
Among these variations, without limitation, are the methods of
prognosis and diagnosis for inflammatory bowel disease related
diseases and/or conditions, compositions of generated by the
aforementioned techniques, treatment of diseases and/or conditions
that relate to the teachings of the invention, techniques and
composition and use of solutions used therein, and the particular
use of the products created through the teachings of the invention.
Various embodiments of the invention can specifically include or
exclude any of these variations or elements.
[0048] In some embodiments, the numbers expressing quantities of
ingredients, properties such as concentration, reaction conditions,
and so forth, used to describe and claim certain embodiments of the
invention are to be understood as being modified in some instances
by the term "about." Accordingly, in some embodiments, the
numerical parameters set forth in the written description and
attached claims are approximations that can vary depending upon the
desired properties sought to be obtained by a particular
embodiment. In some embodiments, the numerical parameters should be
construed in light of the number of reported significant digits and
by applying ordinary rounding techniques. Notwithstanding that the
numerical ranges and parameters setting forth the broad scope of
some embodiments of the invention are approximations, the numerical
values set forth in the specific examples are reported as precisely
as practicable. The numerical values presented in some embodiments
of the invention may contain certain errors necessarily resulting
from the standard deviation found in their respective testing
measurements.
[0049] In some embodiments, the terms "a" and "an" and "the" and
similar references used in the context of describing a particular
embodiment of the invention (especially in the context of certain
of the following claims) can be construed to cover both the
singular and the plural. The recitation of ranges of values herein
is merely intended to serve as a shorthand method of referring
individually to each separate value falling within the range.
Unless otherwise indicated herein, each individual value is
incorporated into the specification as if it were individually
recited herein. All methods described herein can be performed in
any suitable order unless otherwise indicated herein or otherwise
clearly contradicted by context. The use of any and all examples,
or exemplary language (e.g. "such as") provided with respect to
certain embodiments herein is intended merely to better illuminate
the invention and does not pose a limitation on the scope of the
invention otherwise claimed. No language in the specification
should be construed as indicating any non-claimed element essential
to the practice of the invention.
[0050] Groupings of alternative elements or embodiments of the
invention disclosed herein are not to be construed as limitations.
Each group member can be referred to and claimed individually or in
any combination with other members of the group or other elements
found herein. One or more members of a group can be included in, or
deleted from, a group for reasons of convenience and/or
patentability. When any such inclusion or deletion occurs, the
specification is herein deemed to contain the group as modified
thus fulfilling the written description of all Markush groups used
in the appended claims.
[0051] Preferred embodiments of this invention are described
herein, including the best mode known to the inventor for carrying
out the invention. Variations on those preferred embodiments will
become apparent to those of ordinary skill in the art upon reading
the foregoing description. It is contemplated that skilled artisans
can employ such variations as appropriate, and the invention can be
practiced otherwise than specifically described herein.
Accordingly, many embodiments of this invention include all
modifications and equivalents of the subject matter recited in the
claims appended hereto as permitted by applicable law. Moreover,
any combination of the above-described elements in all possible
variations thereof is encompassed by the invention unless otherwise
indicated herein or otherwise clearly contradicted by context.
[0052] Furthermore, numerous references have been made to patents
and printed publications throughout this specification. Each of the
above cited references and printed publications are herein
individually incorporated by reference in their entirety.
[0053] In closing, it is to be understood that the embodiments of
the invention disclosed herein are illustrative of the principles
of the present invention. Other modifications that can be employed
can be within the scope of the invention. Thus, by way of example,
but not of limitation, alternative configurations of the present
invention can be utilized in accordance with the teachings herein.
Accordingly, embodiments of the present invention are not limited
to that precisely as shown and described.
Sequence CWU 1
1
26151DNAHomo sapiensmisc_feature(26)..(26)n is a, c, g, or t
1cattttatga gcaatggcat ctggcnatga acgctgctgc ctgaatcaca g
51251DNAHomo sapiensmisc_feature(26)..(26)n is a, c, g, or t
2tagctgactt aataaaagaa gtccangcac gaaccttgat gacaatgtga c
51351DNAHomo sapiensmisc_feature(26)..(26)n is a, c, g, or t
3aaaaggtctt ccttaccttc attggntttt gaatgagtga gtaataaact t
51451DNAHomo sapiensmisc_feature(26)..(26)n is a, c, g, or t
4atagtaatgt tactggcagt gaaccnatgt aggtctatag aatcctcaat t
51551DNAHomo sapiensmisc_feature(26)..(26)n is a, c, g, or t
5cttaagttcc ccatgaatga cttttncccc ctcctttata aaattgacac c
51651DNAHomo sapiensmisc_feature(26)..(26)n is a, c, g, or t
6gtcaatgaac aaaaggccac ataatnatag atttgaaaaa gacctcagag a
51751DNAHomo sapiensmisc_feature(26)..(26)n is a, c, g, or t
7ggaaccagtt gctacctact tcgcanacag acttggtccc catgaggagc t
51851DNAHomo sapiensmisc_feature(26)..(26)n is a, c, g, or t
8gaaactgtag actttgctta aaaagngtct catatcattt tcaaaataga c
51951DNAHomo sapiensmisc_feature(26)..(26)n is a, c, g, or t
9tcaaagtcct aacttatccc agtctngcta tccattattt acttctctct a
511051DNAHomo sapiensmisc_feature(26)..(26)n is a, c, g, or t
10gggatgagag gtgtgtggtt tgcagnttgg gaaacggaaa tcacatttgc a
511151DNAHomo sapiensmisc_feature(26)..(26)n is a, c, g, or t
11cattgaccat tgtttaatca gagtangagg ccacagatcg aggtgactgt c
511251DNAHomo sapiensmisc_feature(26)..(26)n is a, c, g, or t
12gtgatttaga aaaaaaaaag agatanaatg atcttaattg caattgaaaa t
511351DNAHomo sapiensmisc_feature(26)..(26)n is a, c, g, or t
13tgatgatcat ggctaagtgg gacttnagtg actcaaaccc tgtgttcaga t
511451DNAHomo sapiensmisc_feature(26)..(26)n is a, c, g, or t
14ttggggcctt ttgccccaga agcccntaat tcctcaggcc aacccgaaat t
511551DNAHomo sapiensmisc_feature(26)..(26)n is a, c, g, or t
15acctgctctt acaagtcacc acctgngagc ctcatgagcc gctggtgtga c
511651DNAHomo sapiensmisc_feature(26)..(26)n is a, c, g, or t
16gccgctggtg tgacttggac aggacnaagt tgtggcactg tcaccggggt g
511751DNAHomo sapiensmisc_feature(26)..(26)n is a, c, g, or t
17ctccatcttg gctcagggct ccttgngacc atcttccctg tgcgtccagg t
511851DNAHomo sapiensmisc_feature(26)..(26)n is a, c, g, or t
18gggtcctagg gtcctagacc cctgtnctcc ctgtttctgc ctctgtttgg g
511951DNAHomo sapiensmisc_feature(26)..(26)n is a, c, g, or t
19actacacgca gttctggaac tacctngagc gctgccgcta ctgcaacgtc c
512051DNAHomo sapiensmisc_feature(26)..(26)n is a, c, g, or t
20cctgccgctg ccgcaccggc ttcttngcgc acgctggttt ctgcttggag c
512151DNAHomo sapiensmisc_feature(26)..(26)n is a, c, g, or t
21tgccaggctc ttcctcccat gacacnctgt gcaccagctg cactggcttc c
512251DNAHomo sapiensmisc_feature(26)..(26)n is a, c, g, or t
22tgagccaggg cacagcctcc cctggngagc tctgggaaag tgggcagcaa t
512351DNAHomo sapiensmisc_feature(26)..(26)n is a, c, g, or t
23aaggtggctg gctcctctga cacggngaaa ccgaggcctg atggtaactc t
512451DNAHomo sapiensmisc_feature(26)..(26)n is a, c, g, or t
24gacctcctcc aggcctccca tgcttnccgg gaagtgaagc ttctccctct c
512551DNAHomo sapiensmisc_feature(26)..(26)n is a, c, g, or t
25ggtgggagcc ctgcatcagt gatggnggca gtctgcagtc atggtggctt c
512651DNAHomo sapiensmisc_feature(26)..(26)n is a, c, g, or t
26gcctggggtg tctgggtgca cacctnctcc ccttgctgtg ggggaggctg g 51
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