Variants of tnfsf15 and DCR3 associated with crohn's disease

Abstract

To provide variants of TNFSF15 and DCR3 associated with Crohn's disease.SOLUTION: Described herein are a method and a composition 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 a method 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.SELECTED DRAWING: Figure 4

Description

[Technical field]

[0001] CROSS-REFERENCE TO OTHER APPLICATIONS This application claims priority to US provisional patent applications No. 61 / 824,932, filed May 17, 2013.

[0002] The claimed invention relates to the prognosis, diagnosis and treatment of inflammatory bowel disease and related conditions, including methods and compositions for medical therapy. [Background technology]

[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 contains information that may be useful in understanding the present invention. No admission is made 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), is a chronic inflammatory state with pathological features such as patchy transmural inflammation and fibrous stenosis. Previous studies have shown that TL1A can promote intestinal inflammation through enhancing Th1, Th2 and Th17 effector functions, and TL1A also appears to promote fibrogenesis through increased numbers of fibroblasts and activated fibroblasts, and constitutive TL1A expression in mice was found to exacerbate mouse ileocecal inflammation and intestinal fibrous stenosis. Summary of the Invention [Means for solving the problem]

[0005] SNPs in 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 a higher risk of small intestinal surgery. Decoy Receptor3 (DcR3), a known IBD susceptibility gene, is a decoy receptor that can neutralize pro-inflammatory ligands, including TL1A (TNFSF15). Exemplary embodiments are illustrated in the referenced figures. It is intended that the embodiments and figures disclosed herein be considered illustrative rather than restrictive. [Brief description of the drawings]

[0006] [Figure 1] 1 shows a principal component analysis (PC1 / PC2) according to an embodiment herein. [Diagram 2] According to an embodiment herein, pACT of the TNFSF15 region in NJ (non-Jewish) and AJ (Ashkenazi Jewish) CD is shown. [Diagram 3] According to an embodiment herein, pACT of the DcR3 (TNFRSF6B) region in NJ and AJCD is shown. [Figure 4] 1 shows a linkage disequilibrium map (r2) of associated TNFSF15 SNPs in NJ and SK according to embodiments herein. DETAILED DESCRIPTION OF THE PREFERRED EMBODIMENTS

[0007] Described herein is an assay for quantifying a risk in a subject for Crohn's disease and / or fibrosis, comprising obtaining a sample from the 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 locus, and quantifying the risk in the subject for Crohn's disease and / or fibrosis based on the presence of one or more variants at the TNFSF15 and / or DcR3 locus. In various embodiments, the variants comprise one or more variants selected from the group comprising: 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 variant is 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, Korean or Puerto Rican. In other embodiments, the subject is Korean and the variant is 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 decreased risk in the subject for structural, CD, small intestinal complications and / or need for surgical intervention.

[0008] Also described herein is a method of diagnosing a susceptibility to 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 or absence of one or more variants at the TNFSF15 and / or DcR3 locus, and diagnosing a 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 locus. In other embodiments, the variants consist of one or more variants selected from the group comprising: 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 variant is 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, Korean or Puerto Rican. In other embodiments, the subject is Korean and the variant is SEQ ID NO:3, SEQ ID NO:13 and / or SEQ ID NO:22.

[0009] Also described herein is 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 locus, and treating Crohn's disease and / or fibrosis. In one embodiment, the variants consist of one or more variants selected from the group comprising: 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.

[0010] Description of the Invention All references cited herein are incorporated by reference in their entirety as if fully set forth. Unless otherwise defined, technical and scientific terms used herein have the same meaning as commonly understood by those of ordinary skill in the art to which this invention pertains. Allen et al., Remington: The Science and Practice of Pharmacy 22 nd ed., Pharmaceutical Press (September 15, 2012); Hornyak et al., Introduction to Nanoscience and Nanotechnology, CRC Press (2008); Singleton and Sainsbury, Dictionary of Microbiology and Molecular Biology 3 rd ed., revised ed., J. Wiley & Sons (New York, NY 2006); Smith, March's Advanced Organic Chemistry Reactions, Mechanisms and Structure 7 th ed., J. Wiley & Sons (New York, NY 2013); Singleton, Dictionary of DNA and Genome Technology 3 rd ed., Wiley-Blackwell (November 28, 2012); and Green and Sambrook, Molecular Cloning: A Laboratory Manual 4th ed., Cold Spring Harbor Laboratory Press (Cold Spring Harbor, NY 2012) provides those of skill in the art with a general introduction to many of the terms used in this application. For reference on how to generate antibodies, see Greenfield, Antibodies A Laboratory Manual 2 nd ed., Cold Spring Harbor Press (Cold Spring Harbor NY, 2013); Kohler and Milstein, Derivat ion of specific antibody-producing tissue culture and tumor lines by cell fusion, Eur. J. Immunol. 1976 Jul, 6(7):511-9; See Queen and Selick, Humanized immunoglobulins, US Patent No. 5,585,089 (1996 Dec); and Riechmann et al., Reshaping human antibodies for therapy, Nature 1988 Mar 24, 332(6162):323-7.

[0011] As disclosed herein, the inventors have investigated the effect of the T helper pathway in TL1A-induced colitis and the effect of the T helper pathway in TL1A-induced intestinal fibrosis. The role of TL1A in intestinal mucositis is highlighted by finding that neutralizing TL1A antibodies prevented and treated chronic colitis in mice. However, the contribution of either lymphoid or myeloid derived TL1A to the development of intestinal inflammation is not fully known. TL1A is the product of the TNFSF15 gene, which is expressed by both lymphoid and myeloid derived cells. Variants in the TNFSF15 gene have been found to be associated with IBD. TNFSF15, the protein product of TL1A, is elevated in the intestinal mucosa of IBD patients. Certain TNFSF15 haplotypes are associated with susceptibility to CD and UC in non-Jewish Caucasians. In addition, TNFSF15 haplotype B is associated with severity as well as risk in Jewish CD patients. Furthermore, monocytes from Jewish patients carrying risk haplotype B express higher levels of TL1A in response to FcγR stimulation. These results indicate that CD-associated TNFSF15 genetic mutations contribute to enhanced induction of TL1A resulting in severe chronic mucositis, 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 mucositis. Neutralizing TL1A-antibodies ameliorate inflammation in DSS and Gαi2- / - T cells migrate chronic colitis models. Constitutive TL1A expression in mice leads to mild spontaneous ileitis and increased collagen deposition. TL1A regulates adaptive immune responses in the T helper (Th)-1 effector arm, as shown by enhanced interferon (IFN)-γ production of TL1A from peripheral and mucosal T cells. TL1A is a member of the TNF superfamily. Thus, in summary, TNFSF15 SNPs are associated with IBD, TNFSF15 haplotype B has increased TL1A expression with higher risk of small intestinal surgery, and constitutive Tl1a expression in mice exacerbates murine ileocecal inflammation and intestinal fibrotic stricture.While it is known that TL1A can enhance Th1, Th2 and Th17 effector cell function, it is unclear which TL1A-activated T helper effector pathway induces intestinal inflammation and fibrosis. Therefore, an important scientific question is to understand the effect of T helper pathway on TL1A-induced colitis and the effect of T helper pathway on TL1A-induced intestinal fibrosis.

[0012] As disclosed herein, the inventors performed cross-ethnic fine mapping of TNFSF15 and DcR3 in Caucasian, Puerto Rican and Korean CD. The inventors identified an association between non-Jewish Caucasian (NJ) Crohn's disease (CD) and rare TNFSF15 variants. This association is independent of previously reported common variants. These variants are also much more common in Korean (SK) populations and are also associated with SK CD. DcR3 is significantly associated with NJ CD, a finding replicated in SK and mutations at this locus modify the stenosis phenotype.

[0013] Described herein is an assay for quantifying a risk in a subject for Crohn's disease and / or fibrosis, comprising obtaining a sample from the 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 locus, and quantifying the risk in the subject for Crohn's disease and / or fibrosis based on the presence of one or more variants at the TNFSF15 and / or DcR3 locus. In various embodiments, the variants comprise one or more variants selected from the group comprising: 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 variant is 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, Korean or Puerto Rican. In other embodiments, the subject is Korean and the variant is 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 decreased risk in the subject for structural, CD, small intestinal complications and / or need for surgical intervention.

[0014] Also described herein is a method of diagnosing a susceptibility to 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 or absence of one or more variants at the TNFSF15 and / or DcR3 locus, and diagnosing a 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 locus. In other embodiments, the variants consist of one or more variants selected from the group comprising: 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 variant is 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, Korean or Puerto Rican. In other embodiments, the subject is Korean and the variant is SEQ ID NO:3, SEQ ID NO:13 and / or SEQ ID NO:22.

[0015] Also described herein is 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 locus, and treating Crohn's disease and / or fibrosis. In one embodiment, the variants consist of one or more variants selected from the group comprising: 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.

[0016] In one embodiment, the present invention provides a method of diagnosing a susceptibility to Crohn's disease in a subject by obtaining a sample from the subject, analyzing the sample to determine the presence or absence of one or more risk variants in the subject, and diagnosing the susceptibility to Crohn's disease based on the presence of the one or more risk variants. In another embodiment, the one or more risk variants are at the TNFSF15 and / or DcR3 locus. 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 Korean. In another embodiment, the subject is non-Caucasian.

[0017] 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, analyzing 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 the one or more risk variants. In another embodiment, the one or more risk variants are at the TNFSF15 and / or DcR3 locus. 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 Korean. In another embodiment, the subject is non-Caucasian.

[0018] In one embodiment, the present invention provides methods of treating Crohn's disease in a subject by determining the presence of one or more risk variants in the subject, and treating a subject. In another embodiment, the one or more risk variants are at the TNFSF15 and / or DcR3 locus. 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 Korean. In another embodiment, the subject is non-Caucasian.

[0019] In one embodiment, the present invention provides a method of diagnosing a susceptibility to fibrosis in a subject by obtaining a sample from the subject, analyzing the sample to determine the presence or absence of one or more risk variants in the subject, and diagnosing the susceptibility to fibrosis based on the presence of the one or more risk variants. In another embodiment, the one or more risk variants are at the TNFSF15 and / or DcR3 locus. 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 Korean. In another embodiment, the subject is non-Caucasian.

[0020] In one embodiment, the present invention provides a method of diagnosing a fibrosis subtype in a subject by obtaining a sample from the subject, analyzing 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 the one or more risk variants. In another embodiment, the one or more risk variants are at the TNFSF15 and / or DcR3 locus. 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 Korean. In another embodiment, the subject is non-Caucasian.

[0021] In one embodiment, the present invention provides methods of treating fibrosis in a subject and treating a subject by determining the presence of one or more risk variants in the subject. In another embodiment, the one or more risk variants are at the TNFSF15 and / or DcR3 locus. 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 Korean. In another embodiment, the subject is non-Caucasian.

[0022] The various methods and techniques described above provide a number of ways to implement the present invention. Of course, it should be understood that not necessarily all of the described objectives or advantages can be achieved according to any particular embodiment described herein. Thus, for example, one skilled in the art will recognize that a method can be performed in a manner that achieves or optimizes one advantage or group of advantages taught herein without necessarily achieving other objectives or advantages as may be taught or suggested herein. Various beneficial and disadvantageous options have been mentioned herein. It should be understood that some preferred embodiments specifically include one, another, or several beneficial features, while others specifically exclude one, another, or several disadvantageous features, while still others specifically alleviate existing disadvantageous features by including one, another, or several beneficial features.

[0023] Furthermore, those skilled in the art 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, may be mixed and matched by those skilled in the art to perform methods according to the principles described herein. Among the various elements, features, and steps, some will be specifically included and others will be specifically excluded in various embodiments.

[0024] While the present invention has been disclosed in the context of certain embodiments and examples, it will be appreciated by those skilled in the art that the embodiments of the present invention extend beyond the specifically disclosed embodiments to other alternative embodiments and / or uses thereof, as well as modifications and equivalents.

[0025] Many variations and alternative elements have been disclosed in the embodiments of the present invention. Still further variations and alternative elements will be apparent to those of skill in the art. Among these variations are, but are not limited to, the selection of component modules for the configuration of the present invention and the diseases and other clinical conditions that may be diagnosed, predicted, or treated therewith. Various embodiments of the present invention may specifically include or exclude any of these variations or elements.

[0026] In some embodiments, numbers expressing properties such as amounts of ingredients, concentrations, reaction conditions, and the like used to describe and claim certain embodiments of the present invention should be understood to be modified in some instances by the term "about". Thus, in some embodiments, the numerical parameters set forth in the specification and appended claims are approximations that may vary depending on 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 present invention are approximations, the numerical values ​​set forth in the specific examples are reported as precisely as practicable. The numerical values ​​set forth in some embodiments of the present invention may contain certain errors necessarily resulting from the standard deviation found in their respective testing measurements.

[0027] In some embodiments, the terms "a" and "an" as well as "the" and similar references used in the context of describing particular embodiments of the invention (particularly in certain contexts of the claims below) can be construed to cover both the singular and the plural. Descriptions of ranges of values ​​herein are merely intended to serve as a shorthand method of individually referring to each separate value falling within the range. Unless otherwise indicated herein, each separate value is incorporated into the specification as if it were individually detailed herein. All methods described herein can be performed in any suitable order unless otherwise indicated herein or otherwise clearly contradicted by the context. The use of any and all examples or exemplary words (e.g., "such as") provided herein with respect to certain embodiments is intended merely to better clarify the invention and does not create limitations on the scope of the invention as otherwise claimed. No language herein should be construed as indicating any non-claimed element essential to the practice of the invention.

[0028] Grouping of alternative elements or embodiments of the invention disclosed herein should not be construed as limiting. Each group member may 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 may be included in or deleted from a group for reasons of advantage and / or patentability. When any such inclusion or deletion occurs, the specification is considered to include the group as modified and thus fulfills all Markush group descriptions used herein in the appended claims.

[0029] Preferred embodiments of the present invention are described herein, including the best mode known to the inventor for carrying out the invention. Variations in these preferred embodiments will become apparent to those of skill in the art upon reading the foregoing. Such variations can be used by those of skill in the art as appropriate, and it is believed that the present invention may be practiced otherwise than as specifically described herein. Accordingly, many embodiments of the present 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 present invention unless otherwise expressly set forth herein or otherwise clearly contradicted by the context.

[0030] Furthermore, numerous references are made throughout this specification to patents and printed publications. Each of the above cited literature and printed publications is herein individually incorporated by reference in its entirety.

[0031] Finally, it is to be understood that the embodiments of the invention disclosed herein are illustrative of the principles of the invention. Other modifications that may be employed are within the scope of the invention. Thus, by way of example, but not of limitation, alternative configurations of the invention may be utilized in accordance with the teachings herein. Thus, the embodiments of the invention are not limited to that precisely as shown and described.

[0032] The following examples are provided to better illustrate the claimed invention and should not be construed as limiting the scope of the invention. To the extent that specific materials are mentioned, it is for illustrative purposes only and is not intended to limit the invention. Those skilled in the art will develop equivalent means or reactions without the exercise of inventive faculty and without departing from the scope of the invention. EXAMPLES

[0033] Example 1 method The inventors performed cross-ethnic fine mapping across TNFSF15 and DcR3 in Caucasian, Puerto Rican (PR) and Korean (SK) CD. Immunochip genotyping performed on the following populations shown in Table 1.

[0034] [Table 1]

[0035] To measure the association of TNFSF15 (416 SNPs) and DcR3 (13 SNPs), logistic regression was applied after controlling for population structure using principal component analysis (PCA) (Figure 1). The resulting pACT function was corrected for multiple testing. Values ​​of pACT<0.05 were considered statistically significant. The population attributable risk (PAR) of associated TNFSF15-DcR3 pathway SNPs was then calculated in each population, and the results are shown in Tables 2-4.

[0036] [Table 2]

[0037] [Table 3]

[0038] [Table 4A]

[0039] [Table 4B]

[0040] [Table 5]

[0041] [Table 6]

[0042] [Table 7]

[0043] [Table 8]

[0044] Example 3 TNFSF15 analysis As shown in the results above, 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.

[0045] Importantly, the "rare" and "common" variants could each be tagged by a single SNP (SNP160 and SNP164, respectively) in both NJ and SK (Table 5, Figure 4). The "rare" variants were associated with CD in PR (at higher allele frequencies). No association was found with common variants in PR (Table 4). No significant SNP associations were observed in AJ CD (Figure 2, Table 4). After correction for multiple comparisons, there was no significant association of rare or common CD SNPs with clinical subphenotypes in NJ CD.

[0046] Example 4 DcR3 analysis The above results further showed that rs6062496 in intron 6 was significantly associated with NJ CD (Figure 3, Table 3). The association was confirmed in SK CD, but not in PR and AJ CD (Table 4). We also further identified rs6062496 as being associated with protection against stricture CD, small intestinal complications, and the need for surgery (Table 6).

[0047] Example 5 TNFSF15-DcR3 analysis The above results further suggest that there is no significant DcR3 and TNFSF15 gene-gene interaction in NJ and SK (Table 7). PAR due to the TNFSF15-DcR3 pathway was 32.3% in NJ CD (Table 8). PAR due to TNFSF15 variants in SK was the highest seen in any population, explaining the dominant effect of this locus in Asian CD (Table 8).

[0048] Example 6 conclusion Based on the described results, the inventors identified an association between 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 are also associated with SK CD. DcR3 is significantly associated with NJ CD, a finding replicated in SK and mutations at this locus modify the stenosis phenotype.

[0049] The various methods and techniques described above provide a number of ways to implement the present invention. Of course, it should be understood that not all of the described objectives or advantages can necessarily be achieved according to any particular embodiment described herein. Thus, for example, a person skilled in the art will recognize that a method 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. Various beneficial and disadvantageous options are mentioned herein. It should be understood that some preferred embodiments specifically include one, another, or several beneficial features, while others specifically exclude one, another, or several disadvantageous features, while still others specifically alleviate existing disadvantageous features by the inclusion of one, another, or several beneficial features.

[0050] Furthermore, those skilled in the art will recognize the applicability of various features from different embodiments. Similarly, the various elements, features, and steps discussed above, and other known equivalents for each such element, feature, or step, may be mixed and matched by those skilled in the art to perform methods according to the principles described herein. Among the various elements, features, and steps, some will be specifically included and others will be specifically excluded in various embodiments.

[0051] While the present 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 present invention extend beyond the specifically disclosed embodiments to other alternative embodiments and / or uses and modifications and equivalents thereof.

[0052] Many variations and alternative elements have been disclosed in the embodiments of the present invention. Still further variations and alternative elements will be apparent to those skilled in the art. Among these variations are, but are not limited to, methods of prognosis and diagnosis for inflammatory bowel disease-related diseases and / or conditions, compositions produced by the techniques described above, treatment of diseases and / or conditions related to the teachings of the present invention, techniques and compositions used therein, and uses of the solutions and specific uses of products made via the techniques of the present invention. Various embodiments of the present invention can specifically include or exclude any of these variations or elements.

[0053] In some embodiments, numbers expressing properties such as amounts of ingredients, concentrations, reaction conditions, and the like used to describe and claim certain embodiments of the present invention should be understood to be modified in some instances by the term "about". Accordingly, in some embodiments, the numerical parameters set forth in the specification and appended claims are approximations that may vary depending on 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 present invention are approximations, the numerical values ​​set forth in the specific examples are reported as precisely as practicable. The numerical values ​​set forth in some embodiments of the present invention may contain certain errors necessarily resulting from the standard deviation found in their respective testing measurements.

[0054] In some embodiments, the terms "a" and "one" as well as "the" and similar references used in the context of describing particular embodiments of the invention (particularly in certain contexts of the claims below) can be construed to cover both the singular and the plural. Descriptions of ranges of values ​​herein are merely intended to serve as a shorthand method of individually referring to each separate value falling within the range. Unless otherwise indicated herein, each separate value is incorporated into the specification as if it were individually set forth herein. All methods described herein can be performed in any suitable order unless otherwise indicated herein or otherwise clearly contradicted by the context. The use of any and all examples or exemplary words (e.g., "such as") provided herein with respect to certain embodiments is intended merely to better clarify the invention and does not create limitations on the scope of the invention as otherwise claimed. No language herein should be construed as indicating any non-claimed element essential to the practice of the invention.

[0055] Grouping of alternative elements or embodiments of the invention disclosed herein should not be construed as limiting. 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 may be included in or deleted from a group for reasons of advantage and / or patentability. When any such inclusion or deletion occurs, the specification herein is considered to include the group as modified and thus fulfills all Markush group descriptions used in the appended claims.

[0056] Preferred embodiments of the present invention are described herein, including the best mode known to the inventors for carrying out the invention. Variations in these preferred embodiments will become apparent to those of skill in the art upon reading the foregoing. Such variations can be used by those of skill in the art as appropriate, and it is contemplated that the present invention may be practiced otherwise than as specifically described herein. Accordingly, many embodiments of the present 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 present invention unless otherwise expressly set forth herein or otherwise clearly contradicted by the context.

[0057] Furthermore, numerous references are made throughout this specification to patents and printed publications. Each of the above cited literature and printed publications is herein individually incorporated by reference in its entirety.

[0058] Finally, it is to be understood that the embodiments of the invention disclosed herein are illustrative of the principles of the invention. Other modifications that may be employed are within the scope of the invention. Thus, by way of example, but not of limitation, alternative configurations of the invention may be utilized in accordance with the teachings herein. Thus, the embodiments of the invention are not limited to that precisely as shown and described. For example, the present invention provides the following: (Item 1) 1. An assay for quantifying risk in a subject for 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 in the TNFSF15 and / or DcR3 gene locus; and quantitating the risk in a subject for Crohn's disease and / or fibrosis based on the presence of one or more variants in the TNFSF15 and / or DcR3 gene loci; The assay comprising: (Item 2) The method of item 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. (Item 3) The method of item 1, wherein the mutant is SEQ ID NO:3 and / or SEQ ID NO:13. (Item 4) The method of item 1, wherein the mutant is SEQ ID NO:22. (Item 5) 2. The method of item 1, wherein the subject is non-Jewish Caucasian, Ashkenazi, Korean and / or Puerto Rican. (Item 6) 2. The method of item 1, wherein the subject is Korean and the variant is SEQ ID NO:3, SEQ ID NO:13 and / or SEQ ID NO:22. (Item 7) 2. The method of item 1, wherein the variant is a risk variant. (Item 8) 2. The method of claim 1, wherein the mutant is a protective mutant. (Item 9) 2. The method of item 1, wherein the protective variant quantifies a reduced risk in the subject for structural abnormalities, CD, small intestinal complications and / or need for surgical intervention. (Item 10) 1. A method for diagnosing a 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 in the TNFSF15 and / or DcR3 gene locus; and diagnosing a susceptibility to Crohn's disease and / or fibrosis in a subject based on the presence of one or more variants in said TNFSF15 and / or DcR3 gene loci; The method comprising: (Item 11) 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. (Item 12) The method of item 10, wherein the variant is SEQ ID NO:3 and / or SEQ ID NO:13. (Item 13) 11. The method of item 10, wherein the mutant is SEQ ID NO:22. (Item 14) 11. The method of item 10, wherein the subject is non-Jewish Caucasian, Ashkenazi, Korean or Puerto Rican. (Item 15) 11. The method of item 10, wherein the subject is Korean and the variant is SEQ ID NO:3, SEQ ID NO:13 and / or SEQ ID NO:22. (Item 16) 1. A method of treating 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 of one or more variants in the TNFSF15 and / or DcR3 gene locus; and Treating said Crohn's disease and / or fibrosis; The method comprising: (Item 17) 17. The method of item 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.

Claims

[Claim 1] A method or composition as described in the specification.

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