Abstract: The invention relates to method of diagnosing susceptibility to inflammatory bowel disease (IBD) in an individual by obtaining a sample from the individual, assaying the sample to determine the presence or absence of one or more risk genetic variants and/or an increase in IFNG DNA methylation. In one embodiment, the present invention provides a method of diagnosing susceptibility to inflammatory bowel disease (IBD) in an individual by obtaining a sample from the individual, assaying the sample to determine the presence or absence of one or more risk genetic variants and/or an increase in IFNG DNA methylation relative to a normal subject, and diagnosing susceptibility to inflammatory bowel disease based on the presence of one or more risk genetic variants and/or an increase in IFNG DNA methylation relative to a normal subject. In another embodiment, the IBD is ulcerative colitis.

Abstract: The present invention relates to methods of diagnosing inflammatory bowel disease (IBD) in an individual by determining the presence of at least one risk genetic variant and/or at least one risk serological marker. In one embodiment, the presence of at least one risk genetic variant is indicative of granuloma. In another embodiment, the presence of at least one risk genetic variant is indicative of low bone density (LBD).

Abstract: The present invention relates to methods of prognosing inflammatory bowel disease (IBD) in an individual by determining the presence of at least one risk genetic variant and/or at least one risk serological marker. In one embodiment, the presence of risk serological marker ANCA is indicative of an aggressive form of ulcerative colitis. In another embodiment, the present invention relates to methods of diagnosing a Crohn's disease subtype in an individual, where the presence of risk variants and serological markers I2, OmpC and/or Cbir1 are indicative of the Crohn's disease subtype.

Abstract: A common long term problem after Ileal Pouch-Anal Anastomosis (IPAA) is the inflammation of the pouch, called pouchitis. Additionally, about 5-10% of patients undergoing IPAA with a diagnosis of ulcerative colitis at the time of surgery are subsequently diagnosed with Crohn's disease. In one embodiment, the present invention provides methods of diagnosing and predicting susceptibility to pouchitis after IPAA by detecting the presence or absence of pANCA and/or Cbir1 Flagellin expression.

Abstract: The present invention relates to prognosing, diagnosing and treating of Crohn's disease. The invention also provides prognosis, diagnosis, and treatment that are based upon the presence of one or more genetic risk factors at the FUT2 genetic locus.

Abstract: This invention provides methods of diagnosing or predicting susceptibility to Crohn's Disease by determining the presence or absence of genetic variants. In one embodiment, the present invention provides methods to diagnose and/or predict susceptibility to Crohn's Disease in an individual by determining the presence or absence of anti-Cbir1 reactivity and the presence or absence of TLR5 risk variants. In another embodiment, the present invention provides methods to diagnose Crohn's Disease by determining the presence or absence of NFKB1 haplotype H3 and/or ASCA expression. In another embodiment, the present invention provides methods of diagnosing Crohn's Disease by determining the presence or absence of Cbir1 specific peripheral blood T cell proliferation.

Abstract: Methods of predicting the development of medically refractory ulcerative colitis (MR-UC) in a patient by determining the presence or absence of one or more risk variants, where the presence of one or more risk variants is indicative of a severe and/or aggressive form of ulcerative colitis are disclosed.

Abstract: The present invention relates to prognosing, diagnosing and treating of Crohn's disease.

Abstract: The invention provides a method of diagnosing or predicting susceptibility to a clinical subtype of Crohn's disease in a subject having Crohn's disease by determining the presence or absence of IgA anti-I2 antibodies in the subject, where the presence of the IgA anti-I2 antibodies indicates that the subject has a clinical subtype of Crohn's disease. In one embodiment, a method of the invention is practiced by further determining the presence or absence in the subject of a NOD2 variant, anti-Saccharomyces cerevisiae antibodies (ASCA), IgA anti-OmpC antibodies, or perinuclear anti-neutrophil cytoplasmic antibodies (pANCA). The methods of the invention can be used to diagnose or predict susceptibility to a clinical subtype of Crohn's disease, for example, a fibrostenotic subtype, a subtype characterized by the need for small bowel surgery, or a subtype characterized by the absence of features of ulcerative colitis.

Abstract: The present invention relates to methods of predicting susceptibility to a severe form of Crohn's disease in an individual by determining the presence or absence of one or more risk variants. In one embodiment, the risk variants comprise a combination of genetic risk variants and clinical risk factors. In another embodiment, the genetic risk variants are at the IL12B genetic locus. In another embodiment, the severe form of Crohn's disease is characterized by a rapid progression to a condition requiring surgery for treatment.

Abstract: This invention provides methods of diagnosing or predicting susceptibility to Crohn's Disease by determining the presence or absence of genetic variants. In one embodiment, the present invention provides methods to diagnose and/or predict susceptibility to Crohn's Disease in an individual by determining the presence or absence of anti-Cbir1 reactivity and the presence or absence of TLR5 risk variants. In another embodiment, the present invention provides methods to diagnose Crohn's Disease by determining the presence or absence of NFKB1 haplotype H3 and/or ASCA expression. In another embodiment, the present invention provides methods of diagnosing Crohn's Disease by determining the presence or absence of Cbir1 specific peripheral blood T cell proliferation.

Abstract: The present invention relates to prognosing, diagnosing and treating an aggressive form of Crohn's disease characterized by rapid progression to complication and/or surgery from the time of diagnosis. In one embodiment, the prognosis, diagnosis and treatment is based upon the presence of one or more genetic risk factors.

Abstract: Disclosed are methods of predicting the development of medically refractory ulcerative colitis (MR-UC) in a patient In one embodiment, disclosed is a method of prognosing ulcerative colitis in an individual by determining the presence or absence of one or more risk variants, where the presence of one or more risk variants is indicative of a severe and/or aggressive form of ulcerative colitis. In another embodiment, the severe form of ulcerative colitis is indicative of MR-UC.

Abstract: Disclosed are methods of diagnosing Inflammatory Bowel Disease by determining the presence or absence of genetic variants at SMAD3 and/or JAK2 loci. Provided is a method of diagnosing a Crohn's Disease subtype in an individual by determining the presence or absence of a risk variant at the SMAD3 and/or JAK2 loci.

Abstract: The present invention relates to methods of prognosing responsiveness to anti-TNF? therapy by determining the presence or absence of risk factors in the individual. In one embodiment, the risk factors are genetic markers, serological markers and/or clinical phenotypes associated with non-responsiveness to treatment with anti-TNF? therapy in an individual diagnosed with IBD.

Abstract: The present invention provides a method of diagnosing Crohn's disease in a subject by determining the presence or absence or IgA anti-OmpC antibodies in the subject, where the presence of the IgA anti-OmpC antibodies indicates that the subject has Crohn's disease.

Abstract: The present invention provides a method of diagnosing Crohn's disease in a subject by determining the presence or absence or IgA anti-OmpC antibodies in the subject, where the presence of the IgA anti-OmpC antibodies indicates that the subject has Crohn's disease.

Abstract: The present invention provides a method of diagnosing Crohn's disease in a subject by determining the presence or absence or IgA anti-OmpC antibodies in the subject, where the presence of the IgA anti-OmpC antibodies indicates that the subject has Crohn's disease.

Abstract: The present invention relates to methods of diagnosing and diagnosing susceptibility to Crohn's Disease by determining the presence or absence of risk variants at the JAK3 locus. In one embodiment, the present invention provides a method of diagnosing susceptibility to Crohn's Disease by determining the presence of a risk variant at the JAK3 locus, where the risk variant is associated with positive expression of ASCA and/or anti-I2.

Abstract: The present invention relates to methods of diagnosing susceptibility to Crohn's Diseaese by determining the presence or absence of susceptibility variants at the IL17RD locus. in one embodiment, the present invention provides a method of diagnosing and/or predicting susceptibility to Crohn's Disease by determining the presence or absence of an interaction between IL17RD Block 2 Haplotype 2 and IL23R Block 2 Haplotype 2 and/or IL12RB2 Haplotype 4, where the presence of an interaction between IL17RD Block 2 Haplotype 2 and IL23R Block 2 Haplotype 2 and/or IL12RB2 Haplotype 4 is indicative of susceptibility to Crohn's Disease.