Abstract: The present invention describes a method of prognosing high or low probability of developing an inflammatory bowel disease (IBD) in a subject and a method of diagnosing an inflammatory bowel disease (IBD) in a subject. The invention further provides for a method of identifying genes/genetic loci associated with a disease condition, such as IBD, CD and/or UC.

Abstract: Provided herein are methods and systems for use in identifying a subject with inflammatory bowel disease based on certain criteria, including genetics or serological markers measured in a sample obtained from the subject. Also provided are methods and systems for treatment of the inflammatory bowel disease in the subject. The systems described herein may include polygenic risk score (PRS), which is useful for determining the relative risk of the subject as compared with a reference population.

Abstract: Disclosed herein are methods, kits and compositions for treating an inflammatory disease or condition, or fibrosis in a subject that has been determined to have increased fold-change in Tumor necrosis factor (TNF)-like cytokine 1A (TL1A) expression based, at least partially, on a presence of a combination of genotypes detected in a sample obtained from the subject. In some embodiments, the combination of genotypes is significantly associated with the increased fold-change in TL1A, and in some cases, may also be predictive of severe forms of the inflammatory disease or condition. In some embodiments, the inflammatory disease or condition is an inflammatory bowel disease, such as Crohn's disease or ulcerative colitis.

Abstract: Provided are methods, systems, and kits for selecting a subject for treatment with an inhibitor of Tumor necrosis factor-like cytokine 1A (TL1A) activity or expression based on a presence of one or more genotypes associated with a positive therapeutic response to the inhibitor of TL1A. Also provided are methods, systems and kits for detecting the one or more genotypes described herein.

Abstract: Provided are methods, systems, and kits for selecting a patient for treatment with a therapeutic agent based on a presence of a genotype associated with a positive therapeutic response to the therapeutic agent. The therapeutic agent, in some embodiments, is an inhibitor of TL1A activity or expression, such as for example, an anti-TL1A antibody.

Abstract: The present disclosure provides methods and systems of identifying a fibrotic disease in a subject using a DeepLearning model. The DeepLearning model may be used to predict, treat, monitor, and/or prevent the fibrotic disease in the subject, as well as to characterize a subtype of the fibrotic disease.

Abstract: Provided are methods, systems, and kits for selecting a patient for treatment with a therapeutic agent based on a presence of a genotype associated with a positive therapeutic response to the therapeutic agent. The therapeutic agent, in some embodiments, is an inhibitor of TL1A activity or expression, such as for example, an anti-TL1A antibody.

Abstract: The present invention describes a method of prognosing high or low probability of developing an inflammatory bowel disease (IBD) in a subject and a method of diagnosing an inflammatory bowel disease (IBD) in a subject. The invention further provides for a method of identifying genes/genetic loci associated with a disease condition, such as IBD, CD and/or UC.

Abstract: The present invention describes methods of diagnosing inflammatory bowel disease, including but not limited to Crohn's Disease (CD), Ulcerative Colitis (UC), and/or Medically Refractive Ulcerative Colitis (MR-UC), using RNASET2, TL1A and/or IFN-?. The invention further provides a process for patient identification and/or stratification.

Abstract: Described herein are methods, systems, compositions, and kits useful for the diagnosis and/or treatment of a disease or condition in a subject. The present disclosure relates to methods and systems for identifying and stratifying patients suitable for treatment with an IL18R1 modulator, as described herein.

Abstract: Described herein are methods, systems, compositions, and kits useful for the diagnosis and/or treatment of a disease or condition in a subject. The present disclosure relates to methods and systems for identifying and stratifying patients suitable for treatment with a SKAP2 modulator, as described herein.

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 TNF SF15 (or TL1A) and/or DcR3 genetic loci.

Abstract: Described herein are methods of diagnosing inflammatory bowel disease, including but not limited to Crohn's Disease (CD), Ulcerative Colitis (UC), and/or Medically Refractive Ulcerative Colitis (MR-UC), using RNA-SET2, TL1A and/or IFN-Y. The methods may comprise treating inflammatory bowel disease by administering a therapeutically effective amount of a therapeutic agent to a subject. Described further herein are processes for patient identification and/or stratification.

Abstract: Provided are methods, systems, and kits for selecting a patient for treatment with a therapeutic agent based on a presence of a genotype associated with a positive therapeutic response to the therapeutic agent. The therapeutic agent, in some embodiments, is an inhibitor of TL1A activity or expression, such as for example, an anti-TL1A antibody.

Abstract: Disclosed herein are methods, kits and compositions for treating an inflammatory disease. These methods, kits and compositions may be particularly useful for subjects carrying a risk genotype and/or expressing a transcriptomic risk signature that is indicative of severe inflammatory disease phenotypes for which existing treatment options are limited.

Abstract: Described herein are methods and systems for identifying subjects suitable for treatment with an inhibitor of CD30L activity or expression, such as an anti-CD30L antibody. Methods and systems disclosed herein identify subjects suitable for treatment based on a presence of a genotype that is indicative of a disease or condition in the subject for which an inhibitor of CD30L is a suitable treatment. Exemplary conditions include both Crohns disease and primary sclerosing cholangitis. Compositions used to detect the genotypes described herein, and methods of using them are also provided.

Abstract: Provided are methods, systems, and kits for selecting a patient for treatment with a therapeutic agent based on a presence of a genotype associated with a positive therapeutic response to the therapeutic agent. The therapeutic agent, in some embodiments, is an inhibitor of TL1A activity or expression, such as for example, an anti-TL1A antibody.

Abstract: The present disclosure describes methods, devices and systems of diagnosing, prognosing, and treating subjects with moderate to severe forms of Crohn's disease (CD) that is characterized by stricturing and internal penetrating disease phenotypes. Also described are methods and kits for characterizing a subtype of CD, and identifying a subject as being suitable for a therapy to treat the CD.

Abstract: The present disclosure provides methods and systems of identifying an inflammatory disease or condition, e.g., an inflammatory bowel disease in a subject using a DeepLearning model. The DeepLearning model may be used to predict, treat, monitor, and/or prevent the inflammatory disease or condition in the subject, as well as to characterize a subtype of the inflammatory disease or condition.

Abstract: The present invention describes methods of diagnosing inflammatory bowel disease, including but not limited to Crohn's Disease (CD), Ulcerative Colitis (UC), and/or Medically Refractive Ulcerative Colitis (MR-UC), using RNA-SET2, TL1A and/or IFN-?. The invention further provides a process for patient identification and/or stratification.