Abstract: The present disclosure provides methods for assessing mucosal healing in a patient with Crohn's Disease. The methods include detecting expression levels of analytes in a serum sample from a patient, and applying a mathematical algorithm to the expression levels, thereby producing a Mucosal Healing Index score for the patient. The present disclosure also provides kits that include two or more binding partners, each or which is capable of binding a different analyte measured in the disclosed mucosal healing assessment methods.

Abstract: In some aspects, the present invention provides methods for predicting whether a subject will develop autoantibodies to an anti-TNF? drug during the course of anti-TNF? drug therapy. In other aspects, the present invention provides methods for predicting the level of an anti-TNF? drug in a subject during the course of anti-TNF? drug therapy. Systems for predicting anti-TNF? drug levels and the likelihood of autoantibody formation during the course of anti-TNF? drug therapy are also provided herein. The present invention further provides methods for predicting a clinical outcome (e.g., endoscopic response) of a subject on anti-TNF? drug therapy.

Abstract: In some aspects, the present invention provides methods for predicting whether a subject will develop autoantibodies to an anti-TNF? drug during the course of anti-TNF? drug therapy. In other aspects, the present invention provides methods for predicting the level of an anti-TNF? drug in a subject during the course of anti-TNF? drug therapy. Systems for predicting anti-TNF? drug levels and the likelihood of autoantibody formation during the course of anti-TNF? drug therapy are also provided herein. The present invention further provides methods for predicting a clinical outcome (e.g., endoscopic response) of a subject on anti-TNF? drug therapy.

Abstract: The present disclosure provides methods for assessing mucosal healing in a patient with Crohn's Disease. The methods include detecting expression levels of analytes in a serum sample from a patient, and applying a mathematical algorithm to the expression levels, thereby producing a Mucosal Healing Index score for the patient. The present disclosure also provides kits that include two or more binding partners, each or which is capable of binding a different analyte measured in the disclosed mucosal healing assessment methods.

Abstract: The present disclosure provides methods for assessing mucosal healing in a patient with Chron's Disease. The methods include detecting expression levels of analytes in a serum sample from a patient, and applying a mathematical algorithm to the expression levels, thereby producing a Mucosal Healing Index score for the patient. The present disclosure also provides kits that include two or more binding partners, each or which is capable of binding a different analyte measured in the disclosed mucosal healing assessment methods.

Abstract: of analytes in a serum sample from a patient, and applying a mathematical algorithm to the expression levels, thereby producing a Mucosal Healing Index score for the patient. The present disclosure also provides kits that include two or more binding partners, each or which is capable of binding a different analyte measured in the disclosed mucosal healing assessment methods.

Abstract: In some aspects, the present invention provides methods for predicting whether a subject will develop autoantibodies to an anti-TNF drug during the course of anti-TNF? drug therapy. In other aspects, the present invention provides methods for predicting the level of an anti-TNF? drug in a subject during the course of anti-TNF? drug therapy. Systems for predicting anti-TNF? drug levels and the likelihood of autoantibody formation during the course of anti-TNF? drug therapy are also provided herein. The present invention further provides methods for predicting a clinical outcome (e.g., endoscopic response) of a subject on anti-TNF? drug therapy.

Abstract: In some aspects, the present invention provides methods for predicting whether a subject will develop autoantibodies to an anti-TNF? drug during the course of anti-TNF? drug therapy. In other aspects, the present invention provides methods for predicting the level of an anti-TNF? drug in a subject during the course of anti-TNF? drug therapy. Systems for predicting anti-TNF? drug levels and the likelihood of autoantibody formation during the course of anti-TNF? drug therapy are also provided herein. The present invention further provides methods for predicting a clinical outcome (e.g., endoscopic response) of a subject on anti-TNF? drug therapy.

Abstract: The present invention provides methods for predicting whether an individual having inflammatory bowel disease (IBD) is likely to respond to vedolizumab treatment. Also provided are methods for predicting whether an individual with IBD such as Crohn's disease or ulcerative colitis will develop autoantibodies against vedolizumab. The present invention also provides a treatment regimen for an IBD patient which includes measuring the level of one or more predictive markers of response to vedolizumab prior to administering the anti-?4?7 integrin drug.

Abstract: The present invention relates generally to methods for predicting progression, initiation and susceptibility of osteoarthritis in human subjects using their genotype test results.

Abstract: In some aspects, the present invention provides methods for predicting whether a subject will develop autoantibodies to an anti-TNF? drug during the course of anti-TNF? drug therapy. In other aspects, the present invention provides methods for predicting the level of an anti-TNF? drug in a subject during the course of anti-TNF? drug therapy. Systems for predicting anti-TNF? drug levels and the likelihood of autoantibody formation during the course of anti-TNF? drug therapy are also provided herein. The present invention further provides methods for predicting a clinical outcome (e.g., endoscopic response) of a subject on anti-TNF? drug therapy.

Abstract: The present invention provides methods for predicting whether an individual having inflammatory bowel disease (IBD) is likely to respond to vedolizumab treatment. Also provided are methods for predicting whether an individual with IBD such as Crohn's disease or ulcerative colitis will develop autoantibodies against vedolizumab. The present invention also provides a treatment regimen for an IBD patient which includes measuring the level of one or more predictive markers of response to vedolizumab prior to administering the anti-?4?7 integrin drug.

Abstract: Diagnostics and therapeutics for resistance to weight-loss, which are based upon the identification of a subject's PLIN polymorphisms, haplotype and genotype pattern, are described in this invention.

Abstract: The present invention relates generally to methods for predicting progression, initiation and susceptibility of osteoarthritis in human subjects using their genotype test results.

Abstract: Diagnostics and therapeutics for resistance to weight-loss, which are based upon the identification of a subject's PLIN polymorphisms, haplotype and genotype pattern, are described in this invention.

Abstract: Diagnostics and therapeutics for osteoporosis, which are bases upon the identification of a subjects IL-1 haplotype and genotype pattern are described.

Abstract: This application relates to methods and tests that allow for the establishment of personalized weight-loss programs for a subject based upon the subject's metabolic genotype in key metabolic genes. Kits and methods are disclosed for determining a subject's metabolic genotype, which may be used to select an appropriate therapeutic/dietary regimen or lifestyle recommendation based upon the likelihood of a subject's responsiveness to certain diets and activity levels. Such a personalized weight-loss program will have obvious benefits (e.g., yield better results in terms of weight loss and weight maintenance) over traditional weight-loss programs that do not take into account genetic information.

Abstract: The invention provides methods and compositions for the pharmacogenetic analysis of anti-inflammatory compounds, especially for the pharmacogenetic association of responsiveness to rheumatoid arthritis medications that target TNF?.

Abstract: Methods and apparatus for use in complex genetics classification are disclosed. In one illustrative example, a method is performed using data from a sample population which includes counts of individuals in the sample population associated with both a particular diploid haplotype pair and a particular genetic trait class. A correspondence to analysis (COA) on the data from the sample population is performed (at least in part) so as to determine a first plurality of n-dimensional coordinates for each diploid haplotype pair and a second plurality of n-dimensional coordinates for each genetic trait class. A linear or quadratic classification analysis is then performed based on the first and the second pluralities of n-dimensional coordinates and diploid haplotype pairs of the at least two genes from an individual sample. Advantageously, the individual sample can be accurately classified into one of the genetic trait classes using the method.

Abstract: Software methods for identifying associations between genetic information and particular genetic traits are described. A candidate single nucleotide polymorphism (SNP) combination is selected from a plurality of candidate SNP combinations for a gene associated with (or suspected to be associated with) a genetic trait. Haplotype data associated with this candidate SNP combination are read for a plurality of individuals and grouped into a positive-responding group and a negative-responding group based on whether a predetermined trait criteria for an individual is met. A statistical analysis on the grouped haplotype data is performed to obtain a statistical measurement associated with the candidate SNP combination. The acts of selecting, reading, grouping, and performing are repeated as necessary to identify the candidate SNP combination having the optimal statistical measurement (if one exists). In one approach, all possible SNP combinations are selected and statistically analyzed.