A method for evaluating a gastrointestinal tract may include characterizing one or more disease parameters using objective measures obtained from imaging data of a gastrointestinal tract. The one or more disease parameters reflect a measure of at least one of lesions, ulcers, bleeding, stenosis, and vasculature. The method may also include using the one or more characterized disease parameters to classify a disease state.

The present invention provides antibodies and methods for preparing antibodies to metabolites in the serotonin, tryptophan and kynurenine pathways, such as 5-hydroxyindole-3-acetic acid (5-HIAA), melatonin (MT) and kynurenic acid (KYNA). The specific metabolite antibodies have low cross-reactivity to structurally related metabolites, and are useful reagents for specific and sensitive immunoassays. The present invention also provides methods for using such antibodies to measure the levels of 5-HIAA, melatonin, or kynurenic acid in biological samples from human patients.

The present invention provides methods for aiding in the diagnosis of irritable bowel syndrome (IBS) in an individual. In particular, the present invention is useful for determining whether the individual does not have either celiac disease or inflammatory bowel disease (IBD), and has IBS and/or a subtype thereof. Thus, the present invention provides an accurate diagnostic prediction of IBS and is useful for guiding treatment decisions.

Methods of treating IBD in a subject using an anti-SMAD7 therapy, such as a SMAD7 antisense oligonucleotide, to reduce CCL20, IL8, or TNFα levels are disclosed. Methods of treating and managing IBD in a subject using an anti-SMAD7 therapy, such as a SMAD7 antisense oligonucleotide, based on CCL20, IL8, or TNFα levels are also disclosed. Also disclosed are methods of determining whether a subject with IBD is responsive or likely to be responsive to treatment an anti-SMAD7 therapy. Reduction of CCL20, IL8, or TNFα levels may correlated with IBD remission or decreases in CDAI score.

Methods and materials are disclosed for testing biomarkers in a subject suffering from inflammatory bowel disease (IBD) are described herein. Such detection can be useful for diagnosing and treating ulcerative colitis (UC) and Crohn's disease (CD), two forms of IBD that are otherwise difficult to distinguish. The method includes measuring the level of one or more of several biomarkers, including HD5 or MMP-7, which are expressed differentially in patents with UC and CD. A treatment may be based on the determination of whether the subject has ulcerative colitis or Crohn's disease.

A system and method for using new biomarkers to assess individual diseases is provided. In one embodiment of the present invention, absolute quantification of annotated metabolites by mass spectrometry is used to identify certain biomarkers and derivatives thereof (i.e., signatures), which are then used to screen for, diagnose, predict, prognose, and treat various diseases, including, but not limited to, breast cancer, ovarian cancer, colorectal cancer, pancreatic cancer, and acute graft-versus-host disease.

The methods and systems of the present invention are useful in the diagnosis of inflammatory bowel disease (IBD) and in the prognosis of IBD progression and disease complications. With the present invention, it is possible to predict outcome of disease and patients who will have a particular risk of disease complications and/or progression to surgery.

The present invention provides a method of measuring the levels of BCMA in a biological sample, specifically upon the B cell surface. The diagnostic assays are useful in predicting an individual's likelihood of developing or currently suffering from an autoimmune disease, such as SLE, and for methods for treating an individual clinically diagnosed with an autoimmune disease. This diagnostic test serves to predict a patient's likelihood to respond to a specific drug treatment, in particular treatment with BLyS antagonists, either singly or in combination with other immune suppressive drugs.

A method of diagnosing, monitoring progression of, or monitoring treatment of inflammatory bowel disease comprises determining the levels of CD14.sup.+HLA-DR.sup.hi monocytes or monocytes expressing CCR7 or CCR9 or both CCR7 and CCR9 in a sample obtained from a subject, wherein high levels of CD14.sup.+HLA-DR.sup.hi monocytes or monocytes expressing CCR7 or CCR9 or both CCR7 and CCR9, or increased levels of CD14.sup.+HLA-DR.sup.hi monocytes or monocytes expressing CCR7 or CCR9 or both CCR7 and CCR9 compared to control, indicate the presence or progression of inflammatory bowel disease. Similar methods for diagnosing irritable bowel syndrome are also described. Various companion therapeutic methods and useful binding reagents are also described.

The present invention provides methods for predicting clinical outcome from a sample of a subject having ulcerative colitis (UC), comprising determining a prognostic marker profile and classifying the subject as either a responder or a non-responder. The methods can be used to monitor and to predict the progression of UC, by determining the likelihood for UC to progress either rapidly or slowly in an individual based on the presence or level of at least one marker in a sample. The methods can also be used to predict the regression of UC, by determining the likelihood for UC to regress either rapidly or slowly in an individual.