The present invention provides methods, systems, and code for accurately classifying whether a sample from a pediatric individual is associated with inflammatory bowel disease (IBD) or a clinical subtype thereof, hi particular, the present invention is useful for classifying a sample from a pediatric individual as an IBD sample using a statistical algorithm and/or empirical data. The present invention is also useful for differentiating between a clinical subtype of IBD such as Crohn's disease (CD) and ulcerative colitis (UC) using a statistical algorithm and/or empirical data. Thus, the present invention provides an accurate diagnostic prediction of IBD or a clinical subtype thereof and prognostic information useful for guiding treatment decisions.
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