title: Large sample size, wide variant spectrum, and advanced machine-learning technique boost risk prediction for inflammatory bowel disease.
abstract: We performed risk assessment for Crohn's disease (CD) and ulcerative colitis (UC), the two common forms of inflammatory bowel disease (IBD), by using data from the International IBD Genetics Consortium's Immunochip project. This data set contains ~17,000 CD cases, ~13,000 UC cases, and ~22,000 controls from 15 European countries typed on the Immunochip. This custom chip provides a more comprehensive catalog of the most promising candidate variants by picking up the remaining common variants and certain rare variants that were missed in the first generation of GWAS. Given this unprecedented large sample size and wide variant spectrum, we employed the most recent machine-learning techniques to build optimal predictive models. Our final predictive models achieved areas under the curve (AUCs) of 0.86 and 0.83 for CD and UC, respectively, in an independent evaluation. To our knowledge, this is the best prediction performance ever reported for CD and UC to date.
authors.affiliation: Department of Computer Science, New Jersey Institute of Technology, Newark, NJ 07102, USA. Electronic address: zhiwei04@gmail.com.
authors.forename: Zhi
authors.initials: Z
authors.lastname: Wei
authors.forename: Wei
authors.initials: W
authors.lastname: Wang
authors.forename: Jonathan
authors.initials: J
authors.lastname: Bradfield
authors.forename: Jin
authors.initials: J
authors.lastname: Li
authors.forename: Christopher
authors.initials: C
authors.lastname: Cardinale
authors.forename: Edward
authors.initials: E
authors.lastname: Frackelton
authors.forename: Cecilia
authors.initials: C
authors.lastname: Kim
authors.forename: Frank
authors.initials: F
authors.lastname: Mentch
authors.forename: Kristel
authors.initials: K
authors.lastname: Van Steen
authors.forename: Peter M
authors.initials: PM
authors.lastname: Visscher
authors.forename: Robert N
authors.initials: RN
authors.lastname: Baldassano
authors.forename: Hakon
authors.initials: H
authors.lastname: Hakonarson
mesh_terms: D019540:Area Under Curve; D016022:Case-Control Studies; D003093:Colitis, Ulcerative / Q000235:genetics*; D003424:Crohn Disease / Q000235:genetics*; D056726:Genetic Association Studies; D020022:Genetic Predisposition to Disease; D006801:Humans; D015810:Linkage Disequilibrium; D016015:Logistic Models; D008957:Models, Genetic; D020641:Polymorphism, Single Nucleotide; D018570:Risk Assessment / Q000379:methods; D012307:Risk Factors; D018401:Sample Size; D060388:Support Vector Machine