Computational protocol: Host-microbe interactions have shaped the genetic architecture of inflammatory bowel disease

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Protocol publication

[…] We conducted a meta-analysis of GWAS datasets after imputation to the HapMap3 reference set, and aimed to replicate in the Immunochip data any SNPs with p < 0.01. We compared likelihoods of different disease models to assess whether each locus was associated with CD, UC or both. We used databases of eQTL SNPs and coding SNPs in linkage disequilibrium with our hit SNPs, as well as the network tools GRAIL and DAPPLE, and a co-expression network analysis to prioritize candidate genes in our loci. Gene Ontology, ImmGen mouse immune cell expression resource, the TreeMix selection software, and a Bayesian causal network analysis were used to functionally annotate these genes. […]

Pipeline specifications

Software tools GRAIL, TreeMix
Databases ImmGen
Application Population genetic analysis
Organisms Homo sapiens
Diseases Colitis, Ulcerative, Crohn Disease, Infection, Psoriasis, Spondylitis, Ankylosing, Inflammatory Bowel Diseases