The significance cut-off in the AJ IBD SKAT-O test was relaxed to P < 0.01 in order to capture other possible IBD-associated candidates (127 genes, of which 3 are already known IBD-associated genes: LRRK2, NOD2, and VDR)4, from which a subset of genes was prioritized by 4 complementary pathway enrichment and biological relatedness methods: Ingenuity Pathway Analysis (IPA), ToppGene, Genome-Scale Integrated Analysis of Networks in Tissues (GIANT), and Human Gene Connectome (HGC) (Fig. 2a, “Methods”). Here, LRRK2 is linked to inflammatory bowel disease.