Population-specific rare variants influence age at diagnosis in Korean inflammatory bowel disease

Abstract

Background/Aims Inflammatory bowel disease (IBD), which includes Crohn's disease (CD) and ulcerative colitis (UC), is increasing in East Asia. Most known susceptibility loci, identified primarily in Europeans, remain insufficient to explain clinical heterogeneity in Asians. We performed whole-exome sequencing in Korean IBD patients to identify population-specific variants influencing age at diagnosis. Methods We analyzed 341 Korean IBD patients (192 CD, 149 UC) from three cohorts. Case-control analysis with external controls was confounded by platform heterogeneity, so we used a within-case Cox proportional hazards model instead. Variants were prioritized using a dual-threshold strategy. Gene-level analysis identified subtype-specific pathways, and disease progression was assessed in patients with longitudinal data (n = 206). Results We identified 12 novel rare variants (minor allele frequency < 0.01 in gnomAD) predominantly observed in East Asian populations. One variant in GSG1 (rs146166808) reached genome-wide significance (p = 3.39 × 10−8); carriers showed accelerated disease onset and increased risk of aggressive progression (OR = 12.52, p = 0.050). Subtype-specific analyses identified two variants for CD (GSG1, CYP2D6) and five for UC (including IGLL1). Gene-level analysis revealed distinct genetic architectures: CD showed enrichment for axon guidance pathways (p = 0.000065), whereas UC showed enrichment for calcium signaling and tissue maintenance pathways (p = 0.00068). Conclusions We identified population-specific rare variants influencing disease onset and progression in Korean IBD. Distinct genetic architectures underlying CD and UC provide insight into IBD heterogeneity and potential therapeutic targets in this population.