Rare variant association analysis in 51,256 type 2 diabetes cases and 370,487 controls informs the spectrum of pathogenicity of monogenic diabetes genes

Abstract

AbstractWe meta-analyzed array data imputed with the TOPMed reference panel and whole-genome sequence (WGS) datasets and performed the largest, rare variant (minor allele frequency as low as 5×10−5) GWAS meta-analysis of type 2 diabetes (T2D) comprising 51,256 cases and 370,487 controls.We identified 52 novel variants at genome-wide significance (p<5 × 10−8), including 8 novel variants that were either rare or ancestry-specific. Among them, we identified a rare missense variant inHNF4Ap.Arg114Trp (OR=8.2, 95% confidence interval [CI]=4.6-14.0,p= 1.08×10−13), previously reported as a variant implicated in Maturity Onset Diabetes of the Young (MODY) with incomplete penetrance. We demonstrated that the diabetes risk in carriers of this variant was modulated by a T2D common variant polygenic risk score (cvPRS) (carriers in the top PRS tertile [OR=18.3, 95%CI=7.2-46.9,p=1.2×10−9] vs carriers in the bottom PRS tertile [OR=2.6, 95% CI=0.97-7.09,p= 0.06]. Association results identified eight variants of intermediate penetrance (OR>5) in monogenic diabetes (MD), which in aggregate as a rare variant PRS were associated with T2D in an independent WGS dataset (OR=4.7, 95% CI=1.86-11.77],p= 0.001). Our data also provided support evidence for 21% of the variants reported in ClinVar in these MD genes as benign based on lack of association with T2D.Our work provides a framework for using rare variant imputation and WGS analyses in large-scale population-based association studies to identify large-effect rare variants and provide evidence for informing variant pathogenicity.