Our understanding of the genetic basis of T2D has been significantly advanced by identification of T2D loci through analysis of common variation; however, evidence suggests a role for rare regulatory variation influencing T2D. We leveraged the largest available whole genome sequence (WGS) data from NHLBI’s Trans-Omics for Precision Medicine (TOPMed) initiative and diabetes-centric genomic function data to the interpretation of results. We performed single-variant pooled-ancestry association analyses with (>30x deep sequence) WGS in 13,200 individuals (2,601 T2D and 10,599 controls) from 6 studies. The association analyses were performed in the Analysis Commons hosted on DNANexus. We demonstrated the utility of the OASIS (Omics Analysis, Search and Information System) platform and integrating diabetes-specific functional annotation in a recently discovered locus (GIP-IGF2BP1) to fine-map to the likely causal variants. Our results identified common (minor allele frequency [MAF] > 0.05) variant associations (P < 5 × 10-8) at a known locus with T2D: TCF7L2 (rs7903146, P = 3.8 × 10-12). We also identified a potentially novel association on Chr15q21 with 27 rare variants (MAF = 0.2%, P =1.3 × 10-8, r2=1) spanning a 7.5 MB region. In the Old Order Amish study, 53 individuals carry the haplotype tagged by these 27 variants; 17% of carriers are diagnosed with T2D compared to 3% of the non-carriers. Interrogation of the GIP-IGF2BP1 locus, utilizing diabetes-specific annotation and association evidence of both common and rare non-coding variants, within the OASIS browser implicated nearby genes in the region as being the likely biologic candidates.

In conclusion, preliminary results suggest WGS analysis can discover novel loci for complex traits. Work is ongoing to refine annotation for rare variant association tests and perform functional fine-mapping across the genome. We soon will extend our analysis into the next release of WGS data from TOPMed (N∼69,000 individuals).


J. Wessel: Employee; Spouse/Partner; Eli Lilly and Company. J.A. Brody: None. A. Manning: None.

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