TOPMed T2D whole genome sequence analysis

Publications

Rare Non-coding Variation Identified by Large Scale Whole Genome Sequencing Reveals Unexplained Heritability of Type 2 Diabetes.
Wessel J, et al.
Submitted for publication, 2021.
medRxiv preprint

Phenotypes

  • Type 2 diabetes
  • Type 2 diabetes adj BMI

Subjects

Cases Controls Cohort(Click to view selection criteria for cases and controls) Ancestry
782 2,785 Atherosclerosis Risk in Communities Study VTE cohort (ARIC) Mixed
27 863 Genetics of Cardiometabolic Health in the Amish (Amish) European
14 293 Cleveland Clinic Atrial Fibrillation Study (CCAF) European
173 491 Cleveland Clinic Atrial Fibrillation Study (CFS) Mixed
15 52 Cardiovascular Health Study (CHS) European
1,117 7,500 Genetic Epidemiology of COPD (COPDGene) in the TOPMed Program Mixed
293 18 Diabetes Heart Study (DHS) Mixed
620 3,001 Framingham Heart Study (FHS) European
350 642 Genetic Epidemiology Network of Arteriopathy (GENOA) African
59 708 Genetics of Lipid Lowering Drugs and Diet Network (GOLDN) European
138 1,461 Genetic Epidemiology Network of Salt Sensitivity (GenSALT) Asian
198 1,351 Genetic Studies of Atherosclerosis Risk (GeneSTAR) Mixed
4 59 Heart and Vascular Health Study (HVH) European
323 1,329 Hypertension Genetic Epidemiology Network (HyperGEN) African
1,034 2,076 Jackson Heart Study (JHS) African
1,022 3,766 Multi-Ethnic Study of Atherosclerosis (MESA) Mixed
52 830 Massachusetts General Hospital Atrial Fibrillation Study (MGH_AF) European
16 88 Partners Healthcare Biorepository (Partners) European
232 781 Whole Genome Sequencing to Identify Causal Genetic Variants Influencing CVD Risk - San Antonio Family Studies (SAFS) Hispanic
185 918 Samoan Adiposity Study (Samoan) Samoan
26 128 Vanderbilt Atrial Fibrillation Ablation Registry (VAFAR) European
172 812 Vanderbilt Genetic Basis of Atrial Fibrillation (VU_AF) European
2,787 5,041 Women's Health Initiative (WHI) Mixed

Project

TOPMed logo

The NHLBI Trans-Omics for Precision Medicine program (TOPMed) integrates whole-genome sequencing with other 'omics data to improve scientific understanding of heart, lung, blood, and sleep disorders.

 

Experiment summary

This study is part of the TOPMed project "Whole Genome Sequence Analysis of Type 2 Diabetes Risk". Whole genome sequencing single variant analysis and rare variant analysis of type 2 diabetes was performed in 44,083 TOPMed participants: 9,639 T2D cases and 34,994 controls.

Acknowledgments

The Analysis Commons was funded by R01HL131136. Whole genome sequencing (WGS) for the Trans-Omics in Precision Medicine (TOPMed) program was supported by the National Heart, Lung and Blood Institute (NHLBI). WGS was provided by the following sequencing centers: Broad Genomics (3R01HL121007-01S1); Baylor (3U54HG003273-12S2 / HHSN268201500015C); NWGC (HHSN268201600032I); Psomagen (3R01HL112064-04S1); Illumina (R01HL112064); NYGC (HHSN268201500016C). Centralized read mapping and genotype calling, along with variant quality metrics and filtering, were provided by the TOPMed Informatics Research Center (3R01HL-117626-02S1). Phenotype harmonization, data management, sample-identity QC, and general study coordination, were provided by the TOPMed Data Coordinating Center (3R01HL-120393-02S1). We gratefully acknowledge the studies and participants who provided biological samples and data for TOPMed. The contributions of the investigators of the NHLBI TOPMed Consortium are gratefully acknowledged.

Dataset ID
TOPMed_frz5b_pooled_T2D_WGS