The Cohorts for Heart and Aging Research in Genomic Epidemiology (CHARGE) consortium is an international organization founded to facilitate genome-wide association study meta-analyses and replication opportunities among multiple large and well-phenotyped longitudinal cohort studies.
The goal of the recent CHARGE study is to identify susceptibility genes underlying selected well-replicated GWAS findings for heart, lung, and blood diseases and their risk factors.
To support this work, the BCM-HGSC coordinated receipt of samples from various repositories, and generated sequence data and primary analysis on over 5,000 human genome samples and over 15,000 exome samples.
In addition to generating primary sequence data, the BCM-HGSC completed a project level VCF (pVCF) for both WGS and whole exome data sets across three cohorts: Atherosclerosis Risk in Communities (ARIC); Framingham Heart Study (FHS), National Heart, Lung, and Blood Institute (NHLBI); and Cardiovascular Health Study (CHS).
A project level vcf (pVCF) summarizes variant calls (SNV and Indels) across the entire study such that every call that was ever made on a sample, is made available by the rest of the samples in the study. In this way, we are able to report even reference homozygous calls with the same definition of read depths used in calculating variant calls. This pVCF functions as a unified data set to be delivered to members of the CHARGE consortium, where it is analyzed with extensive metadata to support the research aims of the various CHARGE working groups.
As part of its participation in the CHARGE Consortium, the BCM-HGSC utilized the DNAnexus platform to analyze the genomes of over 15,000 individuals, encompassing over 5,000 whole genomes and 15,000 whole exomes, using our Mercury pipeline.