CHARGE Consortium

CHARGE Consortium

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 Mercury softwaresupport 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.

Related Publications

Jakobsdottir J, van der Lee SJ, Bis JC, Chouraki V, Li-Kroeger D, Yamamoto S, et al. Rare Functional Variant in TM2D3 is Associated with Late-Onset Alzheimer's Disease. PLoS Genet. 2016 ;12(10):e1006327.

Huang Z, Rustagi N, Veeraraghavan N, Carroll A, Gibbs RA, Boerwinkle E, et al. A hybrid computational strategy to address WGS variant analysis in >5000 samples. BMC Bioinformatics. 2016 ;17(1):361.

Yu B, Li AH, Muzny DM, Veeraraghavan N, de Vries PS, Bis JC, et al. Association of Rare Loss-Of-Function Alleles in HAL, Serum Histidine: Levels and Incident Coronary Heart Disease. Circ Cardiovasc Genet. 2015 ;8(2):351-5.

Franceschini N, Hu Y, Reiner AP, Buyske S, Nalls M, Yanek LR, et al. Prospective associations of coronary heart disease loci in African Americans using the MetaboChip: the PAGE study. PLoS One. 2014 ;9(12):e113203.

Grove ML, Yu B, Cochran BJ, Haritunians T, Bis JC, Taylor KD, et al. Best practices and joint calling of the HumanExome BeadChip: the CHARGE Consortium. PLoS One. 2013 ;8(7):e68095.