Genetic loci associated with prevalent and incident myocardial infarction and coronary heart disease in the Cohorts for Heart and Aging Research in Genomic Epidemiology (CHARGE) Consortium

Abstract

64Background 65 Genome-wide association studies have identified multiple genomic loci associated with coronary artery 66 disease, but most are common variants in non-coding regions that provide limited information on causal 67 genes and etiology of the disease. To better understand etiological pathways that might lead to discovery 131 Houston (21); SHIP was called in Illumina GenomeStudio using the CHARGE Consortium joint calling 132 cluster file; GeneSTAR used the Illumina GenomeStudio and zCall software (22); and WGHS data was 133 called using the Illumina BeadStudio v.3.3. Variant quality control (QC) was performed centrally (21) 134 and by the individual studies, including checking concordance with previous GWAS data, and excluding 135 participants with missing >5% genotypes, population clustering outliers, individuals with high inbreeding 136 coefficients or heterozygote rates, gender mismatches, duplicated pairs, and unexpectedly high proportion 137 of identity-by-descent sharing for family studies.