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Analysis Name and Accession
Name: A Genome-Wide Association Meta-Analysis Of Common Carotid Artery IMT
Accession: pha003879.1

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Analysis Description
The Cohorts for Heart and Aging Research in Genomic Epimiology (CHARGE) consortium was formed to facilitate genome-wide association study meta-analyses and replication among large, well-phenotyped cohort studies. Although originally founded by five cohort studies (Age, Gene, Environment, Susceptibility Study - Reykjavik (AGES), Atherosclerosis Risk in Communities (ARIC) study, Cardiovascular Health Study (CHS), Framingham Heart Study, Rotterdam Study, CHARGE has incorporated many genomic and phenotypic data from other cohorts, depending on the phenotype.

Association analysis between genotype and common carotid IMT was done separately within each study cohort according to a pre-specified plan. For each SNP, GWAS-specific results were combined using inverse-variance weighted meta-analysis in METAL.

Analysis Methods
Each study independently implemented a predefined GWAS analysis plan. For the continuous measures of common and internal carotid IMT, cross-sectional associations of ln(IMT) and genetic variation were performed using linear regression models (or linear mixed effects models in the Amish, FHS and ERF data to account for family relatedness). In primary analyses, all studies were adjusted for age and sex. Some studies made additional adjustments, including adjusting for study site, familial structure or for whether the DNA had been whole-genome amplified or not. For each of the 2.5 million SNPs, each study fit additive genetic models regressing trait on genotype dosage (02 copies of the variant allele). For common carotid IMT, the association of each SNP and ln(IMT) was expressed as the regression slope (β), its standard error (s.e.m. (β)) and a corresponding P value, restricted to autosomal SNPs that were reported in at least two studies and had an average minor allele frequency of at least 1%.
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