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Chunk #7 — Methods — Genotyping and quality control

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Genetic risk for major depressive disorder and loneliness in sex-specific associations with coronary artery disease.
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Genetic data from 13,113 ARIC participants were downloaded from dbGaP (phs000280.v3.p1). Genotypes were measured on the Affymetrix 6.0 SNP array, and data were cleaned as previously described [23]. Genetic ancestry was assigned using STRUCTURE [24] in conjunction with HapMap reference populations, and European ancestry was defined as >90% probability of being in the CEU cluster. Genotypes were imputed to the October 2014 Phase 3 release of the 1000 Genomes cosmopolitan reference haplotypes [25] using SHAPEIT [20]/IMPUTE2 [21] and we excluded SNPs with INFO < 0.7, multiallelic SNPs, and structural variants. Dosage data were converted to hard genotyping calls, excluding variants with certainty <0.9, leaving 6,569,625 high quality SNPs for analysis. Inter-individual relatedness and principal components of ancestry were calculated by GCTA [26] and we randomly excluded one individual from pairs of related individuals (pihat > 0.05), leaving 6975 unrelated European ancestry participants.