Chunk #8 — Materials and Methods — Subjects, genotyping and assignment of nominal significance of dependent vs control allele frequencies in each sample — 1) dbGAP samples from the FSCD, COGA and COGEND studies
Genotyping for these samples was performed using Illumina 1 M SNP arrays at the Center for Inherited Disease Research (CIDR), with quality controls and principal components analysis (PCA) controls for racial/ethnic background available at the dbGAP website. Genotypes from dependent and control individuals were selected from dbGAP files, excluding SNPs with minor allele frequencies less than 0.01–0.02 (for European and African American samples, respectively) and those with missing call rates >5%. p values for each SNP were based on χ2 tests.
