DNA from AA-DHS participants was extracted from peripheral blood using the PureGene system (Gentra Systems, Minneapolis, MN). The AA-DHS GWAS utilized the Illumina 5M chip. Quality control (QC) checks in AA-DHS led to the exclusion of 12 individuals from the analyses: six had call rates <95%, two had discordant self-reported and genetically determined sex, one had a heterozygosity score outside of the mean ±4 times the standard error interval, two had the same sample identifiers and one had 100% European ancestry. GWAS analyses were performed on up to 697 individuals.
Imputation was performed using IMPUTE2 with phased haplotype data obtained from SHAPEIT2 [16 (link)]. Directly genotyped variants with a Hardy-Weinberg Equilibrium (HWE) p-value ≥1x10-04 and a call rate ≥95% were included and imputation was based on 3,436,913 autosomal variants. The multi-ethnic 1,000 Genomes Phase I integrated variant set release (v3) was used as the reference panel. Statistical analysis was performed for imputed variants that had an info score above 50%, a minor allele frequency (MAF) >1% and a HWE p-value ≥1x10-04.
Imputation was performed using IMPUTE2 with phased haplotype data obtained from SHAPEIT2 [16 (link)]. Directly genotyped variants with a Hardy-Weinberg Equilibrium (HWE) p-value ≥1x10-04 and a call rate ≥95% were included and imputation was based on 3,436,913 autosomal variants. The multi-ethnic 1,000 Genomes Phase I integrated variant set release (v3) was used as the reference panel. Statistical analysis was performed for imputed variants that had an info score above 50%, a minor allele frequency (MAF) >1% and a HWE p-value ≥1x10-04.
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