Chunk #7 — MATERIALS AND METHODS — Genotyping and quality control

Source

Genome-wide association study of alcohol dependence:significant findings in African- and European-Americans including novel risk loci.

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076 additional SNPs were removed before imputation because of minor allele frequencies (MAF) <1%. After data cleaning and quality control, 5697 individuals and 889 659 SNPs remained for imputation. Further QC information and genotype imputation methods are found in Supplementary Materials. After applying the same QC procedures to the SAGE sample, 39 subjects with call rates <98% were excluded and 726 191 SNPs remained for analysis.