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Chunk #7 — Methods — Measures — Genotyping, ancestry, and genetic relatedness matrix.

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Alcohol use disorder, psychiatric comorbidities, marriage and divorce in a high-risk sample.
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Participants’ DNA samples were genotyped using the Illumina Human1M array, the Illumina Human OmniExpress 12V1 array, the Illumina 2.5M array, or the Smokescreen genotyping arrays. A full description of data processing, quality control, and imputation is available elsewhere (Lai et al., 2019). EA sample data were imputed to Haplotype Reference Consortium, and the AA sample data to the 1000 Genomes Phase 3. Single nucleotide polymorphisms (SNPs) with a genotyping rate < 0.95, that violated Hardy-Weinberg equilibrium (p < 10−6), or had minor allele frequency < 0.01 were excluded from analysis in both the EA and AA samples.