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Chunk #13 — MATERIALS AND METHODS — Target dataset

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Evaluating risk for alcohol use disorder: Polygenic risk scores and family history.
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were considered as having European ancestry. Before imputation, variants with A/T or C/G alleles, missing rate >5%, MAF <3%, and HWE P-value < 0.0001 were excluded. SHAPEIT2 (Delaneau et al., 2013) was used to phase the haplotypes and Minimac3 (Das et al., 2016) was used for imputation to the 1000 Genomes (Phase 3, version 5, NCBI GRCh 37) separately by array. Variants with imputation quality score R2≥0.3 were kept for analysis.