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Chunk #7 — Materials and methods — RNA-seq and genotyping

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Allele-specific expression and high-throughput reporter assay reveal functional genetic variants associated with alcohol use disorders.
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DNA was obtained from the same brain tissues. The Axiom Biobank Genotyping Array (Thermo Fisher Scientific, Waltham, MA, USA) was used for genotyping. Monomorphic variants, variants with call rate ≤0.98 or Hardy–Weinberg equilibrium p < 10−5, and samples with call rate <0.90 were removed using PLINK [16]. Phasing was done using SHAPEIT2 [17]. IMPUTE2 [18] was used for imputation using the 1000 Genomes Phase 1 integrated panel (excluding singleton variants) as the reference. Variants with imputation score ≥0.8 and estimated minor allele frequency (MAF) ≥0.5 were included in the analysis.