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Chunk #9 — MATERIALS AND METHODS — Statistical Analysis — GWAS Analyses and Covariate Adjusment

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Genetic contributors to variation in alcohol consumption vary by race/ethnicity in a large multi-ethnic genome-wide association study.
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GWA analyses were conducted using PLINK44 v1.07 (http://pngu.mgh.harvard.edu/purcell/plink/) and R45 (https://www.R-project.org). Regional Manhattan plots were performed using LocusZoom v1.1 (http://locuszoom.sph.umich.edu/locuszoom/) including SNP association values ± 1Mb upstream and downstream of our peak significant SNPs.46 We assessed single-marker associations with drinker status and with the quantity of alcoholic drinks consumed per week using logistic and linear regression, respectively. We assumed an additive genetic model using allele counts (i.e., 0, 1, or 2 copies of the minor allele) for typed markers or additive dosages for imputed markers. We first analyzed each of the four race/ethnicity groups separately, adjusting for age, and sex, and lean body mass, which serves as a proxy for body size.47 Lean body mass was estimated using the James equation which relies on sex, height (cm), and total body weight (kg).48 We conducted sensitivity analyses without lean body mass as a covariate, and those analyses without lean body mass produced relatively similar results (Supplementary Table 2). To correct for differences in genetic ancestry, we include ancestry principal components (PCs) in our GWA analyses. To calculate the PCs, we used