We used the lavaan (18) v0.6.5 package in R to estimate polychoric phenotypic correlations (rp) among AUDIT items. We used the Genomic Structural Equation Modeling v0.0.2 package in R, which is based on LD score regression (19), to estimate the heritability of each of the ten AUDIT items, and the genetic correlations between them. We applied standard quality control procedures prior to all analyses (e.g., used precomputed LD scores, excluded the major histocompatibility region, SNPs restricted to HapMap 3, applied minor allele frequency ≥1% and information score >.90 filters). Lastly, we used Genomic Structural Equation Modeling (9) to estimate genetic correlations between latent genetic factors and complex traits and disorders broadly related to human health (Supplementary Material 5.1.2). We applied a standard Benjamini–Hochberg false discovery rate correction (FDR 5%) to account for multiple testing.
