Chunk #21 — MATERIALS AND METHODS — Part II: GWAS results from varying p-value thresholds — SNP pruning

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Using genetic information from candidate gene and genome-wide association studies in risk prediction for alcohol dependence.

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The LD-based pruning function in PLINK v1.07 was used to prune the 1,041,983 SNPs genotyped in the combined sample before association analyses were performed. The SNPs were pruned at r2 < 0.50 using a sliding window of 50 base pairs shifted by 5 base pairs following each pruning step.