Each sample was analyzed separately using specific analytic protocols that have been validated for that sample (18;22;25;31;32). Prior to meta-analysis, SNPs that did not satisfy quality control standards imposed for the current study were excluded (see Supplemental Text); only SNPs that survived quality control in all 5 samples were included in the meta-analysis. PLINK (v1.07)(33) was used to analyze allele dosage data for SAGE, CATS and COGA-cc. GWAF-GEE (34) was used to analyze the family data for DSM-IV cannabis dependence from COGA-f and OZALC+. Linear mixed models and Merlin-offline(35) were used to analyze criterion counts in COGA-f and OZALC+ respectively. Logistic and linear regressions were used for the diagnosis and count definitions, respectively (see Table S1 for covariates used for each sample). Results were meta-analyzed in METAL (36) using inverse variance weighting procedures and genomic control correction. Gene-based association analyses were conducted using MAGMA (37) with the 1000 Genomes European data (release version 3, May 22, 2014) as the reference panel. Gene boundaries were extended to include a 10kb window at the 3′ and 5′ ends.
