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Chunk #22 — Online Methods — Genotyping and imputation

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GWAS of lifetime cannabis use reveals new risk loci, genetic overlap with psychiatric traits, and a causal influence of schizophrenia.
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Genotyping was performed on various genotyping platforms and standard quality control checks were performed prior to imputation. Genotype data were imputed using the 1000 Genomes phase 1 release reference set49 for ICC and 23andMe, and the Haplotype Reference Consortium reference set50 for the UK-Biobank sample. Information about samples, genotyping, imputation, and quality control is summarized in Supplementary Table S11 and S12. After quality control, the ICC sample comprised 35,297 individuals and 6,643,927SNPs, the 23andMe sample 22,683 individuals and 7,837,888 SNPs, and the UK-Biobank sample 126,785 individuals and 10,827,718 SNPs.