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Chunk #9 — MATERIALS AND METHODS — Quality control and imputation

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Leveraging genome-wide data to investigate differences between opioid use vs. opioid dependence in 41,176 individuals from the Psychiatric Genomics Consortium.
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IMPUTE221, and the 1000 Genomes Project Phase 3 reference panel, which includes five continental groups19. High-quality imputed SNPs were retained for the association analysis, filtering for imputation INFO score > 0.8 and minor allele frequency (MAF) > 0.01 before analysis. After imputation, we tested for duplicated samples and cryptic relatedness among the cohorts analyzed. The association analysis was conducted considering variants present in at least 80% of the cohorts investigated (Supplementary Table 2).