Chunk #15 — Materials and Methods — QUALITY CONTROL ANALYSES — SNPs — GenRED and GAIN-MDD

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Novel loci for major depression identified by genome-wide association study of Sequenced Treatment Alternatives to Relieve Depression and meta-analysis of three studies.

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SNP QC for the GenRED sample is described in the companion paper4 and Supplementary Methods. We carried out new QC analyses of the GAIN MDD dataset (Supplementary Methods), to ensure consistency across the datasets and because final post-QC data were not available from dbGAP. We included 434,312 SNPs (vs. 435,291 in the published GWAS report5).