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Chunk #5 — Materials and methods — Statistical analyses — Meta-analysis of GWA results across cohorts

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Meta-analysis of Genome-wide Association Studies for Neuroticism, and the Polygenic Association With Major Depressive Disorder.
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6,949,614 SNPs for which results are reported. Genomic control inflation factors (lambda) and Manhattan and quantile–quantile plots per cohort are provided in eTable 3 and eFigures 1 and 2. SNPs with a P-value of 5 × 10−8 or smaller were considered genome-wide significant. In the Generation Scotland cohort, all SNPs with a P-value smaller than 1 × 10−5 were tested for replication. For these SNPs, a meta-analysis of all 30 cohorts was conducted. Because in the Generation Scotland cohort, sum scores were available for neuroticism, this meta-analysis was based on combining P-values, taking into account the direction of effect and weighting by sample size, rather than combining effect sizes.