Chunk #35 — STAR★METHODS — METHOD DETAILS — Genome-wide association study meta-analysis — Technical Quality Control (QC) of the 49 cohorts in the primary PGC sample
Technical QC was performed on single nucleotide polymorphisms (SNPs) in each core PGC study, applying standard PGC criteria including SNP missingness < 0.05 (before sample removal); sample missingness < 0.02; autosomal heterozygosity deviation (| Fhet | < 0.2); SNP missingness < 0.02 (after sample removal); difference in SNP missingness between cases and controls < 0.02; and SNP Hardy-Weinberg equilibrium (HWE: P > 10−6 in controls or P > 10−10 in cases). For chromosome X (chrX) genotypes, we applied the above QC to the males and females separately.41
