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Chunk #9 — METHODS AND MATERIALS — Genotyping, quality control and genetic relationship matrix

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Polygenic dissection of major depression clinical heterogeneity.
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Methods for biological sample collection and DNA extraction have been described previously(25). Autosomal SNPs were genotyped on the Affymetrix 6.0 Human Genome-Wide SNP Array in three separate batches. Main QC steps have been previously described(31;32). Primary analyses included 497,347 SNPs. Additional stringent QC was performed to build a genetic-relationship-matrix (GRM) in order to reduce the possibility that estimates from GRM-based analyses could be inflated by artifacts. The remaining 435,579 SNPs were used to build the GRM using GCTAv.1.24.1(21). All QC steps are described in supplemental methods.