Chunk #31 — Methods — Genome-wide genotyping array data sets used for evaluation of imputation quality and/or phenotype association analysis — Women’s Health Initiative

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Use of >100,000 NHLBI Trans-Omics for Precision Medicine (TOPMed) Consortium whole genome sequences improves imputation quality and detection of rare variant associations in admixed African and Hispanic/Latino populations.

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(~906,600 SNPs, 946,000 copy number variation probes) and on other participants through the MEGA array [44]. Imputation and association analysis was performed separately in individuals with Affymetrix only, MEGA only, and both Affymetrix and MEGA data (S1 Table). For variants with both Affymetrix and MEGA genotypes available, MEGA genotypes were used. In total, 4,318 Hispanic/Latino and 8,494 AA women with blood cell traits were included.