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he primary aim of the Women's Genome Health Study (WGHS) is to create a comprehensive, fully searchable genome-wide database of >360 000 single nucleotide polymorphisms among at least 25 000 initially healthy American women participating in the ongoing NIH-funded Women's Health Study (WHS). These women have already been followed over a 12-year period for major incident health events including but not limited to myocardial infarction, stroke, cancer, diabetes, osteoporosis, venous-thromboembolism, cognitive decline, and common visual disorders such as age- related macular degeneration and cataracts. Investigations within the WGHS will seek to identify relevant patterns of genetic polymorphism that predict future disease states in otherwise healthy American women, and to evaluate patterns of genetic polymorphism that relate to multiple intermediate phenotypes including blood-based determinants of disease that were measured at baseline for each study participant. By linking genome-wide data to the existing epidemiologic databank of the parent WHS, which includes comprehensive dietary, behavioral, and traditional exposure data on each participant since cohort inception in 1992, the WGHS will also allow exploration of gene-environment and gene-gene interactions as they relate to incident disease states. Thus, with continued follow-up of the WHS, the WGHS provides a unique scientific resource-a full-cohort, prospective, genome-wide association study among initially healthy American women.

DNA EXTRACTION AND GENOTYPING PROCEDURES

Genomic DNA extraction was performed on buffycoat samples obtained at baseline from each participant (made possible by funding from Roche Diagnostics, the Doris Duke Charitable Foundation, and the Leducq Foundation). The MagNA Pure LC System (Roche Molecular Biochemicals) based on magnetic bead technology was used according to manufacturer's specifications to perform all DNA isolation steps. The integrity of the isolated DNA was checked randomly on 1% agarose gel together with molecular weight marker III (Roche Molecular Biochemicals). DNA yields were calculated from the OD260 nm measurement, and purity assessed by calculating the ratio of OD260 nm to OD280 nm (24).

SNP genotyping of these DNA samples is performed using the Illumina Infinium II assay (27) to query a genome-wide set of 315 176 haplotype-tagging SNP markers (the Human HAP300 panel) (28). We added to this a focused panel of 45 882 missense and haplotype-tagging SNPs selected to enhance coverage of genomic regions in which we have a strong a priori interest owing to presence of genes believed to be of relevance to cancer as well as metabolic, cardiovascular, and inflammatory diseases (Human HAP300 Duoplus). DNA samples are genotyped in batches of 95 WGHS participants with 1 CEPH (Centre d'Etude de Polymorphism Humain) DNA (NA10846) included to monitor genotyping consistency and plate orientation. Genotyping reactions use 750 μg of genomic DNA where possible, although in some cases successful genotyping has been performed with as little as 45 µg of DNA. The Infinium II process was implemented using Illumina Infinium Robot Control software and monitored using the Illumina Infinium laboratory information management system. The hardware platform consists of 4 Tecan EVO liquid-handling robots, 8 hybridization ovens, 3 Illumina BeadStation confocal scanners, and dual-processor workstations with access to > 1 TB of disk array storage to monitor workflow and generate high-quality reduced data. Genotype calls are generated and subjected to quality control using Illumina BeadStudio v3.1 software.