Ethics approval for the UK Biobank study was obtained from the North West Centre for Research Ethics Committee (11/NW/0382). Blood samples were collected from participants on their visit to a UK Biobank assessment centre and the samples are stored at the UK Biobank facility in Stockport, UK7 (link). Over a period of 18 months samples were retrieved, DNA was extracted, and 96-well plates of 94 × 50-μl aliquots were shipped to Affymetrix Research Services Laboratory for genotyping. Special attention was paid in the automated sample retrieval process at UK Biobank to ensure that experimental units such as plates or timing of extraction did not correlate systematically with baseline phenotypes such as age, sex, and ethnic background, or the time and location of sample collection. Full details of the UK Biobank sample retrieval and DNA extraction process were described previously34 (link).
On receipt of DNA samples, Affymetrix processed samples on the GeneTitan Multi-Channel (MC) Instrument in 96-well plates containing 94 UK Biobank samples and two control samples from the 1000 Genomes Project25 (link). Genotypes were then called from the array intensity data, in units called ‘batches’ which consist of multiple plates. Across the entire cohort, there were 106 batches of 4,700 UK Biobank samples each (Supplementary Information , Supplementary Table 12 ). Following the earlier interim data release, Affymetrix developed a custom genotype calling pipeline that is optimized for biobank-scale genotyping experiments, which takes advantage of the multiple-batch design35 . This pipeline was applied to all samples, including the 150,000 samples that were part of the interim data release. Consequently, some of the genotype calls for these samples may differ between the interim data release and this final data release (see below).
Routine quality checks were carried out during the process of sample retrieval, DNA extraction36 , and genotype calling37 . Any sample that did not pass these checks was excluded from the resulting genotype calls. The custom-designed arrays contain a number of markers that had not been previously typed using Affymetrix genotype array technology. As such, Affymetrix also applied a series of checks to determine whether the genotyping assay for a given marker was successful, either within a single batch, or across all samples. Where these newly attempted assays were not successful, Affymetrix excluded the markers from the data delivery (seeSupplementary Information for details).
On receipt of DNA samples, Affymetrix processed samples on the GeneTitan Multi-Channel (MC) Instrument in 96-well plates containing 94 UK Biobank samples and two control samples from the 1000 Genomes Project25 (link). Genotypes were then called from the array intensity data, in units called ‘batches’ which consist of multiple plates. Across the entire cohort, there were 106 batches of 4,700 UK Biobank samples each (
Routine quality checks were carried out during the process of sample retrieval, DNA extraction36 , and genotype calling37 . Any sample that did not pass these checks was excluded from the resulting genotype calls. The custom-designed arrays contain a number of markers that had not been previously typed using Affymetrix genotype array technology. As such, Affymetrix also applied a series of checks to determine whether the genotyping assay for a given marker was successful, either within a single batch, or across all samples. Where these newly attempted assays were not successful, Affymetrix excluded the markers from the data delivery (see
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