Computational protocol: Gene–obesogenic environment interactions in the UK Biobank study

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Protocol publication

[…] The UK Biobank recruited over 500 000 adults aged 37–73 years in 2006–10 from across the UK. Participants provided samples and a range of information via questionnaires, interviews and measurements. We used up to 119 733 adults of White British descent with genetic data, BMI and at least one obesogenic variable available. We did not include other ethnic groups, because individually they were underpowered to detect previously reported effects. British descent was defined as individuals who both self-identified as White British and were confirmed as ancestrally Caucasian using principal components analyses (PCA) of genome-wide genetic information. This dataset underwent extensive central quality control (http://biobank.ctsu.ox.ac.uk) including the exclusion of the majority of third-degree or closer relatives from a genetic kinship analysis of 96% of individuals. We performed an additional round of PCA on these 120 286 UK Biobank participants. We selected 95 535 independent single-nucleotide polymorphisms (SNPs) (pairwise r < 0.1) directly genotyped with a minor allele frequency (MAF) ≥ 2.5% and missingness < 1.5% across all UK Biobank participants with genetic data available at the time of this study (n = 152 732), and with HWE P > 1 × 10–6 within the White British participants. Principal components were subsequently generated using FlashPCA and the first five adjusted for in all analyses. […]

Pipeline specifications

Software tools kinship, FlashPCA
Databases UK Biobank
Applications Population genetic analysis, GWAS