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The UK Biobank project is a prospective cohort study with deep genetic and phenotypic data collected on approximately 500,000 individuals from across the United Kingdom, aged between 40 and 69 at recruitment. The open resource is unique in its size and scope. A rich variety of phenotypic and health-related information is available on each participant, including biological measurements, lifestyle indicators, biomarkers in blood and urine, and imaging of the body and brain. Follow-up information is provided by linking health and medical records. Genome-wide genotype data have been collected on all participants, providing many opportunities for the discovery of new genetic associations and the genetic bases of complex traits. Here we describe the centralized analysis of the genetic data, including genotype quality, properties of population structure and relatedness of the genetic data, and efficient phasing and genotype imputation that increases the number of testable variants to around 96 million. Classical allelic variation at 11 human leukocyte antigen genes was imputed, resulting in the recovery of signals with known associations between human leukocyte antigen alleles and many diseases.
Understanding the role that genetics has in phenotypic and disease variation, and its potential interactions with other factors, is crucial for a better understanding of human biology. It is hoped that this will lead to more successful drug development1, and potentially to more efficient and personalized treatments. As such, a key component of the UK Biobank resource has been the collection of genome-wide genetic data on every participant using a purpose-designed genotyping array2. An interim release of genotype data on approximately 150,000 UK Biobank participants in May 20 1 53 has already facilitated numerous studies4-6.
In this paper, we summarize the existing and planned content of the phenotype resource and describe the genetic dataset on the full 500,000 participants. To facilitate its wider use, we applied a range of quality control procedures and conducted a set of analyses that reveal properties of the genetic data-such as population structure and relatedness-that can be important for downstream analyses. In addition, we estimated haplotypes and imputed genotypes into the dataset that increases the number oftestable variants by more than 100-fold to approximately 96 million variants. We also imputed classical allelic variation at 11 human leukocyte antigen (HLA) genes, and replicated signals...