The sequences of 150,119 genomes in the UK Biobank
Open accessPublished version of a preprint
Abstract
Detailed knowledge of how diversity in the sequence of the human genome affects phenotypic diversity depends on a comprehensive and reliable characterization of both sequences and phenotypic variation. Over the past decade, insights into this relationship have been obtained from whole-exome sequencing or whole-genome sequencing of large cohorts with rich phenotypic data 1,2 . Here we describe the analysis of whole-genome sequencing of 150,119 individuals from the UK Biobank 3 . This constitutes a set of high-quality variants, including 585,040,410 single-nucleotide polymorphisms, representing 7.0% of all possible human single-nucleotide polymorphisms, and 58,707,036 indels. This large set of variants allows us to characterize selection based on sequence variation within a population through a depletion rank score of windows along the genome. Depletion rank analysis shows that coding exons represent a small fraction of regions in the genome subject to strong sequence conservation. We define three cohorts within the UK Biobank: a large British Irish cohort, a smaller African cohort and a South Asian cohort. A haplotype reference panel is provided that allows reliable imputation of most variants carried by three or more sequenced individuals. We identified 895,055 structural variants and 2,536,688 microsatellites, groups of variants typically excluded from large-scale whole-genome sequencing studies. Using this formidable new resource, we provide several examples of trait associations for rare variants with large effects not found previously through studies based on whole-exome sequencing and/or imputation.
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Almost all UK Biobank participants underwent genome-wide array genotyping and, more recently, proteome, whole-exome sequencing and whole-genome sequencing.
“Further, almost all participants underwent genome-wide array genotyping and, more recently, proteome, whole-exome sequencing 83 and WGS 84 .”
From Multimodal biomedical AI (2022) · cites this paper as [84]
The Main section reports WGS for 150,119 UK Biobank participants, out of 500,000, and says the consortium is sequencing all participants—not that almost all had already undergone WGS. The citation is attached to WGS, so it does not establish the sentence’s separate claims about array genotyping, proteomics or exome sequencing. (LLM, conf=0.88)
Experimental — accuracy not yet measuredMore than 98% of observed genetic variation in humans is non-coding.
“Given that more than 98% of observed genetic variation in humans is non-coding7, global characterization of the complex effects of this vast majority of variants remains intractable without computational predictions.”
From Advancing regulatory variant effect prediction with AlphaGenome (2026) · cites this paper as [7]
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Circulating microRNAs as Potential Biomarkers in Pancreatic Cancer—Advances and Challenges
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Genetic architecture of telomere length in 462,666 UK Biobank whole-genome sequences
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Rare loss of function variants in the hepatokine gene INHBE protect from abdominal obesity
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Cancer cell-intrinsic PD-1: Its role in malignant progression and immunotherapy
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Genetic links between ovarian ageing, cancer risk and de novo mutation rates
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Self-citationGenome-wide association testing beyond SNPs
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Actionable Genotypes and Their Association with Life Span in Iceland
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Repeat polymorphisms underlie top genetic risk loci for glaucoma and colorectal cancer
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The rate and nature of mitochondrial DNA mutations in human pedigrees
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Relating pathogenic loss-of-function mutations in humans to their evolutionary fitness costs
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Addressing the Challenge of Biomedical Data Inequality: An Artificial Intelligence Perspective
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Estimation and mapping of the missing heritability of human phenotypes
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Mapping genetic diversity with the GenomeIndia project
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Not all exons are protein coding: Addressing a common misconception
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The Psychiatric Genomics Consortium: Discoveries and Directions
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A Genomics England haplotype reference panel and imputation of UK Biobank
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A minimal role for synonymous variation in human disease
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Discovering missing heritability in whole-genome sequencing data
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Protein-altering variants at copy number-variable regions influence diverse human phenotypes
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Alzheimer's Disease Sequencing Project release 4 whole genome sequencing dataset
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Sequence variants affecting the genome-wide rate of germline microsatellite mutations
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Self-citationInsertions and Deletions: Computational Methods, Evolutionary Dynamics, and Biological Applications
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Variant effect predictors: a systematic review and practical guide
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Self-citationThe gut microbiota links disease to human genome evolution
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Yield of genetic association signals from genomes, exomes and imputation in the UK Biobank
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Gene-based burden tests of rare germline variants identify six cancer susceptibility genes
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Self-citationLeveraging protein structural information to improve variant effect prediction
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Fast and accurate Bayesian polygenic risk modeling with variational inference
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Quantifying negative selection in human 3ʹ UTRs uncovers constrained targets of RNA-binding proteins
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Preserved Ratio Impaired Spirometry, Metabolomics, and the Risk of Type 2 Diabetes
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Genetic architecture of routinely acquired blood tests in a British South Asian cohort
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Transcription factor networks disproportionately enrich for heritability of blood cell phenotypes
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Genomic and neuroimaging approaches to bipolar disorder
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Genomic structural variation: A complex but important driver of human evolution
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Structural variation across 138,134 samples in the TOPMed consortiumPreprint
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Sequence diversity lost in early pregnancy
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Complex effects of sequence variants on lipid levels and coronary artery disease.
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Self-citationInsufficient evidence for natural selection associated with the Black Death
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Detlefsen, A. J., Paulukinas, R. D., & Penning, T. M. (2023) · International Journal of Molecular Sciences · doi:10.3390/ijms24031873 · Cited by 23 · see citing works
- Authors
- Halldorsson, B. V., Eggertsson, H. P., Moore, K. H. S., Hauswedell, H., Eiriksson, O., Ulfarsson, M. O., Palsson, G., Hardarson, M. T., Oddsson, A., Jensson, B. O., Kristmundsdottir, S., Sigurpalsdottir, B. D., Stefansson, O. A., Beyter, D., Holley, G., Tragante, V., Gylfason, A., Olason, P. I., Zink, F., Asgeirsdottir, M., Sverrisson, S. T., Sigurdsson, B., Gudjonsson, S. A., Sigurdsson, G. T., Halldorsson, G. H., Sveinbjornsson, G., Norland, K., Styrkarsdottir, U., Magnusdottir, D. N., Snorradottir, S., Kristinsson, K., Sobech, E., Jonsson, H., Geirsson, A. J., Olafsson, I., Jonsson, P., Pedersen, O. B., Erikstrup, C., Brunak, S., Ostrowski, S. R., DBDS Genetic Consortium, Andersen, S., Banasik, K., Burgdorf, K., Didriksen, M., Dinh, K. M., Erikstrup, C., Gudbjartsson, D., Hansen, T. F., Hjalgrim, H., Jemec, G., Jennum, P., Johansson, P. I., Larsen, M. A. H., Mikkelsen, S., Nielsen, K. R., Nyegaard, M., Ostrowski, S. R., Sækmose, S., Sørensen, E., Thorsteinsdottir, U., Brun, M. T., Ullum, H., Werge, T., Thorleifsson, G., Jonsson, F., Melsted, P., Jonsdottir, I., Rafnar, T., Holm, H., Stefansson, H., Saemundsdottir, J., Gudbjartsson, D. F., Magnusson, O. T., Masson, G., Thorsteinsdottir, U., Helgason, A., Jonsson, H., Sulem, P., & Stefansson, K.
- Affiliations
- deCODE Genetics (Iceland) (IS)
- Reykjavík University (IS)
- Zealand University Hospital Køge (DK)
- University of Copenhagen (DK)
- Copenhagen Business School (DK)
- Copenhagen University Hospital (DK)
- Aarhus University Hospital (DK)
- Statens Serum Institut (DK)
- Zealand University Hospital (DK)
- Aalborg University Hospital (DK)
- Aarhus University (DK)
- Odense University Hospital (DK)
- Sankt Hans Hospital (DK)
- ORCID
- Halldorsson, Bjarni V.
- Eggertsson, Hannes P.
- Moore, Kristjan H. S.
- Hauswedell, Hannes
- Eiriksson, Ogmundur
- Ulfarsson, Magnus O.
- Palsson, Gunnar
- Hardarson, Marteinn T.
- Oddsson, Asmundur
- Jensson, Brynjar O.
- Sigurpalsdottir, Brynja D.
- Stefansson, Olafur A.
- Beyter, Doruk
- Holley, Guillaume
- Tragante, Vinicius
- Gylfason, Arnaldur
- Olason, Pall I.
- Gudjonsson, Sigurjon A.
- Halldorsson, Gisli H.
- Styrkarsdottir, Unnur
- Pedersen, Ole Birger
- Brunak, Søren
- Banasik, Karina
- Burgdorf, Kristoffer
- Didriksen, Maria
- Dinh, Khoa Manh
- Hansen, Thomas Folkmann
- Hjalgrim, Henrik
- Jemec, Gregor
- Jennum, Poul
- Johansson, Pär Ingemar
- Mikkelsen, Susan
- Nielsen, Kasper Rene
- Nyegaard, Mette
- Sækmose, Susanne
- Sørensen, Erik
- Ullum, Henrik
- Werge, Thomas
- Jonsdottir, Ingileif
- Rafnar, Thorunn
- Holm, Hilma
- Gudbjartsson, Daniel F.
- Helgason, Agnar
- Jonsson, Hakon
- Sulem, Patrick
- Venue
- Nature
- Published
- 2022-07-20
- Volume
- 607
- Issue
- 7920
- Pages
- 732-740
- ISSN
- 0028-0836 (ISSN-L)
- 1476-4687
- PMC
- PMC9329122
- OpenAlex
- W4286005461
- Cited by
- 448
- References
- 113
- Citations by year
- 2026: 68 · 2025: 101 · 2024: 121 · 2023: 120 · 2022: 37 · 2021: 1
- FWCI
- 60.78
- Type
- journal article
- Language
- en
- Open access
- hybrid
- doi.org
- Locations
- Nature (publishedVersion, cc-by)
- bioRxiv (Cold Spring Harbor Laboratory) (acceptedVersion, cc-by-nd)
- PubMed Central (publishedVersion, cc-by)
- PubMed (publishedVersion)
- Research at the University of Copenhagen (University of Copenhagen) (publishedVersion, cc-by)
- VBN Forskningsportal (Aalborg Universitet) (acceptedVersion, other-oa)
- University of Southern Denmark Research Portal (University of Southern Denmark) (acceptedVersion, other-oa)
- Opin vísindi (Opin vísindi) (submittedVersion, cc-by-nc-sa)
- RePEc: Research Papers in Economics (submittedVersion)
- Opin vísindi (Opin vísindi) (submittedVersion, other-oa)
- CBS Research Portal (Copenhagen Business School) (submittedVersion, cc-by)
- Funders
- Amgen
- AstraZeneca
- GlaxoSmithKline
- Wellcome Trust
- Government of the United Kingdom
- UK Research and Innovation
- Medical Research Council (MC_PC_17228)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Genetic Associations and Epidemiology
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Genomics and Rare Diseases
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Phylogenetic Studies
- Keywords
- UK Biobank, whole genome sequencing, human genetic variation, single nucleotide polymorphisms, indels, structural variants, microsatellite markers, haplotype reference panel, genotype imputation, natural selection, sequence conservation, rare variants, trait association, phenotypic diversity
- MeSH terms
- Whole Genome Sequencing, Africa, Asia, Exons, United Kingdom, Haplotypes, Humans, Ireland, Genetic Variation, Cohort Studies, Genome, Human, Conserved Sequence, Biological Specimen Banks, Microsatellite Repeats, Polymorphism, Single Nucleotide, Genomics, Databases, Genetic, INDEL Mutation
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