The UK10K project identifies rare variants in health and disease
Open accessAbstract
The contribution of rare and low-frequency variants to human traits is largely unexplored. Here we describe insights from sequencing whole genomes (low read depth, 7×) or exomes (high read depth, 80×) of nearly 10,000 individuals from population-based and disease collections. In extensively phenotyped cohorts we characterize over 24 million novel sequence variants, generate a highly accurate imputation reference panel and identify novel alleles associated with levels of triglycerides (APOB), adiponectin (ADIPOQ) and low-density lipoprotein cholesterol (LDLR and RGAG1) from single-marker and rare variant aggregation tests. We describe population structure and functional annotation of rare and low-frequency variants, use the data to estimate the benefits of sequencing for association studies, and summarize lessons from disease-specific collections. Finally, we make available an extensive resource, including individual-level genetic and phenotypic data and web-based tools to facilitate the exploration of association results. Low read depth sequencing of whole genomes and high read depth exomes of nearly 10,000 extensively phenotyped individuals are combined to help characterize novel sequence variants, generate a highly accurate imputation reference panel and identify novel alleles associated with lipid-related traits; in addition to describing population structure and providing functional annotation of rare and low-frequency variants the authors use the data to estimate the benefits of sequencing for association studies. This paper, combining data and initial findings from the different arms of the UK10K project, describes insights from low-read-depth sequencing of whole genomes or high-read-depth exome sequencing of nearly 10,000 individuals sampled from a range of disease collections, as well as participants from healthy population based cohorts. The authors characterize novel sequence variants, generate a highly accurate imputation reference panel and identify novel alleles associated with lipid-related traits. In addition to describing population structure and providing functional annotation of rare and low frequency variants, they use the data to estimate the benefits of sequencing for association studies.
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Increased access to exome and whole-genome sequence data has extended discovery to low-frequency and rare alleles previously inaccessible to GWAS, through direct association and imputation.
“Recently, increased access to exome and whole-genome sequence data has, through both direct association analysis45,46 and imputation3,4, extended discovery to low-frequency and rare alleles previously inaccessible to GWAS.”
From A brief history of human disease genetics (2020) · cites this paper as [46]
The remaining 29 are suggested to be due to a combination of incomplete penetrance, late onset of disease, mild symptoms not seeking medical attention, unrecognised technical issues with sequencing or annotation, or dubious evidence to support the gene-phenotype assignment.
“We suggest that the remaining 29 are due to a combination of incomplete penetrance[12–16], late onset of disease (i.e. not yet having occurred), individuals with mild symptoms not seeking medical attention, unrecognised technical issues with sequencing or annotation (e.g. tissue specific alternative splicing), or dubious evidence to support the gene-phenotype assignment”
From Health and population effects of rare gene knockouts in adult humans with related parents (2016) · cites this paper as [14]
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- Authors
- The UK10K Consortium, Writing group, Walter, K., Min, J. L., Huang, J., Crooks, L., Memari, Y., McCarthy, S., Perry, J. R. B., Xu, C., Futema, M., Lawson, D., Iotchkova, V., Schiffels, S., Hendricks, A. E., Danecek, P., Li, R., Floyd, J., Wain, L. V., Barroso, I., Humphries, S. E., Hurles, M. E., Zeggini, E., Barrett, J. C., Plagnol, V., Brent Richards, J., Greenwood, C. M. T., Timpson, N. J., Durbin, R., Soranzo, N., Production group, Bala, S., Clapham, P., Coates, G., Cox, T., Daly, A., Danecek, P., Du, Y., Durbin, R., Edkins, S., Ellis, P., Flicek, P., Guo, X., Guo, X., Huang, L., Jackson, D. K., Joyce, C., Keane, T., Kolb-Kokocinski, A., Langford, C., Li, Y., Liang, J., Lin, H., Liu, R., Maslen, J., McCarthy, S., Muddyman, D., Quail, M. A., Stalker, J., Sun, J., Tian, J., Wang, G., Wang, J., Wang, Y., Wong, K., Zhang, P., Cohorts group, Barroso, I., Birney, E., Boustred, C., Chen, L., Clement, G., Cocca, M., Danecek, P., Davey Smith, G., Day, I. N. M., Day-Williams, A., Down, T., Dunham, I., Durbin, R., Evans, D. M., Gaunt, T. R., Geihs, M., Greenwood, C. M. T., Hart, D., Hendricks, A. E., Howie, B., Huang, J., Hubbard, T., Hysi, P., Iotchkova, V., Jamshidi, Y., Karczewski, K. J., Kemp, J. P., Lachance, G., Lawson, D., Lek, M., Lopes, M., MacArthur, D. G., Marchini, J., Mangino, M., Mathieson, I., McCarthy, S., Memari, Y., Metrustry, S., Min, J. L., Moayyeri, A., Muddyman, D., Northstone, K., Panoutsopoulou, K., Paternoster, L., Perry, J. R. B., Quaye, L., Brent Richards, J., Ring, S., Ritchie, G. R. S., Schiffels, S., Shihab, H. A., Shin, S.-Y., Small, K. S., Soler Artigas, M., Soranzo, N., Southam, L., Spector, T. D., St Pourcain, B., Surdulescu, G., Tachmazidou, I., Timpson, N. J., Tobin, M. D., Valdes, A. M., Visscher, P. M., Wain, L. V., Walter, K., Ward, K., Wilson, S. G., Wong, K., Yang, J., Zeggini, E., Zhang, F., Zheng, H.-F., Neurodevelopmental disorders group, Anney, R., Ayub, M., Barrett, J. C., Blackwood, D., Bolton, P. F., Breen, G., Collier, D. A., Craddock, N., Crooks, L., Curran, S., Curtis, D., Durbin, R., Gallagher, L., Geschwind, D., Gurling, H., Holmans, P., Lee, I., Lönnqvist, J., McCarthy, S., McGuffin, P., McIntosh, A. M., McKechanie, A. G., McQuillin, A., Morris, J., Muddyman, D., O'Donovan, M. C., Owen, M. J., Palotie, A., Parr, J. R., Paunio, T., Pietilainen, O., Rehnström, K., Sharp, S. I., Skuse, D., St Clair, D., Suvisaari, J., Walters, J. T. R., Williams, H. J., Obesity group, Barroso, I., Bochukova, E., Bounds, R., Dominiczak, A., Durbin, R., Farooqi, I. S., Hendricks, A. E., Keogh, J., Marenne, G., McCarthy, S., Morris, A., Muddyman, D., O'Rahilly, S., Porteous, D. J., Smith, B. H., Tachmazidou, I., Wheeler, E., Zeggini, E., Rare disease group, Al Turki, S., Anderson, C. A., Antony, D., Barroso, I., Beales, P., Bentham, J., Bhattacharya, S., Calissano, M., Carss, K., Chatterjee, K., Cirak, S., Cosgrove, C., Durbin, R., Fitzpatrick, D. R., Floyd, J., Reghan Foley, A., Franklin, C. S., Futema, M., Grozeva, D., Humphries, S. E., Hurles, M. E., McCarthy, S., Mitchison, H. M., Muddyman, D., Muntoni, F., O'Rahilly, S., Onoufriadis, A., Parker, V., Payne, F., Plagnol, V., Lucy Raymond, F., Roberts, N., Savage, D. B., Scambler, P., Schmidts, M., Schoenmakers, N., Semple, R. K., Serra, E., Spasic-Boskovic, O., Stevens, E., van Kogelenberg, M., Vijayarangakannan, P., Walter, K., Williamson, K. A., Wilson, C., Whyte, T., Statistics group, Ciampi, A., Greenwood, C. M. T., Hendricks, A. E., Li, R., Metrustry, S., Oualkacha, K., Tachmazidou, I., Xu, C., Zeggini, E., Ethics group, Bobrow, M., Bolton, P. F., Durbin, R., Fitzpatrick, D. R., Griffin, H., Hurles, M. E., Kaye, J., Kennedy, K., Kent, A., Muddyman, D., Muntoni, F., Lucy Raymond, F., Semple, R. K., Smee, C., Spector, T. D., Timpson, N. J., Incidental findings group, Charlton, R., Ekong, R., Futema, M., Humphries, S. E., Khawaja, F., Lopes, L. R., Migone, N., Payne, S. J., Plagnol, V., Pollitt, R. C., Povey, S., Ridout, C. K., Robinson, R. L., Scott, R. H., Shaw, A., Syrris, P., Taylor, R., Vandersteen, A. M., Management committee, Barrett, J. C., Barroso, I., Davey Smith, G., Durbin, R., Farooqi, I. S., Fitzpatrick, D. R., Hurles, M. E., Kaye, J., Kennedy, K., Langford, C., McCarthy, S., Muddyman, D., Owen, M. J., Palotie, A., Brent Richards, J., Soranzo, N., Spector, T. D., Stalker, J., Timpson, N. J., Zeggini, E., Lipid meta-analysis group, Amuzu, A., Pablo Casas, J., Chambers, J. C., Cocca, M., Dedoussis, G., Gambaro, G., Gasparini, P., Gaunt, T. R., Huang, J., Iotchkova, V., Isaacs, A., Johnson, J., Kleber, M. E., Kooner, J. S., Langenberg, C., Luan, J., Malerba, G., März, W., Matchan, A., Min, J. L., Morris, R., Nordestgaard, B. G., Benn, M., Ring, S., Scott, R. A., Soranzo, N., Southam, L., Timpson, N. J., The UCLEB Consortium, Toniolo, D., Traglia, M., Tybjaerg-Hansen, A., van Duijn, C. M., van Leeuwen, E. M., Varbo, A., Whincup, P., Zaza, G., Zeggini, E., & Zhang, W.
- Affiliations
- Wellcome Sanger Institute (GB)
- BGI Group (China) (CN)
- European Bioinformatics Institute (GB)
- Jewish General Hospital (CA)
- Great Ormond Street Hospital (GB)
- University of Trieste (IT)
- University of Cambridge (GB)
- King's College London (GB)
- Biogen (United States) (US)
- Guy's Hospital (GB)
- Translational Research Institute (AU)
- St George's, University of London (GB)
- Broad Institute (US)
- Centre for Human Genetics (GB)
- Harvard University (US)
- University of Leicester (GB)
- The University of Western Australia (AU)
- Royal Edinburgh Hospital (GB)
- University of California, Los Angeles (US)
- University College London (GB)
- St. James's Hospital (IE)
- University of Helsinki (FI)
- Western General Hospital (GB)
- Queen Mary University of London (GB)
- Université du Québec à Montréal (CA)
- National Cancer Research Institute (GB)
- Genetic Alliance UK (United Kingdom) (GB)
- St James's University Hospital (GB)
- University of Lisbon (PT)
- Erasmus MC (NL)
- Medizinische Fakultät Mannheim (DE)
- University of Verona (IT)
- University of Copenhagen (DK)
- University of Bristol (GB)
- Medical University of Graz (AT)
- Copenhagen University Hospital (DK)
- IRCCS Ospedale San Raffaele (IT)
- Imperial College London (GB)
- ORCID
- Coates, Guy
- Edkins, Sarah
- Flicek, Paul
- Guo, Xueqin
- Jackson, David K.
- Keane, Thomas
- Quail, Michael A.
- Sun, Jianping
- Tian, Jing
- Wang, Guangbiao
- Wang, Jun
- Zhang, Pingbo
- Birney, Ewan
- Chen, Lu
- Down, Thomas
- Dunham, Ian
- Evans, David M.
- Geihs, Matthias
- Hart, Deborah
- Hubbard, Tim
- Hysi, Pirro
- Jamshidi, Yalda
- Karczewski, Konrad J.
- Kemp, John P.
- Lek, Monkol
- MacArthur, Daniel G.
- Marchini, Jonathan
- Mangino, Massimo
- Mathieson, Iain
- Moayyeri, Alireza
- Northstone, Kate
- Panoutsopoulou, Kalliope
- Paternoster, Lavinia
- Ritchie, Graham R. S.
- Shin, So-Youn
- Small, Kerrin S.
- Tobin, Martin D.
- Valdes, Ana M.
- Visscher, Peter M.
- Ward, Kirsten
- Wilson, Scott G.
- Yang, Jian
- Zhang, Feng
- Anney, Richard
- Ayub, Muhammad
- Blackwood, Douglas
- Breen, Gerome
- Collier, David A.
- Craddock, Nick
- Curran, Sarah
- Curtis, David
- Gallagher, Louise
- Geschwind, Daniel
- Holmans, Peter
- Lee, Irene
- Lönnqvist, Jouko
- McIntosh, Andrew M.
- McKechanie, Andrew G.
- McQuillin, Andrew
- Morris, James
- Parr, Jeremy R.
- Paunio, Tiina
- Sharp, Sally I.
- Skuse, David
- Suvisaari, Jaana
- Walters, James T. R.
- Williams, Hywel J.
- Bochukova, Elena
- Bounds, Rebecca
- Dominiczak, Anna
- Keogh, Julia
- Marenne, Gaëlle
- Morris, Andrew
- Porteous, David J.
- Smith, Blair H.
- Wheeler, Eleanor
- Anderson, Carl A.
- Bhattacharya, Shoumo
- Carss, Keren
- Chatterjee, Krishna
- Grozeva, Detelina
- Mitchison, Hannah M.
- Onoufriadis, Alexandros
- Payne, Felicity
- Roberts, Nicola
- Savage, David B.
- Scambler, Peter
- Schmidts, Miriam
- Schoenmakers, Nadia
- Serra, Eva
- Williamson, Kathleen A.
- Ciampi, Antonio
- Oualkacha, Karim
- Kent, Alastair
- Ekong, Rosemary
- Pollitt, Rebecca C.
- Robinson, Rachel L.
- Scott, Richard H.
- Shaw, Adam
- Syrris, Petros
- Vandersteen, Anthony M.
- Chambers, John C.
- Dedoussis, George
- Gambaro, Giovanni
- Gasparini, Paolo
- Isaacs, Aaron
- Johnson, Jon
- Kleber, Marcus E.
- Kooner, Jaspal S.
- Langenberg, Claudia
- Luan, Jian'an
- Malerba, Giovanni
- März, Winfried
- Matchan, Angela
- Morris, Richard
- Nordestgaard, Børge G.
- Benn, Marianne
- Toniolo, Daniela
- Traglia, Michela
- Whincup, Peter
- Zaza, Gianluigi
- Zhang, Weihua
- Venue
- Nature
- Published
- 2015-09-14
- Volume
- 526
- Issue
- 7571
- Pages
- 82-90
- ISSN
- 0028-0836 (ISSN-L)
- 1476-4687
- PMC
- PMC4773891
- OpenAlex
- W1907868928
- Cited by
- 1,040
- References
- 49
- Citations by year
- 2026: 26 · 2025: 44 · 2024: 64 · 2023: 57 · 2022: 83 · 2021: 122 · 2020: 99 · 2019: 162 · 2018: 126 · 2017: 129 · 2016: 105 · 2015: 23
- FWCI
- 87.75
- Type
- journal article
- Language
- en
- Open access
- hybrid
- doi.org
- Licence
- Locations
- Nature (publishedVersion, cc-by-nc-sa)
- Europe PMC (PubMed Central) (publishedVersion, cc-by-nc-sa)
- PubMed Central (publishedVersion, cc-by-nc-sa)
- PubMed (publishedVersion)
- Kölner Universitäts PublikationsServer (Universität zu Köln) (publishedVersion)
- Research at the University of Copenhagen (University of Copenhagen) (publishedVersion, other-oa)
- EUR Research Repository (Erasmus University Rotterdam) (publishedVersion)
- Bristol Research (University of Bristol) (publishedVersion, cc-by-nc-sa)
- St George's Online Research Archive (St George's University of London) (acceptedVersion)
- ENLIGHTEN (Jurnal Bimbingan dan Konseling Islam) (acceptedVersion)
- Leicester Research Archive (University of Leicester) (acceptedVersion, other-oa)
- LSHTM Research Online (London School of Hygiene and Tropical Medicine) (acceptedVersion)
- SHURA (Sheffield Hallam University Research Archive) (Sheffield Hallam University) (acceptedVersion)
- DSpace@MIT (Massachusetts Institute of Technology) (submittedVersion, cc-by-nc-sa)
- RePub (Erasmus University Rotterdam) (submittedVersion, other-oa)
- ArTS Archivio della ricerca di Trieste (University of Trieste https://www.units.it/) (submittedVersion, other-oa)
- Minerva Access (University of Melbourne) (submittedVersion, cc-by-nc-sa)
- Research Portal (King's College London) (submittedVersion, cc-by-nc-sa)
- MPG.PuRe (Max Planck Society) (submittedVersion, other-oa)
- Apollo (University of Cambridge) (submittedVersion, cc-by-nc-sa)
- UWA Profiles and Research Repository (UWA) (submittedVersion, other-oa)
- EUR Research Repository (Erasmus University Rotterdam) (submittedVersion)
- UCL Discovery (University College London) (submittedVersion)
- Figshare (submittedVersion)
- Työväentutkimus Vuosikirja (submittedVersion)
- ORCA Online Research @Cardiff (Cardiff University) (submittedVersion)
- Archive of Doctoral Theses and Digital Collections (University of Calabria) (submittedVersion)
- IRIS Research product catalog (Sapienza University of Rome) (submittedVersion)
- Edinburgh Research Explorer (University of Edinburgh) (submittedVersion, other-oa)
- Queen Mary Research Online (Queen Mary University of London) (submittedVersion, cc-by)
- RePub (Erasmus University Rotterdam) (submittedVersion)
- Explore Bristol Research (submittedVersion, cc-by-nc-sa)
- Spiral (Imperial College London) (submittedVersion, cc-by-nc-sa)
- STM:n Hallinnonalan avoin julkaisuarkisto (Julkari) (submittedVersion)
- Apollo
- Newcastle University ePrints (Newcastle Univesity)
- WOS
- Funders
- Wellcome Trust (095515, 091551/Z/10/Z, 091551, 098498/Z/12/Z, 098498, 104125, 100574, 095564/Z/11/Z, UK10K, 102215, 100574/Z/12/Z, 100140, 104125/Z/14/Z, 095564, 100585/Z/12/Z, 095515/Z/11/Z, 104036, 100140/Z/12/Z, WT091310, 096599, 091551/Z/10/A)
- National Institute for Health and Care Research (NF-SI-0513-10109, NF-SI-0508-10198, NF-SI-0514-10176, NF-SI-0510-10268, NF-SI-0507-10380, NF-SI-0514-10027, NIHR-RP-R3-12-013)
- British Heart Foundation (RG/10/13/28570, RG/08/008/25291, RG/10/17/28553, PG/07/045/22690)
- Imperial College London
- Gentofte Hospital
- Rigshospitalet
- Università degli Studi di Verona
- Karl-Franzens-Universität Graz
- Faculty of Health and Medical Sciences, University of Western Australia
- Medizinische Universität Graz
- Medical Research Council (MR/K013351/1, MC_PC_13046, MC_PC_13048, MR/J012165/1, MC_UU_12015/2, MR/L010305/1, MC_PC_15018, MC_UU_12015/1, MR/K000608/1)
- Biotechnology and Biological Sciences Research Council (BB/M020991/1, BB/K015427/1)
- Economic and Social Research Council (ES/M001660/1, ES/J023299/1)
- Det Sundhedsvidenskabelige Fakultet, Københavns Universitet
- 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 › Genetics › Genetic and phenotypic traits in livestock
- Keywords
- rare variants, low-frequency variants, whole genome sequencing, exome sequencing, triglycerides, apolipoprotein B, adiponectin, ADIPOQ, LDL cholesterol, LDL receptor, population structure, functional annotation, population-based cohort
- MeSH terms
- Alleles, Disease, Female, Genetics, Medical, Genetics, Population, United Kingdom, Health, Humans, Male, Receptors, LDL, Reference Standards, Triglycerides, Genetic Variation, Cohort Studies, Genome, Human, Sequence Analysis, DNA, Genetic Predisposition to Disease, Genomics, Lipid Metabolism, Adiponectin, Genome-Wide Association Study, Molecular Sequence Annotation, Exome
About these checks
Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.
Statistics and arithmetic are recomputed, not judged.
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