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The UK10K project identifies rare variants in health and disease

Lookup NU author(s): Professor Jeremy Parr

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Abstract

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, 7x) or exomes (high read depth, 80x) 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.

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Author(s): Walter K, Min JL, Huang J, Crooks L, Memari Y, McCarthy S, Perry JRB, Xu C, Futema M, Lawson D, Iotchkova V, Schiffels S, Hendricks AE, Danecek P, Li R, Floyd J, Wain LV, Barroso I, Humphries SE, Hurles ME, Zeggini E, Barrett JC, Plagnol V, Richards JB, Greenwood CMT, Timpson NJ, Durbin R, Soranzo N, 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 DK, Joyce C, Keane T, Kolb-Kokocinski A, Langford C, Li Y, Liang J, Lin H, Liu R, Maslen J, McCarthy S, Muddyman D, Quail MA, Stalker J, Sun J, Tian J, Wang G, Wang J, Wang Y, Wong K, Zhang P, Barroso I, Birney E, Boustred C, Chen L, Clement G, Cocca M, Danecek P, Smith GD, Day INM, Day-Williams A, Down T, Dunham I, Durbin R, Evans DM, Gaunt TR, Geihs M, Greenwood CMT, Hart D, Hendricks AE, Howie B, Huang J, Hubbard T, Hysi P, Iotchkova V, Jamshidi Y, Karczewski KJ, Kemp JP, Lachance G, Lawson D, Lek M, Lopes M, MacArthur DG, Marchini J, Mangino M, Mathieson I, McCarthy S, Memari Y, Metrustry S, Min JL, Moayyeri A, Muddyman D, Northstone K, Panoutsopoulou K, Paternoster L, Perry JRB, Quaye L, Richards JB, Ring S, Ritchie GRS, Schiffels S, Shihab HA, Shin SY, Small KS, Artigas MS, Soranzo N, Southam L, Spector TD, St Pourcain B, Surdulescu G, Tachmazidou I, Timpson NJ, Tobin MD, Valdes AM, Visscher PM, Wain LV, Walter K, Ward K, Wilson SG, Wong K, Yang J, Zeggini E, Zhang F, Zheng HF, Anney R, Ayub M, Barrett JC, Blackwood D, Bolton PF, Breen G, Collier DA, Craddock N, Crooks L, Curran S, Curtis D, Durbin R, Gallagher L, Geschwind D, Gurling H, Holmans P, Lee I, Lonnqvist J, McCarthy S, McGuffin P, McIntosh AM, McKechanie AG, McQuillin A, Morris J, Muddyman D, O'Donovan MC, Owen MJ, Palotie A, Parr JR, Paunio T, Pietilainen O, Rehnstrom K, Sharp SI, Skuse D, St Clair D, Suvisaari J, Walters JTR, Williams HJ, Barroso I, Bochukova E, Bounds R, Dominiczak A, Durbin R, Farooqi IS, Hendricks AE, Keogh J, Marenne GL, McCarthy S, Morris A, Muddyman D, O'Rahilly S, Porteous DJ, Smith BH, Tachmazidou I, Wheeler E, Zeggini E, Al Turki S, Anderson CA, Antony D, Barroso IS, Beales P, Bentham J, Bhattacharya S, Calissano M, Carss K, Chatterjee K, Cirak S, Cosgrove C, Durbin R, Fitzpatrick DR, Floyd J, Foley AR, Franklin CS, Futema M, Grozeva D, Humphries SE, Hurles ME, McCarthy S, Mitchison HM, Muddyman D, Muntoni F, O'Rahilly S, Onoufriadis A, Parker V, Payne F, Plagnol V, Raymond FL, Roberts N, Savage DB, Scambler P, Schmidts M, Schoenmakers N, Semple RK, Serra E, Spasic-Boskovic O, Stevens E, van Kogelenberg M, Vijayarangakannan P, Walter K, Williamson KA, Wilson C, Whyte T, Ciampi A, Greenwood CMT, Hendricks AE, Li R, Metrustry S, Oualkacha K, Tachmazidou I, Xu CJ, Zeggini E, Bobrow M, Bolton PF, Durbin R, Fitzpatrick DR, Griffin H, Hurles ME, Kaye J, Kennedy K, Kent A, Muddyman D, Muntoni F, Raymond FL, Semple RK, Smee C, Spector TD, Timpson NJ, Charlton R, Ekong R, Futema M, Humphries SE, Khawaja F, Lopes LR, Migone N, Payne SJ, Plagnol V, Pollitt RC, Povey S, Ridout CK, Robinson RL, Scott RH, Shaw A, Syrris P, Taylor R, Vandersteen AM, Barrett JC, Barroso I, Smith GD, Durbin R, Farooqi IS, Fitzpatrick DR, Hurles ME, Kaye J, Kennedy K, Langford C, McCarthy S, Muddyman D, Owen MJ, Palotie A, Richards JB, Soranzo N, Spector TD, Stalker J, Timpson NJ, Zeggini E, Amuzu A, Casas JP, Chambers JC, Cocca M, Dedoussis G, Gambaro G, Gasparini P, Gaunt TR, Huang J, Iotchkova V, Isaacs A, Johnson J, Kleber ME, Kooner JS, Langenberg C, Luan J, Malerba G, Marz W, Matchan A, Min JL, Morris R, Nordestgaard BG, Benn M, Ring S, Scott RA, Soranzo N, Southam L, Timpson NJ, Toniolo D, Traglia M, Tybjaerg-Hansen A, van Duijn CM, van Leeuwen EM, Varbo A, Whincup P, Zaza G, Zeggini E, Zhang WH, UK10K Consortium, UCLEB Consortium

Publication type: Article

Publication status: Published

Journal: Nature

Year: 2015

Volume: 526

Issue: 7571

Pages: 82-90

Print publication date: 01/01/2015

Online publication date: 14/09/2015

Acceptance date: 17/07/2015

ISSN (print): 0028-0836

ISSN (electronic): 1476-4687

Publisher: Nature Publishing Group

URL: http://dx.doi.org/10.1038/nature14962

DOI: 10.1038/nature14962

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