Improved imputation of low-frequency and rare variants using the UK10K haplotype reference panel

Huang, Jie; Howie, Bryan; McCarthy, Shane; Memari, Yasin; Walter, Klaudia; L. Min, Josine; Danecek, Petr; Malerba, Giovanni; Trabetti, Elisabetta; Zheng, Hou‐Feng; Al Turki, Saeed; Amuzu, Antoinette; A. Anderson, Carl; Anney, Richard; Antony, Dinu; Soler Artigas, María; Ayub, Muhammad; Bala, Senduran; C. Barrett, Jeffrey; Barroso, Inês; Beales, Phil; Benn, Marianne; Bentham, Jamie; Bhattacharya, Shoumo; Birney, Ewan; Blackwood, Douglas; Bobrow, Martin; G. Bochukova, Elena; Bolton, Patrick; Bounds, Rebecca; Boustred, Chris; Breen, Gerome; Calissano, Mattia; Carss, Keren; P. Casas, Juan; C. Chambers, John; Charlton, Ruth; Chatterjee, Krishna; Chen, Lu; Ciampi, Antonio; Çırak, Sebahattin; Clapham, Peter; Clement, Gail; Coates, Guy; Cocca, Massimiliano; Collier, David; Cosgrove, Catherine; Cox, Tony; Craddock, Nick; Crooks, Lucy; Curran, Sarah; Curtis, David; Daly, Allan; N.M. Day, Ian; Day-Williams, Aaron; Dedoussis, George; A. Down, Thomas; Du, Yuanping; M. van Duijn, Cornelia; Dunham, Ian; Edkins, Sarah; Ekong, Rosemary; Ellis, Peter; M. Evans, David; Sadaf Farooqi, I.; Fitzpatrick, David; Flicek, Paul; Floyd, James; Reghan Foley, A.; S. Franklin, Christopher; Futema, Marta; Gallagher, Louise; Gasparini, Paolo; R. Gaunt, Tom; Geihs, Matthias; H. Geschwind, Daniel; M.T. Greenwood, Celia; Griffin, Heather; Grozeva, Detelina; Guo, Xiaosen; Guo, Xueqin; Gurling, Hugh; Hart, Deborah; E. Hendricks, Audrey; Holmans, Peter; Huang, Liren; Hubbard, Tim; E. Humphries, Steve; E. Hurles, Matthew; G. Hysi, Pirro; Iotchkova, Valentina; Isaacs, Aaron; K. Jackson, David; Jamshidi, Yalda; Johnson, Jon; Joyce, Christopher; J. Karczewski, Konrad; Kaye, Jane; Keane, Thomas; P. Kemp, John; Kennedy, Karen; Kent, Alastair; M. Keogh, Julia; Khawaja, Farrah; E. Kleber, Marcus; van Kogelenberg, Margriet; Kolb-Kokocinski, Anja; S. Kooner, Jaspal; Lachance, Geneviève; Langenberg, Claudia; Langford, Cordelia; J. Lawson, Daniel; Lee, Irene; M. van Leeuwen, Elisabeth; Lek, Monkol; Li, Rui; Li, Rui; Liang, Jieqin; Lin, Hong; Liu, Ryan; Lönnqvist, Jouko; R. Lopes, Luís; Lopes, Margarida; Luan, Jian’an; G. MacArthur, Daniel; Mangino, Massimo; Marenne, Gaëlle; März, Winfried; Maslen, John; Matchan, Angela; Mathieson, Iain; McGuffin, Peter; M. McIntosh, Andrew; G. McKechanie, Andrew; McQuillin, Andrew; Metrustry, Sarah; Migone, Nicola; M. Mitchison, Hannah; Moayyeri, Alireza; Morris, James; Morris, Richard; Muddyman, Dawn; Muntoni, Francesco; G. Nordestgaard, Børge; Northstone, Kate; O‘Donovan, Michael; O’Rahilly, Stephen; Onoufriadis, Alexandros; Oualkacha, Karim; J. Owen, Michael; Palotie, Aarno; Panoutsopoulou, Kalliope; Parker, Victoria; Parr, Jeremy; Paternoster, Lavinia; Paunio, Tiina; Payne, Felicity; J. Payne, Stewart; R. B. Perry, John; Pietiläinen, Olli; Plagnol, Vincent; C. Pollitt, Rebecca; Povey, Sue; A. Quail, Michael; Quaye, Lydia; Raymond, Lucy; Rehnström, Karola; K. Ridout, Cheryl; M. Ring, Susan; R. S. Ritchie, Graham; Roberts, Nicola; L. Robinson, Rachel; B. Savage, David; Scambler, Peter; Schiffels, Stephan; Schmidts, Miriam; Schoenmakers, Nadia; H. Scott, Richard; A. Scott, Robert; K. Semple, Robert; Serra, Eva; I. Sharp, Sally; Shaw, Adam; A. Shihab, Hashem; Shin, So–Youn; Skuse, David; S. Small, Kerrin; Smee, Carol; Davey Smith, George; Southam, Lorraine; Spasić-Bošković, Olivera; D. Spector, Timothy; St Clair, David; St Pourcain, Beaté; Stalker, Jim; Stevens, Elizabeth; Sun, Jianping; Surdulescu, Gabriela; Suvisaari, Jaana; Syrris, Petros; Tachmazidou, Ioanna; Taylor, Rohan; Tian, Jing; D. Tobin, Martin; Toniolo, Daniela; Traglia, Michela; Tybjærg‐Hansen, Anne; M. Valdes, Ana; M. Vandersteen, Anthony; Varbo, Anette; Vijayarangakannan, Parthiban; M. Visscher, Peter; V. Wain, Louise; Walters, James; Wang, Guangbiao; Wang, Jun; Wang, Yu; Ward, Kirsten; Wheeler, Eleanor; H. Whincup, Peter; Whyte, Tamieka; Williams, Hywel; A. Williamson, Kathleen; Wilson, Crispian; G. Wilson, Scott; Wong, Kim; Xu, Changjiang; Yang, Jian; Zaza, Gianluigi; Zeggini, Eleftheria; Zhang, Feng; Zhang, Pingbo; Zhang, Weihua; Gambaro, Giovanni; Brent Richards, J.; Durbin, Richard; J. Timpson, Nicholas; Marchini, Jonathan; Soranzo, Nicole

doi:10.1038/ncomms9111

Public

Improved imputation of low-frequency and rare variants using the UK10K haplotype reference panel

Published in Nature Communications • Sep 14, 2015

Authors:

Jie Huang

Bryan Howie

Shane McCarthy

Abstract

Imputing genotypes from reference panels created by whole-genome sequencing (WGS) provides a cost-effective strategy for augmenting the single-nucleotide polymorphism (SNP) content of genome-wide arrays. The UK10K Cohorts project has generated a data set of 3,781 whole genomes sequenced at low depth...

Subject

Haplotype

Imputation (statistics)

Allele frequency

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