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Improved imputation of low-frequency and rare variants using the UK10K haplotype reference panel
Authors :
Huang, J. (Jie) Howie, B. (Bryan) McCarthy, S. (Shane) Memari, Y. (Yasin) Walter, K. (Klaudia) Min, J.L. (Josine L.) Danecek, P. (Petr) Malerba, G. (Giovanni) Trabetti, E. (Elisabetta) Zheng, H.-F. (Hou-Feng) Gambaro, G. (Giovanni) Richards, J.B. (Brent) Durbin, R. (Richard) Timpson, N.J. (Nicholas) Marchini, J. (Jonathan) Soranzo, N. (Nicole) Al Turki, S.H. (Saeed) Amuzu, A. (Antoinette) Anderson, C. (Carl) Anney, R. (Richard) Antony, D. (Dinu) Artigas, M.S. Ayub, M. (Muhammad) Bala, S. (Senduran) Barrett, J.C. (Jeffrey) Barroso, I.E. (Inês) Beales, P.L. (Philip) Benn, M. (Marianne) Bentham, J. (Jamie) Bhattacharya, S. (Shoumo) Birney, E. (Ewan) Blackwood, D.H.R. (Douglas) Bobrow, M. (Martin) Bochukova, E. (Elena) Bolton, P.F. (Patrick F.) Bounds, R. (Rebecca) Boustred, C. (Chris) Breen, G. (Gerome) Calissano, M. (Mattia) Carss, K. (Keren) Casas, J.P. (Juan Pablo) Chambers, J.C. (John C.) Charlton, R. (Ruth) Chatterjee, K. (Krishna) Chen, L. (Lu) Ciampi, A. (Antonio) Cirak, S. (Sebahattin) Clapham, P. (Peter) Clement, G. (Gail) Coates, G. (Guy) Cocca, M. (Massimiliano) Collier, D.A. (David) Cosgrove, C. (Catherine) Cox, T. (Tony) Craddock, N.J. (Nick) Crooks, L. (Lucy) Curran, S. (Sarah) Curtis, D. (David) Daly, A. (Allan) Day, I.N.M. (Ian N.M.) Day-Williams, A.G. (Aaron) Dedoussis, G.V. (George) Down, T. (Thomas) Du, Y. (Yuanping) Duijn, C.M. (Cornelia) van Dunham, I. (Ian) Edkins, T. (Ted) Ekong, R. (Rosemary) Ellis, P. (Peter) Evans, D.M. (David) Farooqi, I.S. (I. Sadaf) Fitzpatrick, D.R. (David R.) Flicek, P. (Paul) Floyd, J. (James) Foley, A.R. (A. Reghan) Franklin, C.S. (Christopher S.) Futema, M. (Marta) Gallagher, L. (Louise) Gasparini, P. (Paolo) Gaunt, T.R. (Tom) Geihs, M. (Matthias) Geschwind, D. (Daniel) Greenwood, C.M.T. (Celia) Griffin, H. (Heather) Grozeva, D. (Detelina) Guo, X. (Xiaosen) Guo, X. (Xueqin) Gurling, H. (Hugh) Hart, D. (Deborah) Hendricks, A.E. (Audrey E.) Holmans, P.A. (Peter A.) Huang, L. (Liren) Hubbard, T. (Tim) Humphries, S.E. (Steve E.) Hurles, M.E. (Matthew) Hysi, P.G. (Pirro) Iotchkova, V. (Valentina) Isaacs, A. (Aaron) Jackson, D.K. (David K.) Jamshidi, Y. (Yalda) Johnson, J. (Jon) Joyce, C. (Chris) Karczewski, K.J. (Konrad) Kaye, J. (Jane) Keane, T. (Thomas) Kemp, J.P. (John) Kennedy, K. (Karen) Kent, A. (Alastair) Keogh, J. (Julia) Khawaja, F. (Farrah) Kleber, M.E. (Marcus) Van Kogelenberg, M. (Margriet) Kolb-Kokocinski, A. (Anja) Kooner, J.S. (Jaspal S.) Lachance, G. (Genevieve) Langenberg, C. (Claudia) Langford, C. (Cordelia) Lawson, D. (Daniel) Lee, I. (Irene) Leeuwen, E.M. (Elisa) van Lek, M. (Monkol) Li, R. (Rui) Li, Y. (Yingrui) Liang, J. (Jieqin) Lin, H. (Hong) Liu, R. (Ryan) Lönnqvist, J. (Jouko) Lopes, L.R. (Luis R.) Lopes, M.C. (Margarida) Luan, J. MacArthur, D.G. (Daniel G.) Mangino, M. (Massimo) Marenne, G. (Gaëlle) März, W. (Winfried) Maslen, J. (John) Matchan, A. (Angela) Mathieson, I. (Iain) McGuffin, P. (Peter) McIntosh, A.M. (Andrew) McKechanie, A.G. (Andrew G.) McQuillin, A. (Andrew) Metrustry, S. (Sarah) Migone, N. (Nicola) Mitchison, H.M. (Hannah M.) Moayyeri, A. (Alireza) Morris, J. (James) Morris, R.W. (Richard) Muddyman, D. (Dawn) Muntoni, F. Nordestgaard, B.G. (Børge G.) Northstone, K. (Kate) O'donovan, M.C. (Michael) O'Rahilly, S. (Stephen) Onoufriadis, A. (Alexandros) Oualkacha, K. (Karim) Owen, M.J. (Michael J.) Palotie, A. (Aarno) Panoutsopoulou, K. (Kalliope) Parker, V. (Victoria) Parr, J.R. (Jeremy R.) Paternoster, L. (Lavinia) Paunio, T. (Tiina) Payne, F. (Felicity) Payne, S.J. (Stewart J.) Perry, J.R.B. (John) Pietiläinen, O.P.H. (Olli) Plagnol, V. (Vincent) Pollitt, R.C. (Rebecca C.) Povey, S. (Sue) Quail, M.A. (Michael A.) Quaye, L. (Lydia) Raymond, L. (Lucy) Rehnström, K. (Karola) Ridout, C.K. (Cheryl K.) Ring, S.M. (Susan) Ritchie, G.R.S. (Graham R.S.) Roberts, N. (Nicola) Robinson, R.L. (Rachel L.) Savage, D.B. (David) Scambler, P.J. (Peter) Schiffels, S. (Stephan) Schmidts, M. (Miriam) Schoenmakers, N. (Nadia) Scott, R.H. (Richard H.) Scott, R.A. (Robert) Semple, R.K. (Robert K.) Serra, E. (Eva) Sharp, S.I. (Sally I.) Shaw, A.C. (Adam C.) Shihab, H.A. (Hashem A.) Shin, S.-Y. (So-Youn) Skuse, D. (David) Small, K.S. (Kerrin) Smee, C. (Carol) Smith, A.V. (Davey) Southam, L. (Lorraine) Spasic-Boskovic, O. (Olivera) Spector, T.D. (Timothy) St. Clair, D. (David) St Pourcain, B. (Beate) Stalker, J. (Jim) Stevens, E. (Elizabeth) Sun, J. (Jianping) Surdulescu, G. (Gabriela) Suvisaari, J. (Jaana) Syrris, P. (Petros) Tachmazidou, I. (Ioanna) Taylor, R. (Rohan) Tian, J. (Jing) Tobin, M.D. (Martin) Toniolo, D. (Daniela) Traglia, M. (Michela) Tybjaerg-Hansen, A. (Anne) Valdes, A.M. Vandersteen, A.M. (Anthony M.) Varbo, A. (Anette) Vijayarangakannan, P. (Parthiban) Visscher, P.M. (Peter) Wain, L.V. (Louise) Walters, J.T. (James) Wang, G. (Guangbiao) Wang, J. (Jun) Wang, Y. (Yu) Ward, K. (Kirsten) Wheeler, E. (Eleanor) Whincup, P.H. (Peter) Whyte, T. (Tamieka) Williams, H.J. (Hywel J.) Williamson, K.A. (Kathleen) Wilson, C. (Crispian) Wilson, S.G. (Scott) Wong, K. (Kim) Xu, C. (Changjiang) Yang, J. (Jian) Zaza, G. (Gianluigi) Zeggini, E. (Eleftheria) Zhang, F. (Feng) Zhang, P. (Pingbo) Zhang, W. (Weihua) Huang, J. (Jie) Howie, B. (Bryan) McCarthy, S. (Shane) Memari, Y. (Yasin) Walter, K. (Klaudia) Min, J.L. (Josine L.) Danecek, P. (Petr) Malerba, G. (Giovanni) Trabetti, E. (Elisabetta) Zheng, H.-F. (Hou-Feng) Gambaro, G. (Giovanni) Richards, J.B. (Brent) Durbin, R. (Richard) Timpson, N.J. (Nicholas) Marchini, J. (Jonathan) Soranzo, N. (Nicole) Al Turki, S.H. (Saeed) Amuzu, A. (Antoinette) Anderson, C. (Carl) Anney, R. (Richard) Antony, D. (Dinu) Artigas, M.S. Ayub, M. (Muhammad) Bala, S. (Senduran) Barrett, J.C. (Jeffrey) Barroso, I.E. (Inês) Beales, P.L. (Philip) Benn, M. (Marianne) Bentham, J. (Jamie) Bhattacharya, S. (Shoumo) Birney, E. (Ewan) Blackwood, D.H.R. (Douglas) Bobrow, M. (Martin) Bochukova, E. (Elena) Bolton, P.F. (Patrick F.) Bounds, R. (Rebecca) Boustred, C. (Chris) Breen, G. (Gerome) Calissano, M. (Mattia) Carss, K. (Keren) Casas, J.P. (Juan Pablo) Chambers, J.C. (John C.) Charlton, R. (Ruth) Chatterjee, K. (Krishna) Chen, L. (Lu) Ciampi, A. (Antonio) Cirak, S. (Sebahattin) Clapham, P. (Peter) Clement, G. (Gail) Coates, G. (Guy) Cocca, M. (Massimiliano) Collier, D.A. (David) Cosgrove, C. (Catherine) Cox, T. (Tony) Craddock, N.J. (Nick) Crooks, L. (Lucy) Curran, S. (Sarah) Curtis, D. (David) Daly, A. (Allan) Day, I.N.M. (Ian N.M.) Day-Williams, A.G. (Aaron) Dedoussis, G.V. (George) Down, T. (Thomas) Du, Y. (Yuanping) Duijn, C.M. (Cornelia) van Dunham, I. (Ian) Edkins, T. (Ted) Ekong, R. (Rosemary) Ellis, P. (Peter) Evans, D.M. (David) Farooqi, I.S. (I. Sadaf) Fitzpatrick, D.R. (David R.) Flicek, P. (Paul) Floyd, J. (James) Foley, A.R. (A. Reghan) Franklin, C.S. (Christopher S.) Futema, M. (Marta) Gallagher, L. (Louise) Gasparini, P. (Paolo) Gaunt, T.R. (Tom) Geihs, M. (Matthias) Geschwind, D. (Daniel) Greenwood, C.M.T. (Celia) Griffin, H. (Heather) Grozeva, D. (Detelina) Guo, X. (Xiaosen) Guo, X. (Xueqin) Gurling, H. (Hugh) Hart, D. (Deborah) Hendricks, A.E. (Audrey E.) Holmans, P.A. (Peter A.) Huang, L. (Liren) Hubbard, T. (Tim) Humphries, S.E. (Steve E.) Hurles, M.E. (Matthew) Hysi, P.G. (Pirro) Iotchkova, V. (Valentina) Isaacs, A. (Aaron) Jackson, D.K. (David K.) Jamshidi, Y. (Yalda) Johnson, J. (Jon) Joyce, C. (Chris) Karczewski, K.J. (Konrad) Kaye, J. (Jane) Keane, T. (Thomas) Kemp, J.P. (John) Kennedy, K. (Karen) Kent, A. (Alastair) Keogh, J. (Julia) Khawaja, F. (Farrah) Kleber, M.E. (Marcus) Van Kogelenberg, M. (Margriet) Kolb-Kokocinski, A. (Anja) Kooner, J.S. (Jaspal S.) Lachance, G. (Genevieve) Langenberg, C. (Claudia) Langford, C. (Cordelia) Lawson, D. (Daniel) Lee, I. (Irene) Leeuwen, E.M. (Elisa) van Lek, M. (Monkol) Li, R. (Rui) Li, Y. (Yingrui) Liang, J. (Jieqin) Lin, H. (Hong) Liu, R. (Ryan) Lönnqvist, J. (Jouko) Lopes, L.R. (Luis R.) Lopes, M.C. (Margarida) Luan, J. MacArthur, D.G. (Daniel G.) Mangino, M. (Massimo) Marenne, G. (Gaëlle) März, W. (Winfried) Maslen, J. (John) Matchan, A. (Angela) Mathieson, I. (Iain) McGuffin, P. (Peter) McIntosh, A.M. (Andrew) McKechanie, A.G. (Andrew G.) McQuillin, A. (Andrew) Metrustry, S. (Sarah) Migone, N. (Nicola) Mitchison, H.M. (Hannah M.) Moayyeri, A. (Alireza) Morris, J. (James) Morris, R.W. (Richard) Muddyman, D. (Dawn) Muntoni, F. Nordestgaard, B.G. (Børge G.) Northstone, K. (Kate) O'donovan, M.C. (Michael) O'Rahilly, S. (Stephen) Onoufriadis, A. (Alexandros) Oualkacha, K. (Karim) Owen, M.J. (Michael J.) Palotie, A. (Aarno) Panoutsopoulou, K. (Kalliope) Parker, V. (Victoria) Parr, J.R. (Jeremy R.) Paternoster, L. (Lavinia) Paunio, T. (Tiina) Payne, F. (Felicity) Payne, S.J. (Stewart J.) Perry, J.R.B. (John) Pietiläinen, O.P.H. (Olli) Plagnol, V. (Vincent) Pollitt, R.C. (Rebecca C.) Povey, S. (Sue) Quail, M.A. (Michael A.) Quaye, L. (Lydia) Raymond, L. (Lucy) Rehnström, K. (Karola) Ridout, C.K. (Cheryl K.) Ring, S.M. (Susan) Ritchie, G.R.S. (Graham R.S.) Roberts, N. (Nicola) Robinson, R.L. (Rachel L.) Savage, D.B. (David) Scambler, P.J. (Peter) Schiffels, S. (Stephan) Schmidts, M. (Miriam) Schoenmakers, N. (Nadia) Scott, R.H. (Richard H.) Scott, R.A. (Robert) Semple, R.K. (Robert K.) Serra, E. (Eva) Sharp, S.I. (Sally I.) Shaw, A.C. (Adam C.) Shihab, H.A. (Hashem A.) Shin, S.-Y. (So-Youn) Skuse, D. (David) Small, K.S. (Kerrin) Smee, C. (Carol) Smith, A.V. (Davey) Southam, L. (Lorraine) Spasic-Boskovic, O. (Olivera) Spector, T.D. (Timothy) St. Clair, D. (David) St Pourcain, B. (Beate) Stalker, J. (Jim) Stevens, E. (Elizabeth) Sun, J. (Jianping) Surdulescu, G. (Gabriela) Suvisaari, J. (Jaana) Syrris, P. (Petros) Tachmazidou, I. (Ioanna) Taylor, R. (Rohan) Tian, J. (Jing) Tobin, M.D. (Martin) Toniolo, D. (Daniela) Traglia, M. (Michela) Tybjaerg-Hansen, A. (Anne) Valdes, A.M. Vandersteen, A.M. (Anthony M.) Varbo, A. (Anette) Vijayarangakannan, P. (Parthiban) Visscher, P.M. (Peter) Wain, L.V. (Louise) Walters, J.T. (James) Wang, G. (Guangbiao) Wang, J. (Jun) Wang, Y. (Yu) Ward, K. (Kirsten) Wheeler, E. (Eleanor) Whincup, P.H. (Peter) Whyte, T. (Tamieka) Williams, H.J. (Hywel J.) Williamson, K.A. (Kathleen) Wilson, C. (Crispian) Wilson, S.G. (Scott) Wong, K. (Kim) Xu, C. (Changjiang) Yang, J. (Jian) Zaza, G. (Gianluigi) Zeggini, E. (Eleftheria) Zhang, F. (Feng) Zhang, P. (Pingbo) Zhang, W. (Weihua)
Publication Year :
2015
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 (average 7x), aiming to exhaustively characterize genetic variation down to 0.1% minor allele frequency in the British population. Here we demonstrate the value of this
Details
Database :
OAIster
Notes :
application/pdf, Nature Communications vol. 6, English
Publication Type :
Electronic Resource
Accession number :
edsoai.ocn957100949
Document Type :
Electronic Resource
Full Text :
https://doi.org/10.1038.ncomms9111