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

Autor: Huang, J, Howie, B, Mccarthy, S, Memari, Y, Walter, K, Min, Jl, Danecek, P, Malerba, Giovanni, Trabetti, Elisabetta, Zheng, Hf, Gambaro, G, Richards, Jb, Durbin, R, Timpson, Nj, Marchini, J, Soranzo, N, Al Turki, S, Amuzu, A, Anderson, Ca, Anney, R, Antony, D, Artigas, Ms, Ayub, M, Bala, S, Barrett, Jc, Barroso, I, Beales, P, Benn, M, Bentham, J, Bhattacharya, S, Birney, E, Blackwood, D, Bobrow, M, Bochukova, E, Bolton, Pf, Bounds, R, Boustred, C, Breen, G, Calissano, M, Carss, K, Casas, Jp, Chambers, Jc, Charlton, R, Chatterjee, K, Chen, L, Ciampi, A, Cirak, S, Clapham, P, Clement, G, Coates, G, Cocca, M, Collier, Da, Cosgrove, C, Cox, T, Craddock, N, Crooks, L, Curran, S, Curtis, D, Daly, A, Day, In, Day Williams, A, Dedoussis, G, Down, T, Du, Y, van Duijn, Cm, Dunham, I, Edkins, S, Ekong, R, Ellis, P, Evans, Dm, Farooqi, Is, Fitzpatrick, Dr, Flicek, P, Floyd, J, Foley, Ar, Franklin, Cs, Futema, M, Gallagher, L, Gasparini, P, Gaunt, Tr, Geihs, M, Geschwind, D, Greenwood, C, Griffin, H, Grozeva, D, Guo, X, Gurling, H, Hart, D, Hendricks, Ae, Holmans, P, Huang, L, Hubbard, T, Humphries, Se, Hurles, Me, Hysi, P, Iotchkova, V, Isaacs, A, Jackson, Dk, Jamshidi, Y, Johnson, J, Joyce, C, Karczewski, Kj, Kaye, J, Keane, T, Kemp, Jp, Kennedy, K, Kent, A, Keogh, J, Khawaja, F, Kleber, Me, van Kogelenberg, M, Kolb Kokocinski, A, Kooner, Js, Lachance, G, Langenberg, C, Langford, C, Lawson, D, Lee, I, van Leeuwen, Em, Lek, M, Li, R, Li, Y, Liang, J, Lin, H, Liu, R, Lönnqvist, J, Lopes, Lr, Lopes, M, Luan, J, Macarthur, Dg, Mangino, M, Marenne, G, März, W, Maslen, J, Matchan, A, Mathieson, I, Mcguffin, P, Mcintosh, Am, Mckechanie, Ag, Mcquillin, A, Metrustry, S, Migone, N, Mitchison, Hm, Moayyeri, A, Morris, J, Morris, R, Muddyman, D, Muntoni, F, Nordestgaard, Bg, Northstone, K, O'Donovan, Mc, O'Rahilly, S, Onoufriadis, A, Oualkacha, K, Owen, Mj, Palotie, A, Panoutsopoulou, K, Parker, V, Parr, Jr, Paternoster, L, Paunio, T, Payne, F, Payne, Sj, Perry, Jr, Pietilainen, O, Plagnol, V, Pollitt, Rc, Povey, S, Quail, Ma, Quaye, L, Raymond, L, Rehnström, K, Ridout, Ck, Ring, S, Ritchie, Gr, Roberts, N, Robinson, Rl, Savage, Db, Scambler, P, Schiffels, S, Schmidts, M, Schoenmakers, N, Scott, Rh, Scott, Ra, Semple, Rk, Serra, E, Sharp, Si, Shaw, A, Shihab, Ha, Shin, Sy, Skuse, D, Small, Ks, Smee, C, Smith, Gd, Southam, L, Spasic Boskovic, O, Spector, Td, St Clair, D, St Pourcain, B, Stalker, J, Stevens, E, Sun, J, Surdulescu, G, Suvisaari, J, Syrris, P, Tachmazidou, I, Taylor, R, Tian, J, Tobin, Md, Toniolo, D, Traglia, M, Tybjaerg Hansen, A, Valdes, Am, Vandersteen, Am, Varbo, A, Vijayarangakannan, P, Visscher, Pm, Wain, Lv, Walters, Jt, Wang, G, Wang, J, Wang, Y, Ward, K, Wheeler, E, Whincup, P, Whyte, T, Williams, Hj, Williamson, Ka, Wilson, C, Wilson, Sg, Wong, K, Xu, C, Yang, J, Zaza, Gianluigi, Zeggini, E, Zhang, F, Zhang, P, Zhang, W.

Publikováno v: Nature Communications, 6, 8111
Nature Communications, 6, pp. 8111
Nature Communications
Huang, J, Howie, B, McCarthy, S, Memari, Y, Walter, K, Min, J L, Danecek, P, Malerba, G, Trabetti, E, Zheng, H-F, Gambaro, G, Richards, J B, Durbin, R, Timpson, N J & Marchini, J & Soranzo, N 2015, ' Improved imputation of low-frequency and rare variants using the UK10K haplotype reference panel ', Nature Communications, vol. 6, pp. 8111 . https://doi.org/10.1038/ncomms9111
Huang, J, Howie, B, Mccarthy, S, Memari, Y, Walter, K, Min, J L, Danecek, P, Malerba, G, Trabetti, E, Zheng, H, Al Turki, S, Amuzu, A, Anderson, C A, Anney, R, Antony, D, Artigas, M S, Ayub, M, Bala, S, Barrett, J C, Barroso, I, Beales, P, Benn, M, Bentham, J, Bhattacharya, S, Birney, E, Blackwood, D, Bobrow, M, Bochukova, E, Bolton, P F, Bounds, R, Boustred, C, Breen, G, Calissano, M, Carss, K, Pablo Casas, J, Chambers, J C, Charlton, R, Chatterjee, K, Chen, L, Ciampi, A, Cirak, S, Clapham, P, Clement, G, Coates, G, Cocca, M, Collier, D A, Cosgrove, C, Cox, T, Craddock, N, Crooks, L, Curran, S, Curtis, D, Daly, A, Day, I N M, Day-williams, A, Dedoussis, G, Down, T, Du, Y, Van Duijn, C M, Dunham, I, Edkins, S, Ekong, R, Ellis, P, Evans, D M, Farooqi, I S, Fitzpatrick, D R, Flicek, P, Floyd, J, Foley, A R, Franklin, C S, Futema, M, Gallagher, L, Gasparini, P, Gaunt, T R, Geihs, M, Geschwind, D, Greenwood, C, Griffin, H, Grozeva, D, Guo, X, Guo, X, Gurling, H, Hart, D, Hendricks, A E, Holmans, P, Huang, L, Hubbard, T, Humphries, S E, Hurles, M E, Hysi, P, Iotchkova, V, Isaacs, A, Jackson, D K, Jamshidi, Y, Johnson, J, Joyce, C, Karczewski, K J, Kaye, J, Keane, T, Kemp, J P, Kennedy, K, Kent, A, Keogh, J, Khawaja, F, Kleber, M E, Van Kogelenberg, M, Kolb-kokocinski, A, Kooner, J S, Lachance, G, Langenberg, C, Langford, C, Lawson, D, Lee, I, Van Leeuwen, E M, Lek, M, Li, R, Li, Y, Liang, J, Lin, H, Liu, R, Lönnqvist, J, Lopes, L R, Lopes, M, Luan, J, Macarthur, D G, Mangino, M, Marenne, G, März, W, Maslen, J, Matchan, A, Mathieson, I, Mcguffin, P, Mcintosh, A M, Mckechanie, A G, Mcquillin, A, Metrustry, S, Migone, N, Mitchison, H M, Moayyeri, A, Morris, J, Morris, R, Muddyman, D, Muntoni, F, Nordestgaard, B, Northstone, K, O'donovan, M C, O'rahilly, S, Onoufriadis, A, Oualkacha, K, Owen, M J, Palotie, A, Panoutsopoulou, K, Parker, V, Parr, J R, Paternoster, L, Paunio, T, Payne, F, Payne, S J, Perry, J R B, Pietilainen, O, Plagnol, V, Pollitt, R C, Povey, S, Quail, M A, Quaye, L, Raymond, L, Rehnström, K, Ridout, C K, Ring, S, Ritchie, G R S, Roberts, N, Robinson, R L, Savage, D B, Scambler, P, Schiffels, S, Schmidts, M, Schoenmakers, N, Scott, R H, Scott, R A, Semple, R K, Serra, E, Sharp, S I, Shaw, A, Shihab, H A, Shin, S, Skuse, D, Small, K S, Smee, C, Smith, G D, Southam, L, Spasic-boskovic, O, Spector, T D, St Clair, D, St Pourcain, B, Stalker, J, Stevens, E, Sun, J, Surdulescu, G, Suvisaari, J, Syrris, P, Tachmazidou, I, Taylor, R, Tian, J, Tobin, M D, Toniolo, D, Traglia, M, Tybjærg-Hansen, A, Valdes, A M, Vandersteen, A M, Varbo, A, Vijayarangakannan, P, Visscher, P M, Wain, L V, Walters, J T R, Wang, G, Wang, J, Wang, Y, Ward, K, Wheeler, E, Whincup, P, Whyte, T, Williams, H J, Williamson, K A, Wilson, C, Wilson, S G, Wong, K, Xu, C, Yang, J, Zaza, G, Zeggini, E, Zhang, F, Zhang, P, Zhang, W, Gambaro, G, Richards, J B, Durbin, R, Timpson, N J, Marchini, J & Soranzo, N 2015, ' Improved imputation of low-frequency and rare variants using the UK10K haplotype reference panel ', Nature Communications, vol. 6, 8111 . https://doi.org/10.1038/ncomms9111

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

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http://hdl.handle.net/2066/153109

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