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Cited by 342

The DOI matches its Crossref record; 16 of the 16 references it cites were found in a registry or an index.

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

Open access
Huang, Jie, Howie, Bryan, McCarthy, Shane, Memari, Yasin, Walter, Klaudia, Min, Josine L., Danecek, Petr, Malerba, Giovanni, Trabetti, Elisabetta, Zheng, Hou-Feng, UK10K Consortium, Al Turki, Saeed, Amuzu, Antoinette, Anderson, Carl A., Anney, Richard, Antony, Dinu, Artigas, María Soler, Ayub, Muhammad, Bala, Senduran, Barrett, Jeffrey C., Barroso, Inês, Beales, Phil, Benn, Marianne, Bentham, Jamie, Bhattacharya, Shoumo, Birney, Ewan, Blackwood, Douglas, Bobrow, Martin, Bochukova, Elena, Bolton, Patrick F., Bounds, Rebecca, Boustred, Chris, Breen, Gerome, Calissano, Mattia, Carss, Keren, Pablo Casas, Juan, Chambers, John C., Charlton, Ruth, Chatterjee, Krishna, Chen, Lu, Ciampi, Antonio, Cirak, Sebahattin, Clapham, Peter, Clement, Gail, Coates, Guy, Cocca, Massimiliano, Collier, David A., Cosgrove, Catherine, Cox, Tony, Craddock, Nick, Crooks, Lucy, Curran, Sarah, Curtis, David, Daly, Allan, Day, Ian N. M., Day-Williams, Aaron, Dedoussis, George, Down, Thomas, Du, Yuanping, van Duijn, Cornelia M., Dunham, Ian, Edkins, Sarah, Ekong, Rosemary, Ellis, Peter, Evans, David M., Farooqi, I. Sadaf, Fitzpatrick, David R., Flicek, Paul, Floyd, James, Foley, A. Reghan, Franklin, Christopher S., Futema, Marta, Gallagher, Louise, Gasparini, Paolo, Gaunt, Tom R., Geihs, Matthias, Geschwind, Daniel, Greenwood, Celia, Griffin, Heather, Grozeva, Detelina, Guo, Xiaosen, Guo, Xueqin, Gurling, Hugh, Hart, Deborah, Hendricks, Audrey E., Holmans, Peter, Huang, Liren, Hubbard, Tim, Humphries, Steve E., Hurles, Matthew E., Hysi, Pirro, Iotchkova, Valentina, Isaacs, Aaron, Jackson, David K., Jamshidi, Yalda, Johnson, Jon, Joyce, Chris, Karczewski, Konrad J., Kaye, Jane, Keane, Thomas, Kemp, John P., Kennedy, Karen, Kent, Alastair, Keogh, Julia, Khawaja, Farrah, Kleber, Marcus E., van Kogelenberg, Margriet, Kolb-Kokocinski, Anja, Kooner, Jaspal S., Lachance, Genevieve, Langenberg, Claudia, Langford, Cordelia, Lawson, Daniel, Lee, Irene, van Leeuwen, Elisabeth M., Lek, Monkol, Li, Rui, Li, Yingrui, Liang, Jieqin, Lin, Hong, Liu, Ryan, Lönnqvist, Jouko, Lopes, Luis R., Lopes, Margarida, Luan, Jian'an, MacArthur, Daniel G., Mangino, Massimo, Marenne, Gaëlle, März, Winfried, Maslen, John, Matchan, Angela, Mathieson, Iain, McGuffin, Peter, McIntosh, Andrew M., McKechanie, Andrew G., McQuillin, Andrew, Metrustry, Sarah, Migone, Nicola, Mitchison, Hannah M., Moayyeri, Alireza, Morris, James, Morris, Richard, Muddyman, Dawn, Muntoni, Francesco, Nordestgaard, Børge G., Northstone, Kate, O'Donovan, Michael C., O'Rahilly, Stephen, Onoufriadis, Alexandros, Oualkacha, Karim, Owen, Michael J., Palotie, Aarno, Panoutsopoulou, Kalliope, Parker, Victoria, Parr, Jeremy R., Paternoster, Lavinia, Paunio, Tiina, Payne, Felicity, Payne, Stewart J., Perry, John R. B., Pietilainen, Olli, Plagnol, Vincent, Pollitt, Rebecca C., Povey, Sue, Quail, Michael A., Quaye, Lydia, Raymond, Lucy, Rehnström, Karola, Ridout, Cheryl K., Ring, Susan, Ritchie, Graham R. S., Roberts, Nicola, Robinson, Rachel L., Savage, David B., Scambler, Peter, Schiffels, Stephan, Schmidts, Miriam, Schoenmakers, Nadia, Scott, Richard H., Scott, Robert A., Semple, Robert K., Serra, Eva, Sharp, Sally I., Shaw, Adam, Shihab, Hashem A., Shin, So-Youn, Skuse, David, Small, Kerrin S., Smee, Carol, Smith, George Davey, Southam, Lorraine, Spasic-Boskovic, Olivera, Spector, Timothy D., St Clair, David, St Pourcain, Beate, Stalker, Jim, Stevens, Elizabeth, Sun, Jianping, Surdulescu, Gabriela, Suvisaari, Jaana, Syrris, Petros, Tachmazidou, Ioanna, Taylor, Rohan, Tian, Jing, Tobin, Martin D., Toniolo, Daniela, Traglia, Michela, Tybjaerg-Hansen, Anne, Valdes, Ana M., Vandersteen, Anthony M., Varbo, Anette, Vijayarangakannan, Parthiban, Visscher, Peter M., Wain, Louise V., Walters, James T. R., Wang, Guangbiao, Wang, Jun, Wang, Yu, Ward, Kirsten, Wheeler, Eleanor, Whincup, Peter, Whyte, Tamieka, Williams, Hywel J., Williamson, Kathleen A., Wilson, Crispian, Wilson, Scott G., Wong, Kim, Xu, ChangJiang, Yang, Jian, Zaza, Gianluigi, Zeggini, Eleftheria, Zhang, Feng, Zhang, Pingbo, Zhang, Weihua, Gambaro, Giovanni, Richards, J. Brent, Durbin, Richard, Timpson, Nicholas J., Marchini, Jonathan, Soranzo, Nicole·2015·Nature Communications
DOI 10.1038/ncomms9111
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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 resource for improving imputation accuracy at rare and low-frequency variants in both a UK and an Italian population. We show that large increases in imputation accuracy can be achieved by re-phasing WGS reference panels after initial genotype calling. We also present a method for combining WGS panels to improve variant coverage and downstream imputation accuracy, which we illustrate by integrating 7,562 WGS haplotypes from the UK10K project with 2,184 haplotypes from the 1000 Genomes Project. Finally, we introduce a novel approximation that maintains speed without sacrificing imputation accuracy for rare variants.

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Authors
Huang, J., Howie, B., McCarthy, S., Memari, Y., Walter, K., Min, J. L., Danecek, P., Malerba, G., Trabetti, E., Zheng, H.-F., UK10K Consortium, 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. G., 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.-Y., 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., Tybjaerg-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.
Venue
Nature Communications
Publisher
Springer Science and Business Media LLC
Published
2015-09-14
Volume
6
Issue
1
Pages
8111-8111
ISSN
2041-1723 (ISSN-L)
DOI
10.1038/ncomms9111
OpenAlex
W2216458865
Cited by
342
References
16
FWCI
21.59
Type
journal article
Language
en
Open access
gold

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CoChat. (2026). Citation check: Improved imputation of low-frequency and rare variants using the UK10K haplotype reference panel. https://app.cochat.ai/papers/10.1038/ncomms9111
The paper
Huang, J., Howie, B., McCarthy, S., Memari, Y., Walter, K., Min, J. L., Danecek, P., Malerba, G., Trabetti, E., Zheng, H.-F., UK10K Consortium, Al Turki, S., Amuzu, A., Anderson, C. A., Anney, R., Antony, D., Artigas, M. S., Ayub, M., Bala, S., . . . Soranzo, N. (2015). Improved imputation of low-frequency and rare variants using the UK10K haplotype reference panel. Nature Communications. https://doi.org/10.1038/ncomms9111

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Contains information from the Semantic Scholar Academic Graph Datasets, made available under the ODC Attribution License (ODC-BY 1.0).

Semantic Scholar’s data is described in: Kinney, R., et al. (2023). The Semantic Scholar Open Data Platform. arXiv:2301.10140.