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Cited by 406

The DOI matches its Crossref record; 17 of the 17 references it cites were found in a registry or an index.

Integrating sequence and array data to create an improved 1000 Genomes Project haplotype reference panel

Open access
Delaneau, Olivier, Marchini, Jonathan, The 1000 Genomes Project Consortium, McVean, Gil A., Donnelly, Peter, Lunter, Gerton, Marchini, Jonathan L., Myers, Simon, Gupta-Hinch, Anjali, Iqbal, Zamin, Mathieson, Iain, Rimmer, Andy, Xifara, Dionysia K., Kerasidou, Angeliki, Churchhouse, Claire, Delaneau, Olivier, Altshuler, David M., Gabriel, Stacey B., Lander, Eric S., Gupta, Namrata, Daly, Mark J., DePristo, Mark A., Banks, Eric, Bhatia, Gaurav, Carneiro, Mauricio O., del Angel, Guillermo, Genovese, Giulio, Handsaker, Robert E., Hart, Chris, McCarroll, Steven A., Nemesh, James C., Poplin, Ryan E., Schaffner, Stephen F., Shakir, Khalid, Sabeti, Pardis C., Grossman, Sharon R., Tabrizi, Shervin, Tariya, Ridhi, Li, Heng, Reich, David, Durbin, Richard M., Hurles, Matthew E., Balasubramaniam, Senduran, Burton, John, Danecek, Petr, Keane, Thomas M., Kolb-Kokocinski, Anja, McCarthy, Shane, Stalker, James, Quail, Michael, Ayub, Qasim, Chen, Yuan, Coffey, Alison J., Colonna, Vincenza, Huang, Ni, Jostins, Luke, Scally, Aylwyn, Walter, Klaudia, Xue, Yali, Zhang, Yujun, Blackburne, Ben, Lindsay, Sarah J., Ning, Zemin, Frankish, Adam, Harrow, Jennifer, Tyler-Smith, Chris, Abecasis, Gonalo R., Kang, Hyun Min, Anderson, Paul, Blackwell, Tom, Busonero, Fabio, Fuchsberger, Christian, Jun, Goo, Maschio, Andrea, Porcu, Eleonora, Sidore, Carlo, Tan, Adrian, Trost, Mary Kate, Bentley, David R., Grocock, Russell, Humphray, Sean, James, Terena, Kingsbury, Zoya, Bauer, Markus, Cheetham, R. Keira, Cox, Tony, Eberle, Michael, Murray, Lisa, Shaw, Richard, Chakravarti, Aravinda, Clark, Andrew G., Keinan, Alon, Rodriguez-Flores, Juan L., De La Vega, Francisco M., Degenhardt, Jeremiah, Eichler, Evan E., Flicek, Paul, Clarke, Laura, Leinonen, Rasko, Smith, Richard E., Zheng-Bradley, Xiangqun, Beal, Kathryn, Cunningham, Fiona, Herrero, Javier, McLaren, William M., Ritchie, Graham R. S., Barker, Jonathan, Kelman, Gavin, Kulesha, Eugene, Radhakrishnan, Rajesh, Roa, Asier, Smirnov, Dmitriy, Streeter, Ian, Toneva, Iliana, Gibbs, Richard A., Dinh, Huyen, Kovar, Christie, Lee, Sandra, Lewis, Lora, Muzny, Donna, Reid, Jeff, Wang, Min, Yu, Fuli, Bainbridge, Matthew, Challis, Danny, Evani, Uday S., Lu, James, Nagaswamy, Uma, Sabo, Aniko, Wang, Yi, Yu, Jin, Fowler, Gerald, Hale, Walker, Kalra, Divya, Green, Eric D., Knoppers, Bartha M., Korbel, Jan O., Rausch, Tobias, Sttz, Adrian M., Lee, Charles, Griffin, Lauren, Hsieh, Chih-Heng, Mills, Ryan E., von Grotthuss, Marcin, Zhang, Chengsheng, Shi, Xinghua, Lehrach, Hans, Sudbrak, Ralf, Amstislavskiy, Vyacheslav S., Lienhard, Matthias, Mertes, Florian, Sultan, Marc, Timmermann, Bernd, Yaspo, Marie-Laure, Sudbrak, Herwig, Ralf, Mardis, Elaine R., Wilson, Richard K., Fulton, Lucinda, Fulton, Robert, Weinstock, George M., Chinwalla, Asif, Ding, Li, Dooling, David, Koboldt, Daniel C., McLellan, Michael D., Wallis, John W., Wendl, Michael C., Zhang, Qunyuan, Marth, Gabor T., Garrison, Erik P., Kural, Deniz, Lee, Wan-Ping, Leong, Wen Fung, Ward, Alistair N., Wu, Jiantao, Zhang, Mengyao, Nickerson, Deborah A., Alkan, Can, Hormozdiari, Fereydoun, Ko, Arthur, Sudmant, Peter H., Schmidt, Jeanette P., Davies, Christopher J., Gollub, Jeremy, Webster, Teresa, Wong, Brant, Zhan, Yiping, Sherry, Stephen T., Xiao, Chunlin, Church, Deanna, Ananiev, Victor, Belaia, Zinaida, Beloslyudtsev, Dimitriy, Bouk, Nathan, Chen, Chao, Cohen, Robert, Cook, Charles, Garner, John, Hefferon, Timothy, Kimelman, Mikhail, Liu, Chunlei, Lopez, John, Meric, Peter, Ostapchuk, Yuri, Phan, Lon, Ponomarov, Sergiy, Schneider, Valerie, Shekhtman, Eugene, Sirotkin, Karl, Slotta, Douglas, Zhang, Hua, Wang, Jun, Fang, Xiaodong, Guo, Xiaosen, Jian, Min, Jiang, Hui, Jin, Xin, Li, Guoqing, Li, Jingxiang, Li, Yingrui, Liu, Xiao, Lu, Yao, Ma, Xuedi, Tai, Shuaishuai, Tang, Meifang, Wang, Bo, Wang, Guangbiao, Wu, Honglong, Wu, Renhua, Yin, Ye, Zhang, Wenwei, Zhao, Jiao, Zhao, Meiru, Zheng, Xiaole, Coin, Lachlan J.M., Fang, Lin, Li, Qibin, Li, Zhenyu, Lin, Haoxiang, Liu, Binghang, Luo, Ruibang, Shao, Haojing, Wang, Bingqiang, Xie, Yinlong, Ye, Chen, Yu, Chang, Zheng, Hancheng, Zhu, Hongmei, Cai, Hongyu, Cao, Hongzhi, Su, Yeyang, Tian, Zhongming, Yang, Huanming, Yang, Ling, Zhu, Jiayong, Cai, Zhiming, Wang, Jian, Albrecht, Marcus W., Borodina, Tatiana A., Auton, Adam, Yoon, Seungtai C., Lihm, Jayon, Makarov, Vladimir, Jin, Hanjun, Kim, Wook, Kim, Ki Cheol, Gottipati, Srikanth, Jones, Danielle, Cooper, David N., Ball, Edward V., Stenson, Peter D., Barnes, Bret, Kahn, Scott, Ye, Kai, Batzer, Mark A., Konkel, Miriam K., Walker, Jerilyn A., MacArthur, Daniel G., Lek, Monkol, Shriver, Mark D., Bustamante, Carlos D., Gravel, Simon, Kenny, Eimear E., Kidd, Jeffrey M., Lacroute, Phil, Maples, Brian K., Moreno-Estrada, Andres, Zakharia, Fouad, Henn, Brenna, Sandoval, Karla, Byrnes, Jake K., Halperin, Eran, Baran, Yael, Craig, David W., Christoforides, Alexis, Izatt, Tyler, Kurdoglu, Ahmet A., Sinari, Shripad A., Homer, Nils, Squire, Kevin, Sebat, Jonathan, Bafna, Vineet, Ye, Kenny, Burchard, Esteban G., Hernandez, Ryan D., Gignoux, Christopher R., Haussler, David, Katzman, Sol J., Kent, W. James, Howie, Bryan, Ruiz-Linares, Andres, Dermitzakis, Emmanouil T., Lappalainen, Tuuli, Devine, Scott E., Liu, Xinyue, Maroo, Ankit, Tallon, Luke J., Rosenfeld, Jeffrey A., Michelson, Leslie P., Angius, Andrea, Cucca, Francesco, Sanna, Serena, Bigham, Abigail, Jones, Chris, Reinier, Fred, Li, Yun, Lyons, Robert, Schlessinger, David, Awadalla, Philip, Hodgkinson, Alan, Oleksyk, Taras K., Martinez-Cruzado, Juan C., Fu, Yunxin, Liu, Xiaoming, Xiong, Momiao, Jorde, Lynn, Witherspoon, David, Xing, Jinchuan, Browning, Brian L., Hajirasouliha, Iman, Chen, Ken, Albers, Cornelis A., Gerstein, Mark B., Abyzov, Alexej, Chen, Jieming, Fu, Yao, Habegger, Lukas, Harmanci, Arif O., Mu, Xinmeng Jasmine, Sisu, Cristina, Balasubramanian, Suganthi, Jin, Mike, Khurana, Ekta, Clarke, Declan, Michaelson, Jacob J., OSullivan, Chris, Barnes, Kathleen C., Gharani, Neda, Toji, Lorraine H., Gerry, Norman, Kaye, Jane S., Kent, Alastair, Mathias, Rasika, Ossorio, Pilar N., Parker, Michael, Rotimi, Charles N., Royal, Charmaine D., Tishkoff, Sarah, Via, Marc, Bodmer, Walter, Bedoya, Gabriel, Yang, Gao, You, Chu Jia, Garcia-Montero, Andres, Orfao, Alberto, Dutil, Julie, Brooks, Lisa D., Felsenfeld, Adam L., McEwen, Jean E., Clemm, Nicholas C., Guyer, Mark S., Peterson, Jane L., Duncanson, Audrey, Dunn, Michael, Peltonenz, Leena·2014·Nature Communications
DOI 10.1038/ncomms4934
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Abstract

A major use of the 1000 Genomes Project (1000GP) data is genotype imputation in genome-wide association studies (GWAS). Here we develop a method to estimate haplotypes from low-coverage sequencing data that can take advantage of single-nucleotide polymorphism (SNP) microarray genotypes on the same samples. First the SNP array data are phased to build a backbone (or ‘scaffold’) of haplotypes across each chromosome. We then phase the sequence data ‘onto’ this haplotype scaffold. This approach can take advantage of relatedness between sequenced and non-sequenced samples to improve accuracy. We use this method to create a new 1000GP haplotype reference set for use by the human genetic community. Using a set of validation genotypes at SNP and bi-allelic indels we show that these haplotypes have lower genotype discordance and improved imputation performance into downstream GWAS samples, especially at low-frequency variants. 1000 Genomes imputation can increase the power of genome-wide association studies to detect genetic variants associated with human traits and diseases. Here, the authors develop a method to integrate and analyse low-coverage sequence data and SNP array data, and show that it improves imputation performance.

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Metadata

Authors
Delaneau, O., Marchini, J., The 1000 Genomes Project Consortium, McVean, G. A., Donnelly, P., Lunter, G., Marchini, J. L., Myers, S., Gupta-Hinch, A., Iqbal, Z., Mathieson, I., Rimmer, A., Xifara, D. K., Kerasidou, A., Churchhouse, C., Delaneau, O., Altshuler, D. M., Gabriel, S. B., Lander, E. S., Gupta, N., Daly, M. J., DePristo, M. A., Banks, E., Bhatia, G., Carneiro, M. O., del Angel, G., Genovese, G., Handsaker, R. E., Hart, C., McCarroll, S. A., Nemesh, J. C., Poplin, R. E., Schaffner, S. F., Shakir, K., Sabeti, P. C., Grossman, S. R., Tabrizi, S., Tariya, R., Li, H., Reich, D., Durbin, R. M., Hurles, M. E., Balasubramaniam, S., Burton, J., Danecek, P., Keane, T. M., Kolb-Kokocinski, A., McCarthy, S., Stalker, J., Quail, M., Ayub, Q., Chen, Y., Coffey, A. J., Colonna, V., Huang, N., Jostins, L., Scally, A., Walter, K., Xue, Y., Zhang, Y., Blackburne, B., Lindsay, S. J., Ning, Z., Frankish, A., Harrow, J., Tyler-Smith, C., Abecasis, G. R., Kang, H. M., Anderson, P., Blackwell, T., Busonero, F., Fuchsberger, C., Jun, G., Maschio, A., Porcu, E., Sidore, C., Tan, A., Trost, M. K., Bentley, D. R., Grocock, R., Humphray, S., James, T., Kingsbury, Z., Bauer, M., Cheetham, R. K., Cox, T., Eberle, M., Murray, L., Shaw, R., Chakravarti, A., Clark, A. G., Keinan, A., Rodriguez-Flores, J. L., De La Vega, F. M., Degenhardt, J., Eichler, E. E., Flicek, P., Clarke, L., Leinonen, R., Smith, R. E., Zheng-Bradley, X., Beal, K., Cunningham, F., Herrero, J., McLaren, W. M., Ritchie, G. R. S., Barker, J., Kelman, G., Kulesha, E., Radhakrishnan, R., Roa, A., Smirnov, D., Streeter, I., Toneva, I., Gibbs, R. A., Dinh, H., Kovar, C., Lee, S., Lewis, L., Muzny, D., Reid, J., Wang, M., Yu, F., Bainbridge, M., Challis, D., Evani, U. S., Lu, J., Nagaswamy, U., Sabo, A., Wang, Y., Yu, J., Fowler, G., Hale, W., Kalra, D., Green, E. D., Knoppers, B. M., Korbel, J. O., Rausch, T., Sttz, A. M., Lee, C., Griffin, L., Hsieh, C.-H., Mills, R. E., von Grotthuss, M., Zhang, C., Shi, X., Lehrach, H., Sudbrak, R., Amstislavskiy, V. S., Lienhard, M., Mertes, F., Sultan, M., Timmermann, B., Yaspo, M.-L., Sudbrak, Herwig, R., Mardis, E. R., Wilson, R. K., Fulton, L., Fulton, R., Weinstock, G. M., Chinwalla, A., Ding, L., Dooling, D., Koboldt, D. C., McLellan, M. D., Wallis, J. W., Wendl, M. C., Zhang, Q., Marth, G. T., Garrison, E. P., Kural, D., Lee, W.-P., Leong, W. F., Ward, A. N., Wu, J., Zhang, M., Nickerson, D. A., Alkan, C., Hormozdiari, F., Ko, A., Sudmant, P. H., Schmidt, J. P., Davies, C. J., Gollub, J., Webster, T., Wong, B., Zhan, Y., Sherry, S. T., Xiao, C., Church, D., Ananiev, V., Belaia, Z., Beloslyudtsev, D., Bouk, N., Chen, C., Cohen, R., Cook, C., Garner, J., Hefferon, T., Kimelman, M., Liu, C., Lopez, J., Meric, P., Ostapchuk, Y., Phan, L., Ponomarov, S., Schneider, V., Shekhtman, E., Sirotkin, K., Slotta, D., Zhang, H., Wang, J., Fang, X., Guo, X., Jian, M., Jiang, H., Jin, X., Li, G., Li, J., Li, Y., Liu, X., Lu, Y., Ma, X., Tai, S., Tang, M., Wang, B., Wang, G., Wu, H., Wu, R., Yin, Y., Zhang, W., Zhao, J., Zhao, M., Zheng, X., Coin, L. J. M., Fang, L., Li, Q., Li, Z., Lin, H., Liu, B., Luo, R., Shao, H., Wang, B., Xie, Y., Ye, C., Yu, C., Zheng, H., Zhu, H., Cai, H., Cao, H., Su, Y., Tian, Z., Yang, H., Yang, L., Zhu, J., Cai, Z., Wang, J., Albrecht, M. W., Borodina, T. A., Auton, A., Yoon, S. C., Lihm, J., Makarov, V., Jin, H., Kim, W., Kim, K. C., Gottipati, S., Jones, D., Cooper, D. N., Ball, E. V., Stenson, P. D., Barnes, B., Kahn, S., Ye, K., Batzer, M. A., Konkel, M. K., Walker, J. A., MacArthur, D. G., Lek, M., Shriver, M. D., Bustamante, C. D., Gravel, S., Kenny, E. E., Kidd, J. M., Lacroute, P., Maples, B. K., Moreno-Estrada, A., Zakharia, F., Henn, B., Sandoval, K., Byrnes, J. K., Halperin, E., Baran, Y., Craig, D. W., Christoforides, A., Izatt, T., Kurdoglu, A. A., Sinari, S. A., Homer, N., Squire, K., Sebat, J., Bafna, V., Ye, K., Burchard, E. G., Hernandez, R. D., Gignoux, C. R., Haussler, D., Katzman, S. J., Kent, W. J., Howie, B., Ruiz-Linares, A., Dermitzakis, E. T., Lappalainen, T., Devine, S. E., Liu, X., Maroo, A., Tallon, L. J., Rosenfeld, J. A., Michelson, L. P., Angius, A., Cucca, F., Sanna, S., Bigham, A., Jones, C., Reinier, F., Li, Y., Lyons, R., Schlessinger, D., Awadalla, P., Hodgkinson, A., Oleksyk, T. K., Martinez-Cruzado, J. C., Fu, Y., Liu, X., Xiong, M., Jorde, L., Witherspoon, D., Xing, J., Browning, B. L., Hajirasouliha, I., Chen, K., Albers, C. A., Gerstein, M. B., Abyzov, A., Chen, J., Fu, Y., Habegger, L., Harmanci, A. O., Mu, X. J., Sisu, C., Balasubramanian, S., Jin, M., Khurana, E., Clarke, D., Michaelson, J. J., OSullivan, C., Barnes, K. C., Gharani, N., Toji, L. H., Gerry, N., Kaye, J. S., Kent, A., Mathias, R., Ossorio, P. N., Parker, M., Rotimi, C. N., Royal, C. D., Tishkoff, S., Via, M., Bodmer, W., Bedoya, G., Yang, G., You, C. J., Garcia-Montero, A., Orfao, A., Dutil, J., Brooks, L. D., Felsenfeld, A. L., McEwen, J. E., Clemm, N. C., Guyer, M. S., Peterson, J. L., Duncanson, A., Dunn, M., & Peltonenz, L.
Venue
Nature Communications
Publisher
Springer Science and Business Media LLC
Published
2014-06-13
Volume
5
Issue
1
Pages
3934-3934
ISSN
2041-1723 (ISSN-L)
DOI
10.1038/ncomms4934
OpenAlex
W2095859808
Cited by
406
References
17
FWCI
16.44
Type
journal article
Language
en
Open access
bronze

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CoChat. (2026). Citation check: Integrating sequence and array data to create an improved 1000 Genomes Project haplotype reference panel. https://app.cochat.ai/papers/10.1038/ncomms4934
The paper
Delaneau, O., Marchini, J., The 1000 Genomes Project Consortium, McVean, G. A., Donnelly, P., Lunter, G., Marchini, J. L., Myers, S., Gupta-Hinch, A., Iqbal, Z., Mathieson, I., Rimmer, A., Xifara, D. K., Kerasidou, A., Churchhouse, C., Delaneau, O., Altshuler, D. M., Gabriel, S. B., Lander, E. S., . . . Peltonenz, L. (2014). Integrating sequence and array data to create an improved 1000 Genomes Project haplotype reference panel. Nature Communications. https://doi.org/10.1038/ncomms4934

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