Integrating sequence and array data to create an improved 1000 Genomes Project haplotype reference panel
| العنوان: | Integrating sequence and array data to create an improved 1000 Genomes Project haplotype reference panel |
|---|---|
| المؤلفون: | Delaneau O., Marchini J., McVeanh 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., 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., Hartl, C., McCarroll, S.A., Nemesh J.C., Poplin, R.E., Schaffner, S.F., Shakir, K., Sabeti P.C., Grossman, S.R., Tabrizi, S., Tariyal, 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., Chris, T.-S., 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 LaVega 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., Herwig, S.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., Lachlan H., Fang L., Li Q., Li, Z., Lin H., Liu, B., Luo, R., Shao H., 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., 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., 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., Maroo, A., Tallon L.J., Rosenfeld J.A., Michelson L.P., Angius, A., Cucca F., Sanna, S., Bigham, A., Jones, C., Reinier F., Lyons, R., Schlessinger, D., Awadalla P., Hodgkinson, A., Oleksyk, T.K., Martinez-Cruzado J.C., Fu, Y., 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., 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., Peltonen L. |
| المساهمون: | 1000 Genomes Project Consortium |
| المصدر: | Nature communications Nature Communications Nature communications 5 (2014). doi:10.1038/ncomms4934 info:cnr-pdr/source/autori:Delaneau, Olivier; Marchini, Jonathan; McVeanh, Gil A.; Donnelly, Peter; Lunter, Gerton; Marchini, Jonathan L.; Myers, Simon R.; Gupta-Hinch, Anjali; Iqbal, Zamin; Mathieson, Iain; Rimmer, Andrew J.; Xifara, Dionysia K.; Kerasidou, Angeliki; Churchhouse, Claire; Altshuler, David M.; Gabriel, Stacey Bolk; 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.; Hartl, Chris L.; McCarroll, Steven A.; Nemesh, James C.; Poplin, Ryan E.; Schaffner, Stephen F.; Shakir, Khalid; Sabeti, Pardis C.; Grossman, Sharon R.; Tabrizi, Shervin; Tariyal, Ridhi; Li, Heng; Reich, David E.; Durbin, Richard M.; Hurles, Matthew E.; Balasubramaniam, Senduran; Burton, John S.; Danecek, Petr; Keane, Thomas M.; Kolb-Kokocinski, Anja; McCarthy, Shane E.; Stalker, James W.; Quail, Michael A.; Ayub, Qasim; Chen, Yuan; Coffey, Alison J.; Colonna, Vincenza; Huang, Ni; Jostins, Luke; Scally, Aylwyn; Walter, Klaudia K Ho; Xue, Yali; Zhang, Yujun; Blackburne, Benjamin P.; Lindsay, Sarah J.; Ning, Zemin; Frankish, Adam G.; Harrow, Jennifer L.; Chris, Tyler S.; Abeçasis, Gonçalo R.; Kang, Hyunmin; Anderson, Paul C B; Blackwell, Thomas W.; Busonero, Fabio; Fuchsberger, Christian; Jun, Goo; Maschio, Andrea; Porcu, Eleonora; Sidore, Carlo; Tan, Adrian; Trost, Mary Kate; Bentley, David R.; Grocock, Russell James; Humphray, Sean J.; James, Terena; Kingsbury, Zoya; Bauer, Markus J.; Cheetham, R. Keira; Cox, Tony V.; Eberle, Michael A.; Murray, Lisa J.; Shaw, Richard J.; Chakravarti, Aravinda H.; Clark, Andrew Godfrey B; Keinan, Alon; Rodríguez-Flores, Juan L.; De LaVega, Francisco M.; Degenhardt, Jeremiah D.; Eichler, Evan E.; Flicek, Paul; Clarke, Laura A.; Leinonen, Rasko; Smith, Richard E.; Zheng-Bradley, Xiangqun; Beal, Kathryn F.; Cunningham, Fiona; Herrero, Javier; McLaren, William M.; Ritchie, Graham R S; Barker, Jonathan Nn W N; Kelman, Gavin; Kulesha, Eugene; Radhakrishnan, Rajesh; Roa, Asier; Smirnov, Dmitri S.; Streeter, Ian; Toneva, Iliana; Gibbs, Richard A L; Dinh, Huyen H.; Ková?, Christie L.; Lee, Sandy; Lewis, Lora R.; Muzny, Donna Marie; Reid, Jeffrey G.; Wang, Min; Yu, Fuli; Bainbridge, Matthew N.; Challis, Daniel E.; Evani, Uday S.; Lu, James; Nagaswamy, Uma; Sabo, Aniko M.; Wang, Yi; Yu, Jin; Fowler, Gerald R.; Hale, Walker; Kalra, Divya; Green, Eric D.; Knoppers, Bartha Maria; Korbel, Jan O.; Rausch, Tobias; Sttz, Adrian M.; Lee, Charles; Griffin, Lauren; Hsieh, Chihheng; Mills, Ryan E.; Von Grotthuss, Marcin; Zhang, Chengsheng; Shi, Xinghua; Lehrach, Hans R.; Sudbrak, Ralf; Amstislavskiy, Vyacheslav S.; Lienhard, Matthias; Mertes, Florian; Sultan, Marc; Timmermann, Bernd; Yaspo, Marie Laure; Herwig, Sudbrak Ralf; Mardis, Elaine; Wilson, Richard K.; Fulton, Lucinda L.; Fulton, Robert S.; Weinstock, George M.; Chinwalla, Asif T.; Ding, Li; Dooling, David J.; Koboldt, Daniel C.; McLellan, Michael D.; Wallis, John W.; Wendl, Michael C.; Zhang, Qunyuan; Marth, Gábor T.; Garrison, Erik P.; Kural, Deniz; Lee, Wanping; Leong, Wenfung; Ward, Alistair N.; Wu, Jiantao; Zhang, Mengyao; Nickerson, Deborah A A.; Alkan, Can; Hormozdiari, Fereydoun; Ko, Arthur; Sudmant, Peter H.; Schmidt, Jeanette P.; Davies, Christopher J.; Gollub, Jeremy; Webster, Teresa A.; Wong, Brant; Zhan, Yiping; Sherry, Stephen T.; Xiao, Chunlin; Church, Deanna M.; Ananiev, Victor; Belaia, Zinaida; Beloslyudtsev, Dimitriy; Bouk, Nathan; Chen, Chao; Cohen, Robert F.; Cook, Charles; Garner, John R.; Hefferon, Timothy W.; Kimelman, Mikhail; Liu, Chunlei; Lopez, John R.; Meric, Peter A.; Ostapchuk, Yu L.; Phan, Lon; Ponomarov, Sergiy; Schneider, Valerie A.; Shekhtman, Eugene M.; Sirotkin, Karl M.; Slotta, Douglas J.; 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; Lachlan, Hans; 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, Seungtaichris; Lihm, Jayon; Makarov, Vladimir; Jin, Hanjun; Kim, Wook; Kim, Kicheol; Gottipati, Srikanth; Jones, Danielle; Cooper, David N David N; Ball, Edward V.; Stenson, Peter D.; Barnes, Bret; Kahn, Scott D.; Ye, Kai; Batzer, Mark A.; Konkel, Miriam K.; Walker, Jerilyn A.; Macarthur, Daniel G.; Lek, Monkol; Shriver, Mark D.; Bustamante, Carlos D.; Gravel, Simon Pierre; Kenny, Eimear E.; Kidd, Jeffrey M.; Lacroute, Phil; Maples, Brian K.; Moreno-Estrada, Andrés; Zakharia, Fouad; Henn, Brenna M.; 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 L.; Bafna, Vineet K.; Ye, Kenny; Burchard, Esteban González; Hernandez, Ryan D.; Gignoux, Christopher R.; Haussler, David H.; Katzman, Sol J.; Kent, William James; Howie, Bryan N.; Ruiz-Linarès, Andrés; Dermitzakis, Emmanouil T T.; Lappalainen, Tuuli; Devine, Scott E.; Liu, Xinyue; Maroo, Ankit; Tallon, Luke J.; Rosenfeld, Jeffrey A.; Michelson, Leslie P.; Angius, Andrea G.; Cucca, Francesco; Sanna, Serena; Bigham, Abigail W.; Jones, Chris G.; Reinier, Frédéric; Li, Yun; Lyons, Robert H.; Schlessinger, David; Awadalla, Philip; Hodgkinson, Alan; Oleksyk, Taras K.; Martínez-Cruzado, Juan Carlos; Fu, Yunxin; Liu, Xiaoming; Xiong, Momiao; Jorde, Lynn B.; Witherspoon, David J.; 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 Ozgun; Mu, Xinmengjasmine; Sisu, Cristina; Balasubramanian, Suganthi; Jin, Mike; Khurana, Ekta; Clarke, Declan; Michaelson, Jacob J.; OSullivan, Chris; Barnes, Kathleen Carole; Gharani, Neda; Toji, Lorraine H.; Gerry, Norman P.; Kaye, Jane S.; Kent, Alastair D.; Mathias, Rasika Ann; Ossorio, Pilar N.; Parker, Michael J.; Rotimi, Charles N.; Royal, Charmaine D M; Tishkoff, Sarah A.; Vía, Marc; Bodmer, Walter F.; Bedoya, Gabriel De Jesús; Yang, Gao; You, Chujia; García-Montero, Andrés Celestino; 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 G.; Peltonen, Leena Johanna/titolo:Integrating sequence and array data to create an improved 1000 Genomes Project haplotype reference panel/doi:10.1038%2Fncomms4934/rivista:Nature communications/anno:2014/pagina_da:/pagina_a:/intervallo_pagine:/volume:5 |
| سنة النشر: | 2014 |
| مصطلحات موضوعية: | haplotype, genetic association, genotype, General Physics and Astronomy, Genome-wide association study, genetic analysis, gene sequence, Biology, gene frequency, Polymorphism, Single Nucleotide, General Biochemistry, Genetics and Molecular Biology, Article, polymorphism, Gene Frequency, single nucleotide polymorphism, Humans, chromosome, human, 1000 Genomes Project, indel mutation, genome, Alleles, Genetic association, Genetics, Whole genome sequencing, Multidisciplinary, accuracy, Genome, Human, Haplotype, allele, article, reference database, General Chemistry, Microarray Analysis, chromosome 20, Haplotypes, Human genome, microarray analysis, Imputation (genetics), Algorithms, SNP array, Genome-Wide Association Study |
| الوصف: | 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. © 2014 Macmillan Publishers Limited. All rights reserved. |
| وصف الملف: | application/pdf |
| اللغة: | English |
| الوصول الحر: | https://explore.openaire.eu/search/publication?articleId=doi_dedup___::4e27cd0d1ed4de04db34bcfb769bb534Test https://serval.unil.ch/resource/serval:BIB_FAB25C17CFF9.P001/REF.pdfTest |
| حقوق: | OPEN |
| رقم الانضمام: | edsair.doi.dedup.....4e27cd0d1ed4de04db34bcfb769bb534 |
| قاعدة البيانات: | OpenAIRE |
| الوصف غير متاح. |