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Alignment of 1000 Genomes Project reads to reference assembly GRCh38

Autor: Zheng-Bradley, X., Streeter, I., Fairley, S., Richardson, D., Clarke, L., Flicek, P., 1000 Genomes Project , C., Timmermann, B.

Publikováno v: GigaScience

The 1000 Genomes Project produced more than 100 trillion basepairs of short read sequence from more than 2600 samples in 26 populations over a period of five years. In its final phase, the project released over 85 million genotyped and phased variant

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::04b188c05d96cc652e2ea9b6b8472d2c
https://pubmed.ncbi.nlm.nih.gov/28531267

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

Autor: 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.

Publikováno v: 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

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 pol

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::4e27cd0d1ed4de04db34bcfb769bb534
https://serval.unil.ch/resource/serval:BIB_FAB25C17CFF9.P001/REF.pdf

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