Browsing by Subject "Genetic Variation"

Now showing 1 - 2 of 2

Open Access
The bonobo genome compared with the chimpanzee and human genomes
(2012) Prüfer, K.; Munch, K.; Hellmann I.; Akagi, K.; Miller J.R.; Walenz, B.; Koren, S.; Sutton G.; Kodira, C.; Winer, R.; Knight J.R.; Mullikin J.C.; Meader, S.J.; Ponting, C.P.; Lunter G.; Higashino, S.; Hobolth, A.; Dutheil J.; Karakoç, E.; Alkan, C.; Sajjadian, S.; Catacchio, C.R.; Ventura, M.; Marques-Bonet, T.; Eichler, E.E.; André, C.; Atencia, R.; Mugisha L.; Junhold J.; Patterson, N.; Siebauer, M.; Good J.M.; Fischer, A.; Ptak, S.E.; Lachmann, M.; Symer, D.E.; Mailund, T.; Schierup, M.H.; Andrés, A.M.; Kelso J.; Pääbo, S.
Two African apes are the closest living relatives of humans: the chimpanzee (Pan troglodytes) and the bonobo (Pan paniscus). Although they are similar in many respects, bonobos and chimpanzees differ strikingly in key social and sexual behaviours, and for some of these traits they show more similarity with humans than with each other. Here we report the sequencing and assembly of the bonobo genome to study its evolutionary relationship with the chimpanzee and human genomes. We find that more than three per cent of the human genome is more closely related to either the bonobo or the chimpanzee genome than these are to each other. These regions allow various aspects of the ancestry of the two ape species to be reconstructed. In addition, many of the regions that overlap genes may eventually help us understand the genetic basis of phenotypes that humans share with one of the two apes to the exclusion of the other. © 2012 Macmillan Publishers Limited. All rights reserved.
Open Access
An integrated map of genetic variation from 1,092 human genomes
(Nature Publishing Group, 2012) Altshuler, D.M.; Durbin, R.M.; Abecasis G.R.; Bentley, D.R.; Chakravarti, A.; Clark, A.G.; Donnelly P.; Eichler, E.E.; Flicek P.; Gabriel, S.B.; Gibbs, R.A.; Green, E.D.; Hurles, M.E.; Knoppers, B.M.; Korbel J.O.; Lander, E.S.; Lee, C.; Lehrach H.; Mardis, E.R.; Marth G.T.; McVean G.A.; Nickerson, D.A.; Schmidt J.P.; Sherry, S.T.; Wang, J.; Wilson, R.K.; Dinh H.; Kovar, C.; Lee, S.; Lewis L.; Muzny, D.; Reid J.; Wang, M.; Fang X.; Guo X.; Jian, M.; Jiang H.; Jin X.; Li G.; Li J.; Li Y.; Li, Z.; Liu X.; Lu, Y.; Ma X.; Su, Z.; Tai, S.; Tang, M.; Wang, B.; Wang G.; Wu H.; Wu, R.; Yin, Y.; Zhang W.; Zhao J.; Zhao, M.; Zheng X.; Zhou, Y.; Gupta, N.; Clarke L.; Leinonen, R.; Smith, R.E.; Zheng-Bradley X.; Grocock, R.; Humphray, S.; James, T.; Kingsbury, Z.; Sudbrak, R.; Albrecht, M.W.; Amstislavskiy V.S.; Borodina, T.A.; Lienhard, M.; Mertes F.; Sultan, M.; Timmermann, B.; Yaspo, M.-L.; Fulton L.; Fulton, R.; Weinstock G.M.; Balasubramaniam, S.; Burton J.; Danecek P.; Keane, T.M.; Kolb-Kokocinski, A.; McCarthy, S.; Stalker J.; Quail, M.; Davies, C.J.; Gollub J.; Webster, T.; Wong, B.; Zhan, Y.; Auton, A.; Yu F.; Bainbridge, M.; Challis, D.; Evani, U.S.; Lu J.; Nagaswamy, U.; Sabo, A.; Wang Y.; Yu J.; Coin L.J.M.; Fang L.; Li Q.; Li, Z.; Lin H.; Liu, B.; Luo, R.; Qin, N.; Shao H.; Wang, B.; Xie, Y.; Ye, C.; Yu, C.; Zhang F.; Zheng H.; Zhu H.; Garrison, E.P.; Kural, D.; Lee W.-P.; Fung Leong W.; Ward, A.N.; Wu J.; Zhang, M.; Griffin L.; Hsieh, C.-H.; Mills, R.E.; Shi X.; Von Grotthuss, M.; Zhang, C.; 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.; Yoon, S.C.; Lihm J.; Makarov V.; Jin H.; Kim W.; Cheol Kim, K.; Rausch, T.; Beal, K.; Cunningham F.; Herrero J.; McLaren W.M.; Ritchie G.R.S.; Gottipati, S.; Keinan, A.; Rodriguez-Flores J.L.; Sabeti P.C.; Grossman, S.R.; Tabrizi, S.; Tariyal, R.; Cooper, D.N.; Ball, E.V.; Stenson P.D.; Barnes, B.; Bauer, M.; Keira Cheetham, R.; Cox, T.; Eberle, M.; Kahn, S.; Murray L.; Peden J.; Shaw, R.; Ye, K.; Batzer, M.A.; Konkel, M.K.; Walker J.A.; MacArthur, D.G.; Lek, M.; Herwig, R.; Shriver, M.D.; Bustamante, C.D.; Byrnes J.K.; De La Vega F.M.; Gravel, S.; Kenny, E.E.; Kidd J.M.; Maples, B.K.; Moreno-Estrada, A.; Zakharia F.; Halperin, E.; Baran, Y.; Craig, D.W.; Christoforides, A.; Homer, N.; Izatt, T.; Kurdoglu, A.A.; Sinari, S.A.; Squire, K.; Xiao, C.; Sebat J.; Bafna V.; Ye, K.; Burchard, E.G.; Hernandez, R.D.; Gignoux, C.R.; Haussler, D.; Katzman, S.J.; James Kent W.; 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.; Min Kang H.; Anderson P.; Angius, A.; Bigham, A.; Blackwell, T.; Busonero F.; Cucca F.; Fuchsberger, C.; Jones, C.; Jun G.; Li Y.; Lyons, R.; Maschio, A.; Porcu, E.; Reinier F.; Sanna, S.; Schlessinger, D.; Sidore, C.; Tan, A.; Kate Trost, M.; Awadalla P.; Hodgkinson, A.; Lunter G.; Marchini J.L.; Myers, S.; Churchhouse, C.; Delaneau O.; Gupta-Hinch, A.; Iqbal, Z.; Mathieson I.; Rimmer, A.; Xifara, D.K.; Oleksyk, T.K.; Fu, Y.; Liu X.; Xiong, M.; Jorde L.; Witherspoon, D.; Xing J.; Browning, B.L.; Alkan C.; Hajirasouliha I.; Hormozdiari F.; Ko, A.; Sudmant P.H.; Chen, K.; Chinwalla, A.; Ding L.; Dooling, D.; Koboldt, D.C.; McLellan, M.D.; Wallis J.W.; Wendl, M.C.; Zhang Q.; Tyler-Smith, C.; Albers, C.A.; Ayub Q.; Chen, Y.; Coffey, A.J.; Colonna V.; Huang, N.; Jostins L.; Li H.; Scally, A.; Walter, K.; Xue, Y.; Zhang, Y.; Gerstein, M.B.; Abyzov, A.; Balasubramanian, S.; Chen J.; Clarke, D.; Fu, Y.; Habegger L.; Harmanci, A.O.; Jin, M.; Khurana, E.; Jasmine Mu X.; Sisu, C.; Degenhardt J.; Stütz, A.M.; Keira Cheetham, R.; Church, D.; Michaelson J.J.; Blackburne, B.; Lindsay, S.J.; Ning, Z.; Frankish, A.; Harrow J.; Mu X.J.; Fowler G.; Hale W.; Kalra, D.; Barker J.; Kelman G.; Kulesha, E.; Radhakrishnan, R.; Roa, A.; Smirnov, D.; Streeter I.; Toneva I.; Vaughan, B.; 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.; O'Sullivan, C.; Ostapchuk, Y.; Phan L.; Ponomarov, S.; Schneider V.; Shekhtman, E.; Sirotkin, K.; Slotta, D.; Zhang H.; Barnes, K.C.; Beiswanger, C.; Cai H.; Cao H.; Gharani, N.; Henn, B.; Jones, D.; Kaye J.S.; Kent, A.; Kerasidou, A.; Mathias, R.; Ossorio P.N.; Parker, M.; Reich, D.; Rotimi, C.N.; Royal, C.D.; Sandoval, K.; Su, Y.; Tian, Z.; Tishkoff, S.; Toji L.H.; Via, M.; Wang Y.; Yang H.; Yang L.; Zhu J.; Bodmer W.; Bedoya G.; Ming, C.Z.; Yang G.; Jia You, C.; Peltonen L.; Garcia-Montero, A.; Orfao, A.; Dutil J.; Martinez-Cruzado J.C.; Brooks L.D.; Felsenfeld, A.L.; McEwen J.E.; Clemm, N.C.; Duncanson, A.; Dunn, M.; Guyer, M.S.; Peterson J.L.; Lacroute P.
By characterizing the geographic and functional spectrum of human genetic variation, the 1000 Genomes Project aims to build a resource to help to understand the genetic contribution to disease. Here we describe the genomes of 1,092 individuals from 14 populations, constructed using a combination of low-coverage whole-genome and exome sequencing. By developing methods to integrate information across several algorithms and diverse data sources, we provide a validated haplotype map of 38 million single nucleotide polymorphisms, 1.4 million short insertions and deletions, and more than 14,000 larger deletions. We show that individuals from different populations carry different profiles of rare and common variants, and that low-frequency variants show substantial geographic differentiation, which is further increased by the action of purifying selection. We show that evolutionary conservation and coding consequence are key determinants of the strength of purifying selection, that rare-variant load varies substantially across biological pathways, and that each individual contains hundreds of rare non-coding variants at conserved sites, such as motif-disrupting changes in transcription-factor-binding sites. This resource, which captures up to 98% of accessible single nucleotide polymorphisms at a frequency of 1% in related populations, enables analysis of common and low-frequency variants in individuals from diverse, including admixed, populations. © 2012 Macmillan Publishers Limited. All rights reserved.