Global diversity, population stratification, and selection of human copy-number variation

被引：229

作者：

Sudmant, Peter H. ^{[1
]}

Mallick, Swapan ^{[2
,3
]}

Nelson, Bradley J. ^{[1
]}

Hormozdiari, Fereydoun ^{[1
]}

Krumm, Niklas ^{[1
]}

Huddleston, John ^{[1
,41
]}

Coe, Bradley P. ^{[1
]}

Baker, Carl ^{[1
]}

Nordenfelt, Susanne ^{[2
,3
]}

Bamshad, Michael ^{[4
]}

Jorde, Lynn B. ^{[5
]}

Posukh, Olga L. ^{[6
,7
]}

Sahakyan, Hovhannes ^{[8
,9
]}

Watkins, W. Scott ^{[10
]}

Yepiskoposyan, Levon ^{[9
]}

Abdullah, M. Syafiq ^{[11
]}

Bravi, Claudio M. ^{[12
,13
]}

Capelli, Cristian ^{[14
]}

Hervig, Tor ^{[15
]}

Wee, Joseph T. S. ^{[16
]}

Tyler-Smith, Chris ^{[17
]}

van Driem, George ^{[18
]}

Romero, Irene Gallego ^{[19
]}

Jha, Aashish R. ^{[19
]}

Karachanak-Yankova, Sena ^{[20
]}

Toncheva, Draga ^{[20
]}

Comas, David ^{[21
]}

Henn, Brenna ^{[22
]}

Kivisild, Toomas ^{[23
]}

Ruiz-Linares, Andres ^{[24
]}

Sajantila, Antti ^{[25
]}

Metspalu, Ene ^{[8
,26
]}

Parik, Jueri ^{[8
]}

Villems, Richard ^{[8
]}

Starikovskaya, Elena B. ^{[27
]}

Ayodo, George ^{[28
]}

Beall, Cynthia M. ^{[29
]}

Di Rienzo, Anna ^{[19
]}

Hammer, Michael F. ^{[30
]}

Khusainova, Rita ^{[31
,32
]}

Khusnutdinova, Elza ^{[31
,32
]}

Klitz, William ^{[33
]}

Winkler, Cheryl ^{[34
]}

Labuda, Damian ^{[35
]}

Metspalu, Mait ^{[8
]}

Tishkoff, Sarah A. ^{[36
,37
]}

Dryomov, Stanislav ^{[27
,38
]}

Sukernik, Rem ^{[27
,39
]}

Patterson, Nick ^{[2
,3
]}

Reich, David ^{[2
,3
,40
]}

机构：

[1] Univ Washington, Dept Genome Sci, Seattle, WA 98195 USA

[2] Broad Inst Massachusetts Inst Technol MIT & Harva, Cambridge, MA USA

[3] Harvard Univ, Sch Med, Dept Genet, Boston, MA 02115 USA

[4] Univ Washington, Dept Pediat, Seattle, WA 98119 USA

[5] Univ Utah, Sch Med, Dept Human Genet, Salt Lake City, UT 84112 USA

[6] Russian Acad Sci, Siberian Branch, Inst Cytol & Genet, Novosibirsk 630090, Russia

[7] Novosibirsk State Univ, Novosibirsk 630090, Russia

[8] Estonian Bioctr, Evolutionary Biol Grp, EE-51010 Tartu, Estonia

[9] Natl Acad Sci Armenia, Inst Mol Biol, Lab Ethnogen, Yerevan 0014, Armenia

[10] Univ Utah, Eccles Inst Human Genet, Dept Human Genet, Salt Lake City, UT 84112 USA

[11] Raja Isteri Pengiran Anak Saleha RIPAS Hosp, Bandar Seri Begawan, Brunei Darussal, Brunei

[12] CCT CONICET, Inst Multidisciplinario Biol Celular IMBICE, Lab Genet Mol Poblac, Rio Cuarto, Argentina

[13] CICPBA, Rio Cuarto, Argentina

[14] Univ Oxford, Dept Zool, Oxford OX1 3PS, England

[15] Univ Bergen, Dept Clin Sci, N-5021 Bergen, Norway

[16] Natl Canc Ctr Singapore, Singapore, Singapore

[17] Wellcome Trust Sanger Inst, Hinxton CB10 1SA, Cambs, England

[18] Univ Bern, Inst Linguist, CH-3012 Bern, Switzerland

[19] Univ Chicago, Dept Human Genet, Chicago, IL 60637 USA

[20] Med Univ Sofia, Natl Human Genome Ctr, Dept Med Genet, Sofia 1431, Bulgaria

[21] CSIC UPF, Dept Ciencies Expt, Inst Biol Evolut, Barcelona 08003, Spain

[22] SUNY Stony Brook, Dept Ecol & Evolut, Stony Brook, NY 11794 USA

[23] Univ Cambridge, Div Biol Anthropol, Cambridge CB2 1QH, England

[24] UCL, Dept Genet Evolut & Environm, London WC1E 6BT, England

[25] Univ Helsinki, Dept Forens Med, Helsinki 00014, Finland

[26] Univ Tartu, Dept Evolutionary Biol, EE-5101 Tartu, Estonia

[27] Russian Acad Sci, Siberian Branch, Inst Mol & Cellular Biol, Lab Human Mol Genet, Novosibirsk 630090, Russia

[28] Ctr Global Hlth & Child Dev, Kisumu 40100, Kenya

[29] Case Western Reserve Univ, Dept Anthropol, Cleveland, OH 44106 USA

[30] Univ Arizona, Div Biotechnol, Arizona Res Labs, Tucson, AZ 85721 USA

[31] Russian Acad Sci, Ufa Res Ctr, Inst Biochem & Genet, Ufa 450054, Russia

[32] Bashkir State Univ, Dept Genet & Fundamental Med, Ufa 450074, Russia

[33] Univ Calif Berkeley, Integrat Biol, Berkeley, CA 94720 USA

[34] NCI, Bas Res Lab, Ctr Canc Res, Leidos Biomed Res Inc,Frederick Natl Lab, Ft Detrick, MD 21702 USA

[35] Univ Montreal, Ctr Hosp Univ CHU St Justine, Dept Pediat, Montreal, PQ H3T 1C5, Canada

[36] Univ Penn, Dept Biol, Philadelphia, PA 19104 USA

[37] Univ Penn, Dept Genet, Philadelphia, PA 19104 USA

[38] Russian Acad Sci, Inst Archaeol & Ethnog, Siberian Branch, Dept Paleolith Archaeol, Novosibirsk 630090, Russia

[39] Altai State Univ, Barnaul 656000, Russia

[40] Harvard Univ, Sch Med, Howard Hughes Med Inst, Boston, MA 02115 USA

[41] Univ Washington, Howard Hughes Med Inst, Seattle, WA 98195 USA

来源：

SCIENCE | 2015年 / 349卷 / 6253期

基金：

美国国家科学基金会; 欧洲研究理事会; 英国惠康基金;

关键词：

HUMAN GENOME SEQUENCE; SEGMENTAL DUPLICATIONS; CODING VARIATION; POLYMORPHISMS; ASSOCIATION; DELETION; HISTORY; REGIONS; AUTISM; MICRODELETION;

D O I：

10.1126/science.aab3761

中图分类号：

O [数理科学和化学]; P [天文学、地球科学]; Q [生物科学]; N [自然科学总论];

学科分类号：

07 ; 0710 ; 09 ;

摘要：

In order to explore the diversity and selective signatures of duplication and deletion human copy-number variants (CNVs), we sequenced 236 individuals from 125 distinct human populations. We observed that duplications exhibit fundamentally different population genetic and selective signatures than deletions and are more likely to be stratified between human populations. Through reconstruction of the ancestral human genome, we identify megabases of DNA lost in different human lineages and pinpoint large duplications that introgressed from the extinct Denisova lineage now found at high frequency exclusively in Oceanic populations. We find that the proportion of CNV base pairs to single-nucleotide-variant base pairs is greater among non-Africans than it is among African populations, but we conclude that this difference is likely due to unique aspects of non-African population history as opposed to differences in CNV load.

引用

页数：10

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[1] Copy-number variation in control population cohorts
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[J]. HUMAN MOLECULAR GENETICS, 2007, 16 : R168 - R173
[2] Copy-number variation
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[J]. Nature Reviews Microbiology, 2020, 18 (10) : 542 - 542
[3] Bias of selection on human copy-number variants
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Ponting, Chris P.
[J]. PLOS GENETICS, 2006, 2 (02): : 198 - 207
[4] Copy-number variation: the end of the human genome?
Dear, Paul H.
[J]. TRENDS IN BIOTECHNOLOGY, 2009, 27 (08) : 448 - 454
[5] A crowdsourcing database for the copy-number variation of the Spanish population
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Roldan, Gema
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Ortuno, Francisco
Pita, Guillermo
Nunez-Torres, Rocio
Gonzalez-Neira, Anna
Pena-Chilet, Maria
Dopazo, Joaquin
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[6] A crowdsourcing database for the copy-number variation of the Spanish population
Daniel López-López
Gema Roldán
Jose L. Fernández-Rueda
Gerrit Bostelmann
Rosario Carmona
Virginia Aquino
Javier Perez-Florido
Francisco Ortuño
Guillermo Pita
Rocío Núñez-Torres
Anna González-Neira
María Peña-Chilet
Joaquin Dopazo
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[7] Segmental duplications and copy-number variation in the human genome
Sharp, AJ
Locke, DP
McGrath, SD
Cheng, Z
Bailey, JA
Vallente, RU
Pertz, LM
Clark, RA
Schwartz, S
Segraves, R
Oseroff, VV
Albertson, DG
Pinkel, D
Eichler, EE
[J]. AMERICAN JOURNAL OF HUMAN GENETICS, 2005, 77 (01) : 78 - 88
[8] Copy-number variation and association studies of human disease
Steven A McCarroll
David M Altshuler
[J]. Nature Genetics, 2007, 39 : S37 - S42
[9] Copy-number variation and association studies of human disease
McCarroll, Steven A.
Altshuler, David M.
[J]. NATURE GENETICS, 2007, 39 (Suppl 7) : S37 - S42
[10] Genotype, haplotype and copy-number variation in worldwide human populations
Jakobsson, Mattias
Scholz, Sonja W.
Scheet, Paul
Gibbs, J. Raphael
VanLiere, Jenna M.
Fung, Hon-Chung
Szpiech, Zachary A.
Degnan, James H.
Wang, Kai
Guerreiro, Rita
Bras, Jose M.
Schymick, Jennifer C.
Hernandez, Dena G.
Traynor, Bryan J.
Simon-Sanchez, Javier
Matarin, Mar
Britton, Angela
van de Leemput, Joyce
Rafferty, Ian
Bucan, Maja
Cann, Howard M.
Hardy, John A.
Rosenberg, Noah A.
Singleton, Andrew B.
[J]. NATURE, 2008, 451 (7181) : 998 - 1003

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