Global variation in copy number in the human genome

被引：3101

作者：

Redon, Richard

Ishikawa, Shumpei

Fitch, Karen R.

Feuk, Lars

Perry, George H.

Andrews, T. Daniel

Fiegler, Heike

Shapero, Michael H.

Carson, Andrew R.

Chen, Wenwei

Cho, Eun Kyung

Dallaire, Stephanie

Freeman, Jennifer L.

Gonzalez, Juan R.

Gratacos, Monica

Huang, Jing

Kalaitzopoulos, Dimitrios

Komura, Daisuke

MacDonald, Jeffrey R.

Marshall, Christian R.

Mei, Rui

Montgomery, Lyndal

Nishimura, Kunihiro

Okamura, Kohji

Shen, Fan

Somerville, Martin J.

Tchinda, Joelle

Valsesia, Armand

Woodwark, Cara

Yang, Fengtang

Zhang, Junjun

Zerjal, Tatiana

Zhang, Jane

Armengol, Lluis

Conrad, Donald F.

Estivill, Xavier

Tyler-Smith, Chris

Carter, Nigel P.

Aburatani, Hiroyuki

Lee, Charles

Jones, Keith W.

Scherer, Stephen W.

Hurles, Matthew E.

机构：

[1] Wellcome Trust Sanger Inst, Cambridge CB10 1SA, England

[2] Univ Tokyo, Adv Sci & Technol Res Ctr, Meguro Ku, Tokyo 1538904, Japan

[3] Affymetrix Inc, Santa Clara, CA 95051 USA

[4] Hosp Sick Children, Ctr Appl Genom, Toronto, ON M5G 1L7, Canada

[5] Hosp Sick Children, Program Genet & Genom Biol, Toronto, ON M5G 1L7, Canada

[6] Univ Toronto, Fac Med, Dept Mol & Med Genet, Toronto, ON M5S 1A8, Canada

[7] Brigham & Womens Hosp, Dept Pathol, Boston, MA 02115 USA

[8] Ctr Genom Regulat, Genes & Dis Program, Barcelona 08003, Catalonia, Spain

[9] Univ Alberta, Dept Med Genet, Edmonton, AB T6G 2H7, Canada

[10] Univ Alberta, Dept Pediat, Edmonton, AB T6G 2H7, Canada

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

[12] Pompeu Fabra Univ, Barcelona 08003, Catalonia, Spain

[13] Natl Genotyping Ctr, Barcelona 08003, Catalonia, Spain

[14] Japan Sci & Technol Agcy, Kawaguchi, Saitama 3320012, Japan

[15] Harvard Univ, Sch Med, Boston, MA 02115 USA

来源：

NATURE | 2006年 / 444卷 / 7118期

基金：

英国惠康基金;

关键词：

D O I：

10.1038/nature05329

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：

Copy number variation (CNV) of DNA sequences is functionally significant but has yet to be fully ascertained. We have constructed a first-generation CNV map of the human genome through the study of 270 individuals from four populations with ancestry in Europe, Africa or Asia (the HapMap collection). DNA from these individuals was screened for CNV using two complementary technologies: single-nucleotide polymorphism (SNP) genotyping arrays, and clone-based comparative genomic hybridization. A total of 1,447 copy number variable regions (CNVRs), which can encompass overlapping or adjacent gains or losses, covering 360 megabases (12% of the genome) were identified in these populations. These CNVRs contained hundreds of genes, disease loci, functional elements and segmental duplications. Notably, the CNVRs encompassed more nucleotide content per genome than SNPs, underscoring the importance of CNV in genetic diversity and evolution. The data obtained delineate linkage disequilibrium patterns for many CNVs, and reveal marked variation in copy number among populations. We also demonstrate the utility of this resource for genetic disease studies.

引用

页码：444 / 454

页数：11

共 77 条

[1] Copy number polymorphism in Fcgr3 predisposes to glomerulonephritis in rats and humans [J].

Aitman, TJ ;

Dong, R ;

Vyse, TJ ;

Norsworthy, PJ ;

Johnson, MD ;

Smith, J ;

Mangion, J ;

Roberton-Lowe, C ;

Marshall, AJ ;

Petretto, E ;

Hodges, MD ;

Bhangal, G ;

Patel, SG ;

Sheehan-Rooney, K ;

Duda, M ;

Cook, PR ;

Evans, DJ ;

Domin, J ;

Flint, J ;

Boyle, JJ ;

Pusey, CD ;

Cook, HT .

NATURE, 2006, 439 (7078) :851-855

[2] A haplotype map of the human genome [J].

Altshuler, D ;

Brooks, LD ;

Chakravarti, A ;

Collins, FS ;

Daly, MJ ;

Donnelly, P ;

Gibbs, RA ;

Belmont, JW ;

Boudreau, A ;

Leal, SM ;

Hardenbol, P ;

Pasternak, S ;

Wheeler, DA ;

Willis, TD ;

Yu, FL ;

Yang, HM ;

Zeng, CQ ;

Gao, Y ;

Hu, HR ;

Hu, WT ;

Li, CH ;

Lin, W ;

Liu, SQ ;

Pan, H ;

Tang, XL ;

Wang, J ;

Wang, W ;

Yu, J ;

Zhang, B ;

Zhang, QR ;

Zhao, HB ;

Zhao, H ;

Zhou, J ;

Gabriel, SB ;

Barry, R ;

Blumenstiel, B ;

Camargo, A ;

Defelice, M ;

Faggart, M ;

Goyette, M ;

Gupta, S ;

Moore, J ;

Nguyen, H ;

Onofrio, RC ;

Parkin, M ;

Roy, J ;

Stahl, E ;

Winchester, E ;

Ziaugra, L ;

Shen, Y .

NATURE, 2005, 437 (7063) :1299-1320

[3] Multiple pathogenic and benign genomic rearrangements occur at a 35 kb duplication involving the NEMO and LAGE2 genes [J].

Aradhya, S ;

Bardaro, T ;

Galgóczy, P ;

Yamagata, T ;

Esposito, T ;

Patlan, H ;

Ciccodicola, A ;

Munnich, A ;

Kenwrick, S ;

Platzer, M ;

D'Urso, M ;

Nelson, DL .

HUMAN MOLECULAR GENETICS, 2001, 10 (22) :2557-2567

[4] Recent segmental duplications in the human genome [J].

Bailey, JA ;

Gu, ZP ;

Clark, RA ;

Reinert, K ;

Samonte, RV ;

Schwartz, S ;

Adams, MD ;

Myers, EW ;

Li, PW ;

Eichler, EE .

SCIENCE, 2002, 297 (5583) :1003-1007

[5] Human population genetic structure and inference of group membership [J].

Bamshad, MJ ;

Wooding, S ;

Watkins, WS ;

Ostler, CT ;

Batzer, MA ;

Jorde, LB .

AMERICAN JOURNAL OF HUMAN GENETICS, 2003, 72 (03) :578-589

[6] Haploview: analysis and visualization of LD and haplotype maps [J].

Barrett, JC ;

Fry, B ;

Maller, J ;

Daly, MJ .

BIOINFORMATICS, 2005, 21 (02) :263-265

[7] Ultraconserved elements in the human genome [J].

Bejerano, G ;

Pheasant, M ;

Makunin, I ;

Stephen, S ;

Kent, WJ ;

Mattick, JS ;

Haussler, D .

SCIENCE, 2004, 304 (5675) :1321-1325

[8] Natural genetic variation caused by transposable elements in humans [J].

Bennettt, EA ;

Coleman, LE ;

Tsui, C ;

Pittard, WS ;

Devine, SE .

GENETICS, 2004, 168 (02) :933-951

[9] A chromosomal duplication map of malformations: Regions of suspected haplo- and triplolethality - and tolerance of segmental aneuploidy - in humans [J].

Brewer, C ;

Holloway, S ;

Zawalnyski, P ;

Schinzel, A ;

FitzPatrick, D .

AMERICAN JOURNAL OF HUMAN GENETICS, 1999, 64 (06) :1702-1708

[10] The Bar "gene" - A duplication [J].

Bridges, CB .

SCIENCE, 1936, 83 :210-211

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