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http://www.nature.com/nature/journal/v444/n7118/full/nature05329.html    

Nature 444, 444-454 (23 November 2006) | doi:10.1038/nature05329; Received 13 June 2006; Accepted 10 October 2006

Global variation in copy number in the human genome

Richard Redon¹, Shumpei Ishikawa^2,3, Karen R. Fitch⁴, Lars Feuk^5,6, George H. Perry⁷, T. Daniel Andrews¹, Heike Fiegler¹, Michael H. Shapero⁴, Andrew R. Carson^5,6, Wenwei Chen⁴, Eun Kyung Cho⁷, Stephanie Dallaire⁷, Jennifer L. Freeman⁷, Juan R. González⁸, Mònica Gratacòs⁸, Jing Huang⁴, Dimitrios Kalaitzopoulos¹, Daisuke Komura³, Jeffrey R. MacDonald⁵, Christian R. Marshall^5,6, Rui Mei⁴, Lyndal Montgomery¹, Kunihiro Nishimura², Kohji Okamura^5,6, Fan Shen⁴, Martin J. Somerville⁹, Joelle Tchinda⁷, Armand Valsesia¹, Cara Woodwark¹, Fengtang Yang¹, Junjun Zhang⁵, Tatiana Zerjal¹, Jane Zhang⁴, Lluis Armengol⁸, Donald F. Conrad¹⁰, Xavier Estivill^8,11, Chris Tyler-Smith¹, Nigel P. Carter¹, Hiroyuki Aburatani^2,12, Charles Lee^7,13, Keith W. Jones⁴, Stephen W. Scherer^5,6 and Matthew E. Hurles¹

1. The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SA, UK
2. Genome Science, and,
3. Dependable and High Performance Computing, Research Center for Advanced Science and Technology, University of Tokyo, 4-6-1 Komaba, Meguro, Tokyo 153-8904, Japan
4. Affymetrix, Inc., Santa Clara, California 95051, USA
5. The Centre for Applied Genomics and Program in Genetics and Genomic Biology, The Hospital for Sick Children, MaRS Centre–East Tower, 101 College Street, Room 14-701, Toronto, Ontario M5G 1L7, Canada
6. Department of Molecular and Medical Genetics, Faculty of Medicine, University of Toronto M5S 1A8, Canada
7. Department of Pathology, Brigham and Women's Hospital, Boston, Massachusetts 02115, USA
8. Genes and Disease Program, Center for Genomic Regulation, Charles Darwin s/n, Barcelona Biomedical Research Park, 08003 Barcelona, Catalonia, Spain
9. Departments of Medical Genetics and Pediatrics, University of Alberta, Edmonton, Alberta T6G 2H7, Canada
10. Department of Human Genetics, University of Chicago, 920 East 58th Street, Chicago, Illinois 60637, USA
11. Pompeu Fabra University, Charles Darwin s/n, and National Genotyping Centre (CeGen), Passeig Marítim 37-49, Barcelona Biomedical Research Park, 08003 Barcelona, Catalonia, Spain
12. Japan Science and Technology Agency, Kawaguchi, Saitama 332-0012, Japan
13. Harvard Medical School, Boston, Massachusetts 02115, USA

Correspondence to: Stephen W. Scherer^5,6Matthew E. Hurles¹ Correspondence and requests for materials should be addressed to M.E.H. (Email: meh@sanger.ac.uk) or S.W.S (Email: steve@genet.sickkids.on.ca).

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Abstract

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.

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