Global variation in copy number in the human genome

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.; González, Juan R.; Gratacòs, Mònica; 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.

Global variation in copy number in the human genome

Richard Redon, Shumpei Ishikawa, Karen R. Fitch, Lars Feuk, George H. Perry, T. Daniel Andrews, Heike Fiegler, Michael H. Shapero, Andrew R. Carson, Wenwei Chen, Eun Kyung Cho, Stephanie Dallaire, Jennifer L. Freeman, Juan R. González, Mònica Gratacòs, Jing Huang, Dimitrios Kalaitzopoulos, Daisuke Komura, Jeffrey R. MacDonald, Christian R. Marshall, Rui Mei, Lyndal Montgomery, Kunihiro Nishimura, Kohji Okamura, Fan Shen, Martin J. Somerville, Joelle Tchinda, Armand Valsesia, Cara Woodwark, Fengtang Yang, Junjun Zhang, Tatiana Zerjal, Jane Zhang, Lluis Armengol, Donald F. Conrad, Xavier Estivill, Chris Tyler-Smith, Nigel P. Carter, Hiroyuki Aburatani, Charles Lee, Keith W. Jones, Stephen W. Scherer () and Matthew E. Hurles ()
Additional contact information
Richard Redon: The Wellcome Trust Sanger Institute
Shumpei Ishikawa: Genome Science
Karen R. Fitch: Affymetrix, Inc.
Lars Feuk: The Hospital for Sick Children
George H. Perry: Brigham and Women’s Hospital
T. Daniel Andrews: The Wellcome Trust Sanger Institute
Heike Fiegler: The Wellcome Trust Sanger Institute
Michael H. Shapero: Affymetrix, Inc.
Andrew R. Carson: The Hospital for Sick Children
Wenwei Chen: Affymetrix, Inc.
Eun Kyung Cho: Brigham and Women’s Hospital
Stephanie Dallaire: Brigham and Women’s Hospital
Jennifer L. Freeman: Brigham and Women’s Hospital
Juan R. González: Center for Genomic Regulation, Charles Darwin s/n, Barcelona Biomedical Research Park
Mònica Gratacòs: Center for Genomic Regulation, Charles Darwin s/n, Barcelona Biomedical Research Park
Jing Huang: Affymetrix, Inc.
Dimitrios Kalaitzopoulos: The Wellcome Trust Sanger Institute
Daisuke Komura: Research Center for Advanced Science and Technology, University of Tokyo
Jeffrey R. MacDonald: The Hospital for Sick Children
Christian R. Marshall: The Hospital for Sick Children
Rui Mei: Affymetrix, Inc.
Lyndal Montgomery: The Wellcome Trust Sanger Institute
Kunihiro Nishimura: Genome Science
Kohji Okamura: The Hospital for Sick Children
Fan Shen: Affymetrix, Inc.
Martin J. Somerville: University of Alberta
Joelle Tchinda: Brigham and Women’s Hospital
Armand Valsesia: The Wellcome Trust Sanger Institute
Cara Woodwark: The Wellcome Trust Sanger Institute
Fengtang Yang: The Wellcome Trust Sanger Institute
Junjun Zhang: The Hospital for Sick Children
Tatiana Zerjal: The Wellcome Trust Sanger Institute
Jane Zhang: Affymetrix, Inc.
Lluis Armengol: Center for Genomic Regulation, Charles Darwin s/n, Barcelona Biomedical Research Park
Donald F. Conrad: University of Chicago
Xavier Estivill: Center for Genomic Regulation, Charles Darwin s/n, Barcelona Biomedical Research Park
Chris Tyler-Smith: The Wellcome Trust Sanger Institute
Nigel P. Carter: The Wellcome Trust Sanger Institute
Hiroyuki Aburatani: Genome Science
Keith W. Jones: Affymetrix, Inc.
Stephen W. Scherer: The Hospital for Sick Children
Matthew E. Hurles: The Wellcome Trust Sanger Institute

Nature, 2006, vol. 444, issue 7118, 444-454

Abstract: 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.

Date: 2006
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DOI: 10.1038/nature05329

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