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Global variation in copy number in the human genome

Author

Listed:
  • Richard Redon

    (The Wellcome Trust Sanger Institute)

  • Shumpei Ishikawa

    (Genome Science
    Research Center for Advanced Science and Technology, University of Tokyo)

  • Karen R. Fitch

    (Affymetrix, Inc.)

  • Lars Feuk

    (The Hospital for Sick Children
    University of Toronto)

  • 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
    University of Toronto)

  • 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
    University of Toronto)

  • Rui Mei

    (Affymetrix, Inc.)

  • Lyndal Montgomery

    (The Wellcome Trust Sanger Institute)

  • Kunihiro Nishimura

    (Genome Science)

  • Kohji Okamura

    (The Hospital for Sick Children
    University of Toronto)

  • 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
    Pompeu Fabra University, Charles Darwin s/n, and National Genotyping Centre (CeGen))

  • Chris Tyler-Smith

    (The Wellcome Trust Sanger Institute)

  • Nigel P. Carter

    (The Wellcome Trust Sanger Institute)

  • Hiroyuki Aburatani

    (Genome Science
    Japan Science and Technology Agency)

  • Charles Lee

    (Brigham and Women’s Hospital
    Harvard Medical School)

  • Keith W. Jones

    (Affymetrix, Inc.)

  • Stephen W. Scherer

    (The Hospital for Sick Children
    University of Toronto)

  • Matthew E. Hurles

    (The Wellcome Trust Sanger Institute)

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.

Suggested Citation

  • 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 Da, 2006. "Global variation in copy number in the human genome," Nature, Nature, vol. 444(7118), pages 444-454, November.
    • Handle: RePEc:nat:nature:v:444:y:2006:i:7118:d:10.1038_nature05329
    DOI: 10.1038/nature05329
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    Cited by:

    1. Yichen Henry Liu & Can Luo & Staunton G. Golding & Jacob B. Ioffe & Xin Maizie Zhou, 2024. "Tradeoffs in alignment and assembly-based methods for structural variant detection with long-read sequencing data," Nature Communications, Nature, vol. 15(1), pages 1-22, December.
    2. Gaëlle Marenne & Stephen J Chanock & Núria Malats & Emmanuelle Génin, 2013. "Advantage of Using Allele-Specific Copy Numbers When Testing for Association in Regions with Common Copy Number Variants," PLOS ONE, Public Library of Science, vol. 8(9), pages 1-1, September.
    3. Jae Eun Lee & Jung Hye Sung & Daniel Sarpong & Jimmy T. Efird & Paul B. Tchounwou & Elizabeth Ofili & Keith Norris, 2018. "Knowledge Management for Fostering Biostatistical Collaboration within a Research Network: The RTRN Case Study," IJERPH, MDPI, vol. 15(11), pages 1-13, November.
    4. Yang Guo & Shuzhen Wang & A. K. Alvi Haque & Xiguo Yuan, 2022. "WAVECNV: A New Approach for Detecting Copy Number Variation by Wavelet Clustering," Mathematics, MDPI, vol. 10(12), pages 1-11, June.
    5. Soohyun Lee & Simon Kasif & Zhiping Weng & Charles R Cantor, 2008. "Quantitative Analysis of Single Nucleotide Polymorphisms within Copy Number Variation," PLOS ONE, Public Library of Science, vol. 3(12), pages 1-10, December.
    6. Albertas Dvirnas & Callum Stewart & Vilhelm Müller & Santosh Kumar Bikkarolla & Karolin Frykholm & Linus Sandegren & Erik Kristiansson & Fredrik Westerlund & Tobias Ambjörnsson, 2021. "Detection of structural variations in densely-labelled optical DNA barcodes: A hidden Markov model approach," PLOS ONE, Public Library of Science, vol. 16(11), pages 1-15, November.
    7. Andrew K MacLeod & Gail Davies & Antony Payton & Albert Tenesa & Sarah E Harris & David Liewald & Xiayi Ke & Michelle Luciano & Lorna M Lopez & Alan J Gow & Janie Corley & Paul Redmond & Geraldine McN, 2012. "Genetic Copy Number Variation and General Cognitive Ability," PLOS ONE, Public Library of Science, vol. 7(12), pages 1-9, December.
    8. Nur Zarina Ali Hassan & Norfilza Mohd Mokhtar & Teow Kok Sin & Isa Mohamed Rose & Ismail Sagap & Roslan Harun & Rahman Jamal, 2014. "Integrated Analysis of Copy Number Variation and Genome-Wide Expression Profiling in Colorectal Cancer Tissues," PLOS ONE, Public Library of Science, vol. 9(4), pages 1-11, April.
    9. Patrick Breheny & Prabhakar Chalise & Anthony Batzler & Liewei Wang & Brooke L Fridley, 2012. "Genetic Association Studies of Copy-Number Variation: Should Assignment of Copy Number States Precede Testing?," PLOS ONE, Public Library of Science, vol. 7(4), pages 1-9, April.
    10. Yu Wang & Wei Li & Yingying Xia & Chongzhi Wang & Y Tom Tang & Wenying Guo & Jinliang Li & Xia Zhao & Yepeng Sun & Juan Hu & Hefu Zhen & Xiandong Zhang & Chao Chen & Yujian Shi & Lin Li & Hongzhi Cao , 2015. "Identifying Human Genome-Wide CNV, LOH and UPD by Targeted Sequencing of Selected Regions," PLOS ONE, Public Library of Science, vol. 10(4), pages 1-18, April.
    11. Joanna E Cobb & Stefan J White & Stephen B Harrap & Justine A Ellis, 2009. "Androgen Receptor Copy Number Variation and Androgenetic Alopecia: A Case-Control Study," PLOS ONE, Public Library of Science, vol. 4(4), pages 1-4, April.
    12. Kyungjoon Lee & John S Brownstein & Richard G Mills & Isaac S Kohane, 2010. "Does Collocation Inform the Impact of Collaboration?," PLOS ONE, Public Library of Science, vol. 5(12), pages 1-6, December.
    13. Leonid Iakoubov & Malgorzata Mossakowska & Malgorzata Szwed & Zhibing Duan & Federico Sesti & Monika Puzianowska-Kuznicka, 2013. "A Common Copy Number Variation (CNV) Polymorphism in the CNTNAP4 Gene: Association with Aging in Females," PLOS ONE, Public Library of Science, vol. 8(11), pages 1-1, November.
    14. Michael I Falola & Howard W Wiener & Nathan E Wineinger & Gary R Cutter & Robert P Kimberly & Jeffrey C Edberg & Donna K Arnett & Richard A Kaslow & Jianming Tang & Sadeep Shrestha, 2013. "Genomic Copy Number Variants: Evidence for Association with Antibody Response to Anthrax Vaccine Adsorbed," PLOS ONE, Public Library of Science, vol. 8(5), pages 1-9, May.
    15. Yu Chen & Amy Y. Wang & Courtney A. Barkley & Yixin Zhang & Xinyang Zhao & Min Gao & Mick D. Edmonds & Zechen Chong, 2023. "Deciphering the exact breakpoints of structural variations using long sequencing reads with DeBreak," Nature Communications, Nature, vol. 14(1), pages 1-12, December.
    16. Prashanthi Dharanipragada & Sriharsha Vogeti & Nita Parekh, 2018. "iCopyDAV: Integrated platform for copy number variations—Detection, annotation and visualization," PLOS ONE, Public Library of Science, vol. 13(4), pages 1-37, April.
    17. Soumya Raychaudhuri & Joshua M Korn & Steven A McCarroll & The International Schizophrenia Consortium & David Altshuler & Pamela Sklar & Shaun Purcell & Mark J Daly, 2010. "Accurately Assessing the Risk of Schizophrenia Conferred by Rare Copy-Number Variation Affecting Genes with Brain Function," PLOS Genetics, Public Library of Science, vol. 6(9), pages 1-12, September.
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