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; Matthew E. Hurles

doi:10.1038/nature05329

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. MarshallRui 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^*, Matthew E. Hurles

^*Corresponding author for this work

Research output: Contribution to journal › Article › peer-review

3496 Citations (Scopus)

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.

Original language	English
Pages (from-to)	444-454
Number of pages	11
Journal	Nature
Volume	444
Issue number	7118
DOIs	https://doi.org/10.1038/nature05329
Publication status	Published - 23 Nov 2006

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Redon, R., Ishikawa, S., Fitch, K. R., Feuk, L., Perry, G. H., Andrews, T. D., Fiegler, H., Shapero, M. H., Carson, A. R., Chen, W., Cho, E. K., Dallaire, S., Freeman, J. L., González, J. R., Gratacòs, M., Huang, J., Kalaitzopoulos, D., Komura, D., MacDonald, J. R., ... Hurles, M. E. (2006). Global variation in copy number in the human genome. Nature, 444(7118), 444-454. https://doi.org/10.1038/nature05329

@article{29598dd76dcd4a968e761309f2d77e5e,

title = "Global variation in copy number in the human genome",

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.",

author = "Richard Redon and Shumpei Ishikawa and Fitch, {Karen R.} and Lars Feuk and Perry, {George H.} and Andrews, {T. Daniel} and Heike Fiegler and Shapero, {Michael H.} and Carson, {Andrew R.} and Wenwei Chen and Cho, {Eun Kyung} and Stephanie Dallaire and Freeman, {Jennifer L.} and Gonz{\'a}lez, {Juan R.} and M{\`o}nica Gratac{\`o}s and Jing Huang and Dimitrios Kalaitzopoulos and Daisuke Komura and MacDonald, {Jeffrey R.} and Marshall, {Christian R.} and Rui Mei and Lyndal Montgomery and Kunihiro Nishimura and Kohji Okamura and Fan Shen and Somerville, {Martin J.} and Joelle Tchinda and Armand Valsesia and Cara Woodwark and Fengtang Yang and Junjun Zhang and Tatiana Zerjal and Jane Zhang and Lluis Armengol and Conrad, {Donald F.} and Xavier Estivill and Chris Tyler-Smith and Carter, {Nigel P.} and Hiroyuki Aburatani and Charles Lee and Jones, {Keith W.} and Scherer, {Stephen W.} and Hurles, {Matthew E.}",

year = "2006",

month = nov,

day = "23",

doi = "10.1038/nature05329",

language = "English",

volume = "444",

pages = "444--454",

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Redon, R, Ishikawa, S, Fitch, KR, Feuk, L, Perry, GH, Andrews, TD, Fiegler, H, Shapero, MH, Carson, AR, Chen, W, Cho, EK, Dallaire, S, Freeman, JL, González, JR, Gratacòs, M, Huang, J, Kalaitzopoulos, D, Komura, D, MacDonald, JR, Marshall, CR, Mei, R, Montgomery, L, Nishimura, K, Okamura, K, Shen, F, Somerville, MJ, Tchinda, J, Valsesia, A, Woodwark, C, Yang, F, Zhang, J, Zerjal, T, Zhang, J, Armengol, L, Conrad, DF, Estivill, X, Tyler-Smith, C, Carter, NP, Aburatani, H, Lee, C, Jones, KW, Scherer, SW & Hurles, ME 2006, 'Global variation in copy number in the human genome', Nature, vol. 444, no. 7118, pp. 444-454. https://doi.org/10.1038/nature05329

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T1 - Global variation in copy number in the human genome

AU - Redon, Richard

AU - Ishikawa, Shumpei

AU - Fitch, Karen R.

AU - Feuk, Lars

AU - Perry, George H.

AU - Andrews, T. Daniel

AU - Fiegler, Heike

AU - Shapero, Michael H.

AU - Carson, Andrew R.

AU - Chen, Wenwei

AU - Cho, Eun Kyung

AU - Dallaire, Stephanie

AU - Freeman, Jennifer L.

AU - González, Juan R.

AU - Gratacòs, Mònica

AU - Huang, Jing

AU - Kalaitzopoulos, Dimitrios

AU - Komura, Daisuke

AU - MacDonald, Jeffrey R.

AU - Marshall, Christian R.

AU - Mei, Rui

AU - Montgomery, Lyndal

AU - Nishimura, Kunihiro

AU - Okamura, Kohji

AU - Shen, Fan

AU - Somerville, Martin J.

AU - Tchinda, Joelle

AU - Valsesia, Armand

AU - Woodwark, Cara

AU - Yang, Fengtang

AU - Zhang, Junjun

AU - Zerjal, Tatiana

AU - Zhang, Jane

AU - Armengol, Lluis

AU - Conrad, Donald F.

AU - Estivill, Xavier

AU - Tyler-Smith, Chris

AU - Carter, Nigel P.

AU - Aburatani, Hiroyuki

AU - Lee, Charles

AU - Jones, Keith W.

AU - Scherer, Stephen W.

AU - Hurles, Matthew E.

PY - 2006/11/23

Y1 - 2006/11/23

N2 - 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.

AB - 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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U2 - 10.1038/nature05329

DO - 10.1038/nature05329

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SN - 0028-0836

VL - 444

SP - 444

EP - 454

JO - Nature

JF - Nature

IS - 7118

ER -

Global variation in copy number in the human genome

Abstract

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