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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.

SUBMITTER: Redon R 

PROVIDER: S-EPMC2669898 | biostudies-literature | 2006 Nov

REPOSITORIES: biostudies-literature

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Global variation in copy number in the human genome.

Redon Richard R   Ishikawa Shumpei S   Fitch Karen R KR   Feuk Lars L   Perry George H GH   Andrews T Daniel TD   Fiegler Heike H   Shapero Michael H MH   Carson Andrew R AR   Chen Wenwei W   Cho Eun Kyung EK   Dallaire Stephanie S   Freeman Jennifer L JL   González Juan R JR   Gratacòs Mònica M   Huang Jing J   Kalaitzopoulos Dimitrios D   Komura Daisuke D   MacDonald Jeffrey R JR   Marshall Christian R CR   Mei Rui R   Montgomery Lyndal L   Nishimura Kunihiro K   Okamura Kohji K   Shen Fan F   Somerville Martin J MJ   Tchinda Joelle J   Valsesia Armand A   Woodwark Cara C   Yang Fengtang F   Zhang Junjun J   Zerjal Tatiana T   Zhang Jane J   Armengol Lluis L   Conrad Donald F DF   Estivill Xavier X   Tyler-Smith Chris C   Carter Nigel P NP   Aburatani Hiroyuki H   Lee Charles C   Jones Keith W KW   Scherer Stephen W SW   Hurles Matthew E ME  

Nature 20061101 7118


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 tota  ...[more]

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