Global variation in copy number in the human genome

By R. Redon, Shumpei Ishikawa, Karen R. Fitch, Lars Feuk, G. Perry, T. Daniel Andrews, H. Fiegler, M. Shapero, Andrew R. Carson, Wenwei Chen and 33 more. Nature, 2006

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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.

Subfields: Genetics, Plant Science

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Citations in the corpus

Robustness: mechanisms and consequences (2009, background): “In addition, the widespread nature of copy number polymorphism [40] suggests that there might be significant genetic variation in the degree of redundancy-driven robustness.”
The Impact of Genetic Architecture on Genome-Wide Evaluation Methods (2010, background): “First, it is likely that the number of SNP on current chips is not high enough to tag all the genetic variance and variation not associated with SNP (e.g., copy number variation; Redon et al. 2006) will also be missed.”
Copy-number variations associated with neuropsychiatric conditions (2008, background): “These quantitative structural variants often encompass one or more genes and collectively include more nucleotides per genome than the total number of single-nucleotide polymorphisms (SNPs”
European guidelines on cardiovascular disease prevention in clinical practice: executive summary: Fourth Joint Task Force of the European Society of Cardiology and Other Societies on Cardiovascular Disease Prevention in Clinical Practice (Constituted by representatives of nine societies and by invit (2007, positive): “These include single nucleotide polymorphisms (SNPs) as well as insertion/deletion and copy number variants which have recently been reported to be very common.(183) A large number of ‘candidate’ genes have already been investigated in relation to CHD traits and to risk of CHD itself.”
High-resolution mapping and analysis of copy number variations in the human genome: a data resource for clinical and research applications. (2009, methodology): “Copy number variation (CNV) in the human genome significantly influences human diversity and predisposition to disease (Sebat et al. 2004, 2007; Sharp et al. 2005; Conrad et al. 2006; Feuk et al. 2006; Hinds et al. 2006; McCarroll et al. 2006; Redon et al. 2006; Kidd et al. 2008; Perry et al. 2008;…”
A DNA replication mechanism for generating nonrecurrent rearrangements associated with genomic disorders. (2007, background): “…evolutionary changes (Dumas et al., 2007; Ohno, 1970) including the emergence of novel gene function, the generation of advantageous and/or benign CNVs (Redon et al., 2006) in response to environmental factors, as well as the generation of Inc. complex segmental duplications or regional LCRs.”
A Copy Number Variation Morbidity Map of Developmental Delay (2011, neutral): “below average (a measure of cluster separation); and no overlap of the target exon (note that individual probes were not filtered given the heterogeneity of platforms and the potential for atypical CNVs) with common copy number polymorphisms or deletions seen in multiple control individual”