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CNV and Human Health
CNV and Human Health
Analysis of individual human genomes has revealed an unexpected amount of variability in human
populations. The most common form of genetic variation involves small changes in the genetic code that alter
a single base pair. Other types of mutations range from small insertions to large chromosomal rearrangements
that can be detected cytogenetically using a microscope. The term "copy number variation" refers to an
intermediate-scale genetic change, operationally defined as segments greater than 1,000 base pairs in length
but typically less than 5 megabases, which is the cytogenetic level of resolution. CNVs include both additional
copies of sequence (duplications) and losses of genetic material (deletions). Because CNVs change the
structure of the genome, such mutations, together with inversions and translocations, are collectively classified
as forms of genome structural variation. Recently, scientists have come to appreciate that CNVs account for
much of human variability.
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genome. For instance, Figure 1 summarizes the results of one study that compared the sequence of
euchromatic regions from one human female with a reference human genome sequence (Tuzun et al., 2005).
(The reference sequence is thought to largely represent the sequence of one human male.) This particular
study identified 297 sites of potential structural variation between the two sequences, including 139 insertions,
102 deletions, and 56 inversions. The positions of these structural variations are shown for each chromosome.
Based on these and other results (Redon et al., 2006, Kidd et al., 2008; Conrad et al. 2006, McCarroll et al.,
2006), human CNV is now thought to affect more base pairs than other forms of mutation. In other words, if
two humans were compared, the number of base pairs affected by structural differences in the organization
and copy number status of DNA segments would be greater than the sum of all single-base-pair substitution
differences. Recent evidence also suggests that changes in copy number play an important role in evolution.
For example, a comparison of the human and chimpanzee genetic sequences found that copy number
changes account for more differences between the two species than do other forms of mutation (Cheng et al.,
2005). Research also reveals that copy number changes can affect the expression of genes, alter the
organization of chromatin, and/or influence the regulation of genes in the vicinity.
The second class of CNVs includes relatively rare variants that are much longer than CNPs, ranging in size
from hundreds of thousands of base pairs to over 1 million base pairs in length. Also known as microdeletions
and microduplications, these variants usually have a much more recent origin within a family. These CNVs
may have arisen during production of the sperm or egg that gave rise to a particular individual, or they may
have been passed down for only a few generations within a family. These large and rare structural variants
have been observed disproportionately in patients with mental retardation, developmental delay,
schizophrenia, and autism (de Vries et al., 2005, Sharp et al. 2006, Sebat et al., 2007, Walsh et al., 2008).
Their appearance in such patients has led to speculation that large and rare CNVs may be more important in
neurocognitive diseases than other forms of inherited mutations, including single nucleotide substitutions.
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mechanisms are needed to explain the origin of those CNVs whose breakpoints do not map to segmental
duplications.)
Aitman, T. J. et al. Copy number polymorphism in Fcgr3 predisposes to glomerulonephritis in rats and humans. Nature 439, 851-5 (2006) (link to
article)
Bailey, J. A., et al. Recent segmental duplications in the human genome. Science 297, 1003-1007 (2002)
Cheng, Z., et al. A genome-wide comparison of recent chimpanzee and human segmental duplications. Nature 437, 88-93 (2005)
doi:10.1038/nature04000 (link to article)
Conrad, D. F., Andrews, T. D., Carter, N. P., Hurles, M. E. & Pritchard, J. K. A high-resolution survey of deletion polymorphisms in the human
genome. Nat Genet 38, 75-81 (2006) (link to article)
de Vries, B. B. et al. Diagnostic genome profiling in mental retardation. Am J Hum Genet 77, 606-16 (2005)
Fellermann, K. et al. A chromosome 8 gene-cluster polymorphism with low human Beta-defensin 2 gene copy number predisposes to crohn disease
of the colon. Am J Hum Genet 79, 439-48 (2006)
Hollox, E. J. et al. Psoriasis is associated with increased beta-defensin genomic copy number. Nat Genet 40, 23-5 (2008) (link to article)
Iafrate, A. J., et al. Detection of large-scale variation in the human genome. Nature Genetics 36, 949-951 (2004) doi:10.1038/ng1416 (link to
article)
International Human Genome Sequencing Consortium. Initial sequencing and analysis of the human genome. Nature 409, 860-921 (2001) (link to
article)
Kidd, J. M., et al. Mapping and sequencing of structural variation from eight human genomes. Nature 453, 56-64 (2008) doi:10.1038/nature06862
Lupski, J. R. Genomic disorders: Structural features of the genome can lead to DNA rearrangements and human disease traits. Trends in Genetics
14, 417-422 (1998)
McCarroll, S. A. et al. Common deletion polymorphisms in the human genome. Nat Genet 38, 86-92 (2006).
Redon, R., et al. Global variation in copy number in the human genome. Nature 444, 444-454 (2006) doi:10.1038/nature05329 (link to article)
Sebat, J., et al. Large-scale copy number polymorphism in the human genome. Science 305, 525-528 (2004)
Sebat, J., et al. Strong association of de novo copy number mutations with autism. Science 316, 445-449 (2007)
Sharp, A. J., et al. Discovery of previously unidentified genomic disorders from the duplication architecture of the human genome. Nature Genetics
38, 1038-1042 (2006) doi:10.1038/ng1862 (link to article)
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Stranger, B. E., et al. Relative impact of nucleotide and copy number variation on gene expression phenotypes. Science 315, 848-853 (2007)
Tuzun, E., et al. Fine-scale structural variation of the human genome. Nature Genetics 37, 727-732 (2005) doi:10.1038/ng1562 (link to article)
Walsh, T., et al. Rare structural variants disrupt multiple genes in neurodevelopmental pathways in
schizophrenia. Science 320, 539-543 (2008)
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