Copy-number variation

This gene duplication has created a copy-number variation. The chromosome now has two copies of this section of DNA, rather than one.

Copy-number variations (CNVs)—a form of structural variation—are alterations of the DNA of a genome that results in the cell having an abnormal or, for certain genes, a normal variation in the number of copies of one or more sections of the DNA. CNVs correspond to relatively large regions of the genome that have been deleted (fewer than the normal number) or duplicated (more than the normal number) on certain chromosomes. For example, the chromosome that normally has sections in order as A-B-C-D might instead have sections A-B-C-C-D (a duplication of "C") or A-B-D (a deletion of "C").

This variation accounts for roughly 12% of human genomic DNA and each variation may range from about one kilobase (1,000 nucleotide bases) to several megabases in size.^[1] CNVs contrast with single-nucleotide polymorphisms (SNPs), which affect only one single nucleotide base.

Sources

CNVs may either be inherited or caused by de novo mutation. A 2007 study proposed mechanism for the cause of some CNVs was fork stalling and template switching, a replication misstep.^[2] However, this model was subsequently superseded by microhomology-mediated break-induced replication (MMBIR).^[3]

CNVs can be caused by structural rearrangements of the genome such as deletions, duplications, inversions, and translocations. Low copy repeats (LCRs), which are region-specific repeat sequences, are susceptible to such genomic rearrangements resulting in CNVs. Factors such as size, orientation, percentage similarity and the distance between the copies influence the susceptibility of LCRs to genomic rearrangement.^[4] Segmental Duplications (SDs) map near ancestral duplication sites in a phenomenon called duplication shadowing which describes the observation of a ~10 fold increased probability of duplication in regions flanking duplications versus other random regions.^[5]

Identification

Copy number variation can be discovered by cytogenetic techniques such as fluorescent in situ hybridization, comparative genomic hybridization, array comparative genomic hybridization, and by virtual karyotyping with SNP arrays. Recent advances in DNA sequencing technology have further enabled the identification of CNVs by next-generation sequencing.^[6][7][8][9]

CNVs can be limited to a single gene or include a contiguous set of genes. CNVs can result in having either too many or too few of the dosage-sensitive genes, which may be responsible for a substantial amount of human phenotypic variability, complex behavioral traits and disease susceptibility.^[10][11]

In certain cases, such as rapidly growing Escherichia coli cells, the gene copy number can be 4-fold greater for genes located near the origin of DNA replication, rather than at the terminus of DNA replication. Elevating the gene copy number of a particular gene can increase the expression of the protein that it encodes.^{[12] [13]}

Prevalence in humans

The fact that DNA copy number variation is a widespread and common phenomenon among humans was first uncovered following the completion of the human genome project.^[14][15] It is estimated that approximately 0.4% of the genome of unrelated people typically differ with respect to copy number.^[16] De novo CNVs have been observed between identical twins who otherwise have identical genomes.^[17]

Role in disease

Like other types of genetic variation, some CNVs have been associated with susceptibility or resistance to disease. Gene copy number can be elevated in cancer cells. For instance, the EGFR copy number can be higher than normal in non-small cell lung cancer.^[18] In addition, a higher copy number of CCL3L1 has been associated with lower susceptibility to HIV infection,^[19] and a low copy number of FCGR3B (the CD16 cell surface immunoglobulin receptor) can increase susceptibility to systemic lupus erythematosus and similar inflammatory autoimmune disorders.^[20] Copy number variation has also been associated with autism,^{[21][22][23][24]} schizophrenia,^[21][25] and idiopathic learning disability.^[26]

However, although once touted as the explanation for the elusive hereditary causes of complex diseases like rheumatoid arthritis, the most common CNVs have little or no role in causing disease.^[27]

Among common functional CNVs, gene gains outnumber losses, suggesting that many of them are favored in evolution and, therefore, beneficial in some way.^[28] One example of CNV is the human salivary amylase gene (AMY1). This gene is typically present as two diploid copies in chimpanzees. Humans average over 6 copies and may have as many as 15. This is thought to be an adaptation to a high-starch diet that improves the ability to digest starchy foods.^[13]

See also

• Comparative genomics
• Copy number analysis
• Human genome
• Inparanoid
• Molecular evolution
• Pseudogenes
• Segmental duplication
• Tandem exon duplication
• Virtual Karyotype

References

Further reading

• Genome-wide analysis of DNA copy-number changes using cDNA microarrays "Gene amplifications and deletions frequently contribute to tumorigenesis. Characterization of these DNA copy-number changes is important for both the basic understanding of cancer and its diagnosis".
• "Huge genetic variation in healthy people". New Scientist. 7 August 2004. 
• "As normal as normal can be". Nature Genetics. 1 September 2004. 
• "Human Genome: Patchwork people". Nature. 20 October 2005. 
• "Gene duplications may define who you are". New Scientist. 22 November 2006. 
• "DNA varies more widely from person to person, Genetic maps reveal". National Geographic. 22 November 2006. 
• "Finding the right lenses" (PDF). Nature Genetics. 1 July 2007. 
• "Nucleotide-resolution analysis of structural variants using BreakSeq and a breakpoint library" (PDF). Nature Biotechnoloty. 1 January 2010. 
• "New Research Sheds Light on Autism's Genetic Causes". Singularity Hub. 15 June 2010. 

External links

• Copy Number Variation Project, Sanger Institute
• Integrative annotation platform for copy number variations in humans
• A bibliography on copy number variation
• Database of Genomic Variants, a database of structural variants in the human genome
• Copy Number Variation Detection via High-Density SNP Genotyping
• Oxford Gene Technology
• High-resolution mapping of copy number variations in 2,026 healthy individuals
• The 1000 Genomes Project
• cn.FARMS: a latent variable model to detect copy number variations in microarray data with a low false discovery rate, an R package —software

• cn.MOPS: mixture of Poissons for discovering copy number variations in next generation sequencing data —software