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Genomic variation

Copy number variation doesn't copy SNPs

Nature Reviews Genetics volume 8, page 247 (2007)Cite this article

Manolis Dermitzakis, Matthew Hurles and colleagues carried out an association analysis of gene expression in cell lines from the HapMap individuals with both SNPs and CNVs, focusing on the genomic regions around the expressed genes. Of the 14,072 genes for which expression levels were measured, they found association with a local SNP in between 323 genes (in Europeans) and 411 genes (in Africans). For CNVs, the numbers were lower — local CNVs were associated with the expression levels of between 44 genes (in Chinese) and 96 genes (in Africans). On the basis of these data and corrections for the proportion of total copy number variation observed in this study, the authors estimate that 8.75–17.7% of heritable variation in gene expression is due to copy number variation.

So what types of effect are the CNVs having? Altering gene dosage through deletion or duplication is the obvious possibility, but over half the CNVs were outside the probed region of the gene with whose expression they were associated. This implies that they are affecting gene structure or regulation rather than dosage. There were even a small minority of cases in which increased transcription was associated with reduced copy number, implying a complex relationship.

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References

ORIGINAL RESEARCH PAPER

  1. Stranger, B. E. et al. Relative impact of nucleotide and copy number variation on gene expression phenotypes. Science 315, 848–853 (2007)

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FURTHER READING

  1. Feuk, L., Carson, A. R. & Scherer, S. W. Structural variation in the human genome. Nature Rev. Genet. 7, 85–97 (2006)

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  2. Redon, R. et al. Global variation in copy number in the human genome. Nature 444, 444–454 (2006)

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Authors
  1. Patrick Goymer
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Goymer, P. Copy number variation doesn't copy SNPs. Nat Rev Genet 8, 247 (2007). https://doi.org/10.1038/nrg2088

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