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. 2006 May 23;103(21):8006-11.
doi: 10.1073/pnas.0602318103. Epub 2006 May 15.

Hotspots for copy number variation in chimpanzees and humans

George H Perry  1 , Joelle Tchinda, Sean D McGrath, Junjun Zhang, Simon R Picker, Angela M Cáceres, A John Iafrate, Chris Tyler-Smith, Stephen W Scherer, Evan E Eichler, Anne C Stone, Charles Lee
Affiliations

Hotspots for copy number variation in chimpanzees and humans

George H Perry et al. Proc Natl Acad Sci U S A. .

Abstract

Copy number variation is surprisingly common among humans and can be involved in phenotypic diversity and variable susceptibility to complex diseases, but little is known of the extent of copy number variation in nonhuman primates. We have used two array-based comparative genomic hybridization platforms to identify a total of 355 copy number variants (CNVs) in the genomes of 20 wild-born chimpanzees (Pan troglodytes) and have compared the identified chimpanzee CNVs to known human CNVs from previous studies. Many CNVs were observed in the corresponding regions in both chimpanzees and humans; especially those CNVs of higher frequency. Strikingly, these loci are enriched 20-fold for ancestral segmental duplications, which may facilitate CNV formation through nonallelic homologous recombination mechanisms. Therefore, some of these regions may be unstable "hotspots" for the genesis of copy number variation, with recurrent duplications and deletions occurring across and within species.

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Conflict of interest statement

Conflict of interest statement: No conflicts declared.

Figures

Fig. 1.
Fig. 1.
Map of CNVs shared between humans and chimpanzees and found in chimpanzees only. The genomic positions of chimpanzee CNVs that do not overlap with any currently known human CNVs are depicted as red squares, and CNVs observed at the same loci in both chimpanzees and humans are depicted as blue diamonds.
Fig. 2.
Fig. 2.
Copy number variation at the RP11-88L18 locus. The RP11-88L18 BAC clone (human chromosome 5p15.1) is an example of a CNV that is shared by humans and chimpanzees. Arrows on the aCGH chromosome-specific plots depict (a) a genomic loss for chimpanzee Andy, relative to the reference chimpanzee Clint; (b) a genomic loss for chimpanzee Vincent, relative to Clint; and (c) a genomic gain for human NA17026, relative to human individual 113. (d) These observations were confirmed by qPCR. Genomic DNA from the reference chimpanzee Clint (relative quantity = 1) was used for the standard curve. Error bars depict ±2 SD (95% confidence interval).
Fig. 3.
Fig. 3.
Model for evolution of CNV hotspots. Certain segmental duplications that arose in a human–chimpanzee common ancestor (depicted at point A) may facilitate separate nonallelic homologous recombination (NAHR) in both chimpanzees (B) and humans (C), leading to the genesis of CNVs in both species. If NAHR in these regions occurs frequently, it may be expected to lead to the maintenance of common CNVs by way of recurrent duplications and deletions.
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