28 Sep 2012: Jin X, He M, Ferguson B, Meng Y, Ouyang L, et al. (2012) Correction: An Effort to Use Human-Based Exome Capture Methods to Analyze Chimpanzee and Macaque Exomes. PLOS ONE 7(9): 10.1371/annotation/450f85d8-03c6-4bd4-aa8e-b5b5894b4593. https://doi.org/10.1371/annotation/450f85d8-03c6-4bd4-aa8e-b5b5894b4593 View correction
Non-human primates have emerged as an important resource for the study of human disease and evolution. The characterization of genomic variation between and within non-human primate species could advance the development of genetically defined non-human primate disease models. However, non-human primate specific reagents that would expedite such research, such as exon-capture tools, are lacking. We evaluated the efficiency of using a human exome capture design for the selective enrichment of exonic regions of non-human primates. We compared the exon sequence recovery in nine chimpanzees, two crab-eating macaques and eight Japanese macaques. Over 91% of the target regions were captured in the non-human primate samples, although the specificity of the capture decreased as evolutionary divergence from humans increased. Both intra-specific and inter-specific DNA variants were identified; Sanger-based resequencing validated 85.4% of 41 randomly selected SNPs. Among the short indels identified, a majority (54.6%–77.3%) of the variants resulted in a change of 3 base pairs, consistent with expectations for a selection against frame shift mutations. Taken together, these findings indicate that use of a human design exon-capture array can provide efficient enrichment of non-human primate gene regions. Accordingly, use of the human exon-capture methods provides an attractive, cost-effective approach for the comparative analysis of non-human primate genomes, including gene-based DNA variant discovery.
Citation: Jin X, He M, Ferguson B, Meng Y, Ouyang L, Ren J, et al. (2012) An Effort to Use Human-Based Exome Capture Methods to Analyze Chimpanzee and Macaque Exomes. PLoS ONE 7(7): e40637. https://doi.org/10.1371/journal.pone.0040637
Editor: Karol Sestak, Tulane University, United States of America
Received: February 14, 2012; Accepted: June 11, 2012; Published: July 27, 2012
Copyright: © Jin et al. This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.
Funding: This study was funded by the National Science and Technology Major Project of Key Drug Innovation and Development (2011ZX09307-303-03), the Science and Technology Planning Project of Guangdong Province, China (2010B060200007) and the Fundamental Research Funds for the Central Universities (2012zz0091, 2012ZZ0093 and 2011ZM0111). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.
Competing interests: The authors have declared that no competing interests exist. Some of the authors are from Copenhagen Zoo, which is a non-profit organization and is listed as a cultural institution. In addition, Copenhagen Zoo has no commercial goals linked to the study, and this does not alter the authors’ adherence to all the PLoS ONE policies on sharing data and materials.
Non-human primates are increasingly studied as highly relevant animal models for human biomedical diseases and disorders. Members of the Macaca genus are among the most commonly studied non-human primates, due to their close evolutionary relationship to humans, analogous disease susceptibilities, and wide-spread commercial availability. The rhesus macaque (Macaca mulatta), estimated to have shared a common ancestor with humans approximately 25 million years ago (MYA) , is one of the most widely studied macaques. Genetic studies have shown the rhesus macaque to have common genetic risk factors with humans for age-related macular degeneration  behavioral disorders , _ENREF_4 and reproductive disorders such as amennorhea . A close relative of the rhesus macaque, the Japanese macaque (M. fuscata) has served as a model for multiple sclerosis  and ischemia , _ENREF_8. The crab-eating or cynomolgus macaque (M. fascicularis) is widely used in studies of amyotrophic lateral sclerosis , and depression , among other disorders.
The chimpanzee (Pan troglodytes), is more closely related to humans than the macaques, sharing a common ancestor approximately 5–7 MYA . The more recent divergence between humans and the chimpanzee has been of particular importance to the study of human evolution and speciation , _ENREF_12. In the field of comparative genomics, the chimpanzee genome provides a critical insight into studies of positive selection in primate genomes . The chimpanzee has also served as a important model for neuroscience research, including studies of cognition , neurobiology , and behavior .
With the recent advance in genomic technologies, interest in comparative analysis of non-human primates, particularly as they relate to biomedical and evolutionary studies, has been rapidly expanding , . However, such studies are limited by the financial costs, computational requirements and effort required to generate genome-wide variant data on a large scale. Although improvements in next-generation sequencing (NGS) technology have already sharply reduced the cost of sequencing, the non-human primate still significantly lags behind in the comprehensive characterization of genome variation.
Exome sequencing has proven to be a powerful and efficient approach in human genetics studies , as it allows an unbiased investigation of almost all protein-coding regions in a large sample of individuals, at a fraction of the cost of whole genome sequencing. The method has been successfully applied to causative gene identification of several rare monogenic diseases such as Miller syndrome  spinocerebellar ataxias  and retinitis pigementosa . A study of 50 Tibetan exomes uncovered a number of high-altitude adaptation related genes . If the human exome-capture tools can be applied to the closely related non-human primate species, it could provide an opportunity to efficiently advance the pace of discovery of non-human primate sequence variants.
The human and chimpanzee genomes are about 99% identical, while macaques and human genomes are an estimated 93% conserved , . Given the high level of sequence conservation for coding regions among primates, we considered whether it would be feasible to efficiently enrich the exonic sequences of primate species using human-based exon capture designs. Applying exon-capture technology to non-human primate research would not only minimize cost, but it would also reduce the computational effort required for deep sequence analysis. Importantly, exome-sequencing approaches would expedite the discovery sequence variants of greatest interest to many investigators, those located in gene coding regions.
Similar efforts have been used to successfully enrich and sequence target regions of the Neanderthal genome . More than a megabase of captured sequence was recovered from Neanderthal DNA, despite DNA degradation and the presence of significant microbial DNA contamination. This achievement provides support for the use of human exon-capture reagents for the study of more distantly related human ancestors.
Here we report an effort to use human based exome capture to analyze chimpanzee and macaque exomes. Nineteen non-human primates, involving 3 species, were evaluated. We report the utility of the human exon array tool for exon enrichment, DNA variant discovery, and for comparative genomic analysis.