NDLI: An Effort to Use Human-Based Exome Capture Methods to Analyze Chimpanzee and Macaque Exomes

Content Provider	PubMed Central
Author	Jin, Xin He, Mingze Ferguson, Betsy Meng, Yuhuan Ouyang, Limei Ren, Jingjing Thomas, Mailund Sun, Fei Sun, Liangdan Shen, Juan Zhuo, Min Song, Li Wang, Jufang Ling, Fei Zhu, Yuqi Hvilsom, Christina Siegismund, Hans Liu, Xiaoming Gong, Zhuolin Ji, Fang Wang, Xinzhong Liu, Boqing Zhang, Yu Hou, Jianguo Wang, Jing Zhao, Hua Wang, Yanyi Fang, Xiaodong Zhang, Guojie Wang, Jian Zhang, Xuejun Schierup, Mikkel H. Du, Hongli Wang, Jun Wang, Xiaoning
Editor	Sestak, Karol
Copyright Year	2012
Abstract	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.
Related Links	http://dx.doi.org/10.1371/journal.pone.0040637
Starting Page	40637
File Format	PDF
ISSN	19326203
e-ISSN	19326203
Journal	PLoS ONE
Issue Number	7
Volume Number	7
Language	English
Publisher	Public Library of Science
Publisher Date	2012-07-01
Access Restriction	Open
Rights Holder	Public Library of Science
Subject Keyword	Biochemistry, Genetics and Molecular Biology(all) Agricultural and Biological Sciences(all) Medicine(all) Research in Higher Education
Content Type	Text
Resource Type	Article
Subject	Multidisciplinary

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1	Ministry of Education (GoI), Department of Higher Education	Sanctioning Authority	https://www.education.gov.in/ict-initiatives
2	Indian Institute of Technology Kharagpur	Host Institute of the Project: The host institute of the project is responsible for providing infrastructure support and hosting the project	https://www.iitkgp.ac.in
3	National Digital Library of India Office, Indian Institute of Technology Kharagpur	The administrative and infrastructural headquarters of the project	Dr. B. Sutradhar bsutra@ndl.gov.in
4	Project PI / Joint PI	Principal Investigator and Joint Principal Investigators of the project	Dr. B. Sutradhar bsutra@ndl.gov.in Prof. Saswat Chakrabarti will be added soon
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