An effort to use human-based exome capture methods to analyze chimpanzee and macaque exomes

Research output: Contribution to journal/Conference contribution in journal/Contribution to newspaperJournal articleResearchpeer-review

  • Xin Jin
  • ,
  • Mingze He
  • ,
  • Betsy Ferguson
  • ,
  • Yuhuan Meng
  • ,
  • Limei Ouyang
  • ,
  • Jingjing Ren
  • ,
  • Thomas Mailund
  • Fei Sun
  • ,
  • Liangdan Sun
  • ,
  • Juan Shen, Department of Physics, Denmark
  • Min Zhuo
  • ,
  • Li Song
  • ,
  • Jufang Wang
  • ,
  • Fei Ling
  • ,
  • Yuqi Zhu
  • ,
  • Christina Hvilsom, Biologisk institut, Denmark
  • Hans Siegismund, Denmark
  • Xiaoming Liu, Department of Solid Mechanics, Denmark
  • Zhuolin Gong
  • ,
  • Fang Ji
  • ,
  • Xinzhong Wang
  • ,
  • Boqing Liu
  • ,
  • Yu Zhang, Centre for Biological Sequence Analysis, Denmark
  • Jianguo Hou
  • ,
  • Jing Wang, Denmark
  • Hua Zhao
  • ,
  • Yanyi Wang
  • ,
  • Xiaodong Fang
  • ,
  • Guojie Zhang
  • ,
  • Jian Wang
  • ,
  • Xuejun Zhang
  • ,
  • Mikkel H Schierup
  • Hongli Du
  • ,
  • Jun Wang, Denmark
  • Xiaoning Wang
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.
Original languageEnglish
JournalP L o S One
Volume7
Issue7
Pages (from-to)e40637
ISSN1932-6203
DOIs
Publication statusPublished - 2012

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