title: An effort to use human-based exome capture methods to analyze chimpanzee and macaque exomes.
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.
authors: School of Bioscience and Bioengineering, South China University of Technology, Guangzhou, China.
authors: Xin
authors: X
authors: Jin
authors: Mingze
authors: M
authors: He
authors: Betsy
authors: B
authors: Ferguson
authors: Yuhuan
authors: Y
authors: Meng
authors: Limei
authors: L
authors: Ouyang
authors: Jingjing
authors: J
authors: Ren
authors: Thomas
authors: T
authors: Mailund
authors: Fei
authors: F
authors: Sun
authors: Liangdan
authors: L
authors: Sun
authors: Juan
authors: J
authors: Shen
authors: Min
authors: M
authors: Zhuo
authors: Li
authors: L
authors: Song
authors: Jufang
authors: J
authors: Wang
authors: Fei
authors: F
authors: Ling
authors: Yuqi
authors: Y
authors: Zhu
authors: Christina
authors: C
authors: Hvilsom
authors: Hans
authors: H
authors: Siegismund
authors: Xiaoming
authors: X
authors: Liu
authors: Zhuolin
authors: Z
authors: Gong
authors: Fang
authors: F
authors: Ji
authors: Xinzhong
authors: X
authors: Wang
authors: Boqing
authors: B
authors: Liu
authors: Yu
authors: Y
authors: Zhang
authors: Jianguo
authors: J
authors: Hou
authors: Jing
authors: J
authors: Wang
authors: Hua
authors: H
authors: Zhao
authors: Yanyi
authors: Y
authors: Wang
authors: Xiaodong
authors: X
authors: Fang
authors: Guojie
authors: G
authors: Zhang
authors: Jian
authors: J
authors: Wang
authors: Xuejun
authors: X
authors: Zhang
authors: Mikkel H
authors: MH
authors: Schierup
authors: Hongli
authors: H
authors: Du
authors: Jun
authors: J
authors: Wang
authors: Xiaoning
authors: X
authors: Wang
mesh_terms: D000818:Animals; D059472:Exome; D006801:Humans; D008252:Macaca fascicularis / Q000235:genetics*; D020411:Oligonucleotide Array Sequence Analysis; D002679:Pan troglodytes / Q000235:genetics*; D020641:Polymorphism, Single Nucleotide