An effort to use human-based exome capture methods to analyze chimpanzee and macaque exomes
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An effort to use human-based exome capture methods to analyze chimpanzee and macaque exomes. / Jin, Xin; He, Mingze; Ferguson, Betsy; Meng, Yuhuan; Ouyang, Limei; Ren, Jingjing; Mailund, Thomas; Sun, Fei; Sun, Liangdan; Shen, Juan; Zhuo, Min; Song, Li; Wang, Jufang; Ling, Fei; Zhu, Yuqi; Hvilsom, Christina; Siegismund, Hans Redlef; 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.
In: P L o S One, Vol. 7, No. 7, 2012.Research output: Contribution to journal › Journal article › Research › peer-review
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TY - JOUR
T1 - An effort to use human-based exome capture methods to analyze chimpanzee and macaque exomes
AU - Jin, Xin
AU - He, Mingze
AU - Ferguson, Betsy
AU - Meng, Yuhuan
AU - Ouyang, Limei
AU - Ren, Jingjing
AU - Mailund, Thomas
AU - Sun, Fei
AU - Sun, Liangdan
AU - Shen, Juan
AU - Zhuo, Min
AU - Song, Li
AU - Wang, Jufang
AU - Ling, Fei
AU - Zhu, Yuqi
AU - Hvilsom, Christina
AU - Siegismund, Hans Redlef
AU - Liu, Xiaoming
AU - Gong, Zhuolin
AU - Ji, Fang
AU - Wang, Xinzhong
AU - Liu, Boqing
AU - Zhang, Yu
AU - Hou, Jianguo
AU - Wang, Jing
AU - Zhao, Hua
AU - Wang, Yanyi
AU - Fang, Xiaodong
AU - Zhang, Guojie
AU - Wang, Jian
AU - Zhang, Xuejun
AU - Schierup, Mikkel H.
AU - Du, Hongli
AU - Wang, Jun
AU - Wang, Xiaoning
N1 - e40637
PY - 2012
Y1 - 2012
N2 - 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.
AB - 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.
U2 - 10.1371/journal.pone.0040637
DO - 10.1371/journal.pone.0040637
M3 - Journal article
C2 - 22848389
VL - 7
JO - PLoS ONE
JF - PLoS ONE
SN - 1932-6203
IS - 7
ER -
ID: 38565242