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

Research output: Contribution to journal › Journal article › Research › peer-review

Standard

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

Harvard

Jin, X, He, M, Ferguson, B, Meng, Y, Ouyang, L, Ren, J, Mailund, T, Sun, F, Sun, L, Shen, J, Zhuo, M, Song, L, Wang, J, Ling, F, Zhu, Y, Hvilsom, C, Siegismund, HR, Liu, X, Gong, Z, Ji, F, Wang, X, Liu, B, Zhang, Y, Hou, J, Wang, J, Zhao, H, Wang, Y, Fang, X, Zhang, G, Wang, J, Zhang, X, Schierup, MH, Du, H, Wang, J & Wang, X 2012, 'An effort to use human-based exome capture methods to analyze chimpanzee and macaque exomes', P L o S One, vol. 7, no. 7. https://doi.org/10.1371/journal.pone.0040637

APA

Jin, X., He, M., Ferguson, B., Meng, Y., Ouyang, L., Ren, J., Mailund, T., Sun, F., Sun, L., Shen, J., Zhuo, M., Song, L., Wang, J., Ling, F., Zhu, Y., Hvilsom, C., Siegismund, H. R., Liu, X., Gong, Z., ... Wang, X. (2012). An effort to use human-based exome capture methods to analyze chimpanzee and macaque exomes. P L o S One, 7(7). https://doi.org/10.1371/journal.pone.0040637

Vancouver

Jin X, He M, Ferguson B, Meng Y, Ouyang L, Ren J et al. An effort to use human-based exome capture methods to analyze chimpanzee and macaque exomes. P L o S One. 2012;7(7). https://doi.org/10.1371/journal.pone.0040637

Author

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. / An effort to use human-based exome capture methods to analyze chimpanzee and macaque exomes. In: P L o S One. 2012 ; Vol. 7, No. 7.

Bibtex

@article{c85aba88c00240dc870798ce3fbe50bd,
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.",
author = "Xin Jin and Mingze He and Betsy Ferguson and Yuhuan Meng and Limei Ouyang and Jingjing Ren and Thomas Mailund and Fei Sun and Liangdan Sun and Juan Shen and Min Zhuo and Li Song and Jufang Wang and Fei Ling and Yuqi Zhu and Christina Hvilsom and Siegismund, {Hans Redlef} and Xiaoming Liu and Zhuolin Gong and Fang Ji and Xinzhong Wang and Boqing Liu and Yu Zhang and Jianguo Hou and Jing Wang and Hua Zhao and Yanyi Wang and Xiaodong Fang and Guojie Zhang and Jian Wang and Xuejun Zhang and Schierup, {Mikkel H.} and Hongli Du and Jun Wang and Xiaoning Wang",
note = "e40637",
year = "2012",
doi = "10.1371/journal.pone.0040637",
language = "English",
volume = "7",
journal = "PLoS ONE",
issn = "1932-6203",
publisher = "Public Library of Science",
number = "7",

}

RIS

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