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

  • Xin Jin ,

    Contributed equally to this work with: Xin Jin, Mingze He, Betsy Ferguson, Yuhuan Meng, Limei Ouyang, Jingjing Ren

    Affiliations School of Bioscience and Bioengineering, South China University of Technology, Guangzhou, China, BGI-Shenzhen, Shenzhen, China

  • Mingze He ,

    Contributed equally to this work with: Xin Jin, Mingze He, Betsy Ferguson, Yuhuan Meng, Limei Ouyang, Jingjing Ren

    Affiliations School of Bioscience and Bioengineering, South China University of Technology, Guangzhou, China, BGI-Shenzhen, Shenzhen, China

  • Betsy Ferguson ,

    Contributed equally to this work with: Xin Jin, Mingze He, Betsy Ferguson, Yuhuan Meng, Limei Ouyang, Jingjing Ren

    Affiliation Primate Genetics Program, Oregon National Primate Research Center, Oregon Health and Sciences University, Beaverton, Oregon, United States of America

  • Yuhuan Meng ,

    Contributed equally to this work with: Xin Jin, Mingze He, Betsy Ferguson, Yuhuan Meng, Limei Ouyang, Jingjing Ren

    Affiliation School of Bioscience and Bioengineering, South China University of Technology, Guangzhou, China

  • Limei Ouyang ,

    Contributed equally to this work with: Xin Jin, Mingze He, Betsy Ferguson, Yuhuan Meng, Limei Ouyang, Jingjing Ren

    Affiliation BGI-Shenzhen, Shenzhen, China

  • Jingjing Ren ,

    Contributed equally to this work with: Xin Jin, Mingze He, Betsy Ferguson, Yuhuan Meng, Limei Ouyang, Jingjing Ren

    Affiliations BGI-Shenzhen, Shenzhen, China, School of Biological Science and Medical Engineering, Southeast University, Nanjing, China

  • Thomas Mailund,

    Affiliation Bioinformatics Research Center, Aarhus University, Aarhus C, Denmark

  • Fei Sun,

    Affiliation School of Bioscience and Bioengineering, South China University of Technology, Guangzhou, China

  • Liangdan Sun,

    Affiliations Institute of Dermatology and Department of Dermatology, No.1 Hospital, Anhui Medical University, Hefei, Anhui, China, State Key Laboratory Incubation Base of Dermatology, Ministry of National Science and Technology, Hefei, Anhui, China

  • Juan Shen,

    Affiliation BGI-Shenzhen, Shenzhen, China

  • Min Zhuo,

    Affiliation School of Bioscience and Bioengineering, South China University of Technology, Guangzhou, China

  • Li Song,

    Affiliation BGI-Shenzhen, Shenzhen, China

  • Jufang Wang,

    Affiliation School of Bioscience and Bioengineering, South China University of Technology, Guangzhou, China

  • Fei Ling,

    Affiliation School of Bioscience and Bioengineering, South China University of Technology, Guangzhou, China

  • Yuqi Zhu,

    Affiliation BGI-Shenzhen, Shenzhen, China

  • Christina Hvilsom,

    Affiliations Science and Conservation, Copenhagen Zoo, Frederiksberg, Denmark, Bioinformatics, Department of Biology, University of Copenhagen, Copenhagen, Denmark

  • Hans Siegismund,

    Affiliation Bioinformatics, Department of Biology, University of Copenhagen, Copenhagen, Denmark

  • Xiaoming Liu,

    Affiliation South-China Primate Research and Development Center, Guangdong Entomological Institute, Guangzhou, China

  • Zhuolin Gong,

    Affiliation BGI-Shenzhen, Shenzhen, China

  • Fang Ji,

    Affiliation South-China Primate Research and Development Center, Guangdong Entomological Institute, Guangzhou, China

  • Xinzhong Wang,

    Affiliation South-China Primate Research and Development Center, Guangdong Entomological Institute, Guangzhou, China

  • Boqing Liu,

    Affiliation South-China Primate Research and Development Center, Guangdong Entomological Institute, Guangzhou, China

  • Yu Zhang,

    Affiliation Guangdong Laboratory Animals Monitoring Institute, Guangzhou, China

  • Jianguo Hou,

    Affiliation Guangdong Laboratory Animals Monitoring Institute, Guangzhou, China

  • Jing Wang,

    Affiliation Guangdong Laboratory Animals Monitoring Institute, Guangzhou, China

  • Hua Zhao,

    Affiliation Chinese PLA General Hospital, Beijing, China

  • Yanyi Wang,

    Affiliation Chinese PLA General Hospital, Beijing, China

  • Xiaodong Fang,

    Affiliation BGI-Shenzhen, Shenzhen, China

  • Guojie Zhang,

    Affiliation BGI-Shenzhen, Shenzhen, China

  • Jian Wang,

    Affiliation BGI-Shenzhen, Shenzhen, China

  • Xuejun Zhang,

    Affiliations Institute of Dermatology and Department of Dermatology, No.1 Hospital, Anhui Medical University, Hefei, Anhui, China, State Key Laboratory Incubation Base of Dermatology, Ministry of National Science and Technology, Hefei, Anhui, China

  • Mikkel H. Schierup,

    Affiliation Guangdong Laboratory Animals Monitoring Institute, Guangzhou, China

  • Hongli Du ,

    hldu@scut.edu.cn (HD); wangj@genomics.cn (JW); xnwang@scut.edu.cn (XW)

    Affiliation School of Bioscience and Bioengineering, South China University of Technology, Guangzhou, China

  • Jun Wang ,

    hldu@scut.edu.cn (HD); wangj@genomics.cn (JW); xnwang@scut.edu.cn (XW)

    Affiliations BGI-Shenzhen, Shenzhen, China, Bioinformatics, Department of Biology, University of Copenhagen, Copenhagen, Denmark

  •  [ ... ],
  • Xiaoning Wang

    hldu@scut.edu.cn (HD); wangj@genomics.cn (JW); xnwang@scut.edu.cn (XW)

    Affiliations School of Bioscience and Bioengineering, South China University of Technology, Guangzhou, China, Chinese PLA General Hospital, Beijing, China

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

  • Xin Jin, 
  • Mingze He, 
  • Betsy Ferguson, 
  • Yuhuan Meng, 
  • Limei Ouyang, 
  • Jingjing Ren, 
  • Thomas Mailund, 
  • Fei Sun, 
  • Liangdan Sun, 
  • Juan Shen
PLOS
x

Correction

28 Sep 2012: Jin X, He M, Ferguson B, Meng Y, Ouyang L, et al. (2012) Correction: An Effort to Use Human-Based Exome Capture Methods to Analyze Chimpanzee and Macaque Exomes. PLOS ONE 7(9): 10.1371/annotation/450f85d8-03c6-4bd4-aa8e-b5b5894b4593. https://doi.org/10.1371/annotation/450f85d8-03c6-4bd4-aa8e-b5b5894b4593 View correction

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.

Introduction

Non-human primates are increasingly studied as highly relevant animal models for human biomedical diseases and disorders. Members of the Macaca genus are among the most commonly studied non-human primates, due to their close evolutionary relationship to humans, analogous disease susceptibilities, and wide-spread commercial availability. The rhesus macaque (Macaca mulatta), estimated to have shared a common ancestor with humans approximately 25 million years ago (MYA) [1], is one of the most widely studied macaques. Genetic studies have shown the rhesus macaque to have common genetic risk factors with humans for age-related macular degeneration [2] behavioral disorders [3], [4]_ENREF_4 and reproductive disorders such as amennorhea [5]. A close relative of the rhesus macaque, the Japanese macaque (M. fuscata) has served as a model for multiple sclerosis [6] and ischemia [7], [8]_ENREF_8. The crab-eating or cynomolgus macaque (M. fascicularis) is widely used in studies of amyotrophic lateral sclerosis [9], and depression [10], among other disorders.

The chimpanzee (Pan troglodytes), is more closely related to humans than the macaques, sharing a common ancestor approximately 5–7 MYA [1]. The more recent divergence between humans and the chimpanzee has been of particular importance to the study of human evolution and speciation [11], [12]_ENREF_12. In the field of comparative genomics, the chimpanzee genome provides a critical insight into studies of positive selection in primate genomes [13]. The chimpanzee has also served as a important model for neuroscience research, including studies of cognition [14], neurobiology [15], and behavior [16].

With the recent advance in genomic technologies, interest in comparative analysis of non-human primates, particularly as they relate to biomedical and evolutionary studies, has been rapidly expanding [17], [18]. However, such studies are limited by the financial costs, computational requirements and effort required to generate genome-wide variant data on a large scale. Although improvements in next-generation sequencing (NGS) technology have already sharply reduced the cost of sequencing, the non-human primate still significantly lags behind in the comprehensive characterization of genome variation.

Exome sequencing has proven to be a powerful and efficient approach in human genetics studies [19], as it allows an unbiased investigation of almost all protein-coding regions in a large sample of individuals, at a fraction of the cost of whole genome sequencing. The method has been successfully applied to causative gene identification of several rare monogenic diseases such as Miller syndrome [20] spinocerebellar ataxias [21] and retinitis pigementosa [22]. A study of 50 Tibetan exomes uncovered a number of high-altitude adaptation related genes [23]. If the human exome-capture tools can be applied to the closely related non-human primate species, it could provide an opportunity to efficiently advance the pace of discovery of non-human primate sequence variants.

The human and chimpanzee genomes are about 99% identical, while macaques and human genomes are an estimated 93% conserved [17], [18]. Given the high level of sequence conservation for coding regions among primates, we considered whether it would be feasible to efficiently enrich the exonic sequences of primate species using human-based exon capture designs. Applying exon-capture technology to non-human primate research would not only minimize cost, but it would also reduce the computational effort required for deep sequence analysis. Importantly, exome-sequencing approaches would expedite the discovery sequence variants of greatest interest to many investigators, those located in gene coding regions.

Similar efforts have been used to successfully enrich and sequence target regions of the Neanderthal genome [24]. More than a megabase of captured sequence was recovered from Neanderthal DNA, despite DNA degradation and the presence of significant microbial DNA contamination. This achievement provides support for the use of human exon-capture reagents for the study of more distantly related human ancestors.

Here we report an effort to use human based exome capture to analyze chimpanzee and macaque exomes. Nineteen non-human primates, involving 3 species, were evaluated. We report the utility of the human exon array tool for exon enrichment, DNA variant discovery, and for comparative genomic analysis.

Results and Discussion

Capture and Sequencing

We sequenced the exomes of