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A genome-wide characterization of copy number variations in native populations of Peninsular Malaysia

European Journal of Human Geneticsvolume 26pages886897 (2018) | Download Citation

Abstract

Copy number variations (CNVs) are genomic structural variations that result from the deletion or duplication of large genomic segments. The characterization of CNVs is largely underrepresented, particularly those of indigenous populations, such as the Orang Asli in Peninsular Malaysia. In the present study, we first characterized the genome-wide CNVs of four major native populations from Peninsular Malaysia, including the Malays and three Orang Asli populations; namely, Proto-Malay, Senoi, and Negrito (collectively called PM). We subsequently assessed the distribution of CNVs across the four populations. The resulting global CNV map revealed 3102 CNVs, with an average of more than 100 CNVs per individual. We identified genes harboring CNVs that are highly differentiated between PM and global populations, indicating that these genes are predominantly enriched in immune responses and defense functions, including APOBEC3A_B, beta-defensin genes, and CCL3L1, followed by other biological functions, such as drug and toxin metabolism and responses to radiation, suggesting some attributions between CNV variations and adaptations of the PM groups to the local environmental conditions of tropical rainforests.

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Additional information

These authors contributed equally: Ruiqing Fu, Boon-Peng Hoh.

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Acknowledgements

We thank the Department of Orang Asli Development (JAKOA) and especially all subjects who voluntarily participated in this study. SX acknowledges financial support from the Strategic Priority Research Program (XDB13040100) and Key Research Program of Frontier Sciences (QYZDJ-SSW-SYS009) of the Chinese Academy of Sciences (CAS), the National Natural Science Foundation of China (NSFC) grant (91331204, 91731303, 31771388, and 31711530221), the National Science Fund for Distinguished Young Scholars (31525014), the National Key Research and Development Program (2016YFC0906403), and the Program of Shanghai Academic Research Leader (16XD1404700). B-PH acknowledges the Chinese Academy of Sciences President’s International Fellowship Initiatives (2017VBA0008) awarded to him. This study is also supported by Ministry of Science, Technology and Innovation (MOSTI) grant erBiotek Grant #100-RM/BIOTEK 16/6/2 B (1/2011) and [100- RMI/GOV 16/6/2 (19/2011)] awarded to B-PH and MEP. SX is Max-Planck Independent Research Group Leader and member of CAS Youth Innovation Promotion Association. SX also gratefully acknowledges the support of the National Program for Top-notch Young Innovative Talents of The “Wanren Jihua” Project. We thank LetPub (www.letpub.com) for providing linguistic assistance during the preparation of this manuscript. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.

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Author notes

    Affiliations

    1. Chinese Academy of Sciences (CAS), Key Laboratory of Computational Biology, Max Planck Independent Research Group on Population Genomics, CAS-MPG Partner Institute for Computational Biology, Shanghai Institutes for Biological Sciences, Shanghai, 200031, China

      • Ruiqing Fu
      • , Boon-Peng Hoh
      •  & Shuhua Xu
    2. University of Chinese Academy of Sciences, Beijing, 100049, China

      • Ruiqing Fu
      •  & Shuhua Xu
    3. Institute of Medical Molecular Biotechnology, Faculty of Medicine, Universiti Teknologi MARA, Sungai Buloh Campus, Selangor, Malaysia

      • Siti Shuhada Mokhtar
    4. School of Medicine, Monash University Sunway Campus, Petaling Jaya, Malaysia

      • Maude Elvira Phipps
    5. Faculty of Medicine and Health Sciences, UCSI University, Jalan Menara Gading, Taman Connaught, Cheras, Kuala Lumpur, Malaysia

      • Boon-Peng Hoh
    6. School of Life Science and Technology, ShanghaiTech University, Shanghai, 201210, China

      • Shuhua Xu
    7. Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming, 650223, China

      • Shuhua Xu

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    The authors declare that they have no conflict of interest.

    Corresponding author

    Correspondence to Shuhua Xu.

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    DOI

    https://doi.org/10.1038/s41431-018-0120-8