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Structural variants in the Chinese population and their impact on phenotypes, diseases and population adaptation

Author

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  • Zhikun Wu

    (Zhongshan Ophthalmic Center, Sun Yat-sen University)

  • Zehang Jiang

    (Zhongshan Ophthalmic Center, Sun Yat-sen University)

  • Tong Li

    (Zhongshan Ophthalmic Center, Sun Yat-sen University)

  • Chuanbo Xie

    (Sun Yat-sen University Cancer Center, Sun Yat-sen University)

  • Liansheng Zhao

    (Mental Health Center and Psychiatric Laboratory, the State Key Laboratory of Biotherapy, West China Hospital of Sichuan University
    Guangdong-Hong Kong-Macao Greater Bay Area Center for Brain Science and Brain-Inspired Intelligence)

  • Jiaqi Yang

    (Zhongshan Ophthalmic Center, Sun Yat-sen University)

  • Shuai Ouyang

    (Zhongshan Ophthalmic Center, Sun Yat-sen University)

  • Yizhi Liu

    (Zhongshan Ophthalmic Center, Sun Yat-sen University)

  • Tao Li

    (Mental Health Center and Psychiatric Laboratory, the State Key Laboratory of Biotherapy, West China Hospital of Sichuan University
    Guangdong-Hong Kong-Macao Greater Bay Area Center for Brain Science and Brain-Inspired Intelligence)

  • Zhi Xie

    (Zhongshan Ophthalmic Center, Sun Yat-sen University)

Abstract

A complete characterization of genetic variation is a fundamental goal of human genome research. Long-read sequencing has improved the sensitivity of structural variant discovery. Here, we conduct the long-read sequencing-based structural variant analysis for 405 unrelated Chinese individuals, with 68 phenotypic and clinical measurements. We discover a landscape of 132,312 nonredundant structural variants, of which 45.2% are novel. The identified structural variants are of high-quality, with an estimated false discovery rate of 3.2%. The concatenated length of all the structural variants is approximately 13.2% of the human reference genome. We annotate 1,929 loss-of-function structural variants affecting the coding sequence of 1,681 genes. We discover rare deletions in HBA1/HBA2/HBB associated with anemia. Furthermore, we identify structural variants related to immunity which differentiate the northern and southern Chinese populations. Our study describes the landscape of structural variants in the Chinese population and their contribution to phenotypes and disease.

Suggested Citation

  • Zhikun Wu & Zehang Jiang & Tong Li & Chuanbo Xie & Liansheng Zhao & Jiaqi Yang & Shuai Ouyang & Yizhi Liu & Tao Li & Zhi Xie, 2021. "Structural variants in the Chinese population and their impact on phenotypes, diseases and population adaptation," Nature Communications, Nature, vol. 12(1), pages 1-12, December.
    • Handle: RePEc:nat:natcom:v:12:y:2021:i:1:d:10.1038_s41467-021-26856-x
    DOI: 10.1038/s41467-021-26856-x
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    1. Lingling Shi & Yunfei Guo & Chengliang Dong & John Huddleston & Hui Yang & Xiaolu Han & Aisi Fu & Quan Li & Na Li & Siyi Gong & Katherine E. Lintner & Qiong Ding & Zou Wang & Jiang Hu & Depeng Wang & , 2016. "Long-read sequencing and de novo assembly of a Chinese genome," Nature Communications, Nature, vol. 7(1), pages 1-10, November.
    2. Haley J. Abel & David E. Larson & Allison A. Regier & Colby Chiang & Indraniel Das & Krishna L. Kanchi & Ryan M. Layer & Benjamin M. Neale & William J. Salerno & Catherine Reeves & Steven Buyske & Tar, 2020. "Mapping and characterization of structural variation in 17,795 human genomes," Nature, Nature, vol. 583(7814), pages 83-89, July.
    3. Mircea Cretu Stancu & Markus J. Roosmalen & Ivo Renkens & Marleen M. Nieboer & Sjors Middelkamp & Joep Ligt & Giulia Pregno & Daniela Giachino & Giorgia Mandrile & Jose Espejo Valle-Inclan & Jerome Ko, 2017. "Mapping and phasing of structural variation in patient genomes using nanopore sequencing," Nature Communications, Nature, vol. 8(1), pages 1-13, December.
    4. Ryan L. Collins & Harrison Brand & Konrad J. Karczewski & Xuefang Zhao & Jessica Alföldi & Laurent C. Francioli & Amit V. Khera & Chelsea Lowther & Laura D. Gauthier & Harold Wang & Nicholas A. Watts , 2020. "A structural variation reference for medical and population genetics," Nature, Nature, vol. 581(7809), pages 444-451, May.
    5. Karen H. Miga & Sergey Koren & Arang Rhie & Mitchell R. Vollger & Ariel Gershman & Andrey Bzikadze & Shelise Brooks & Edmund Howe & David Porubsky & Glennis A. Logsdon & Valerie A. Schneider & Tamara , 2020. "Telomere-to-telomere assembly of a complete human X chromosome," Nature, Nature, vol. 585(7823), pages 79-84, September.
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    2. Jinlong Shi & Zhilong Jia & Jinxiu Sun & Xiaoreng Wang & Xiaojing Zhao & Chenghui Zhao & Fan Liang & Xinyu Song & Jiawei Guan & Xue Jia & Jing Yang & Qi Chen & Kang Yu & Qian Jia & Jing Wu & Depeng Wa, 2023. "Structural variants involved in high-altitude adaptation detected using single-molecule long-read sequencing," Nature Communications, Nature, vol. 14(1), pages 1-15, December.

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