IDEAS home Printed from https://ideas.repec.org/a/nat/natcom/v12y2021i1d10.1038_s41467-021-26856-x.html
   My bibliography  Save this article

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

Author

Listed:
  • 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
    as

    Download full text from publisher

    File URL: https://www.nature.com/articles/s41467-021-26856-x
    File Function: Abstract
    Download Restriction: no
    File URL: https://libkey.io/10.1038/s41467-021-26856-x?utm_source=ideas
    LibKey link: if access is restricted and if your library uses this service, LibKey will redirect you to where you can use your library subscription to access this item
    ---><---

    References listed on IDEAS

    as
    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.
    Full references (including those not matched with items on IDEAS)

    Citations

    Citations are extracted by the CitEc Project, subscribe to its RSS feed for this item.
    as


    Cited by:

    1. Xiaoling Tong & Min-Jin Han & Kunpeng Lu & Shuaishuai Tai & Shubo Liang & Yucheng Liu & Hai Hu & Jianghong Shen & Anxing Long & Chengyu Zhan & Xin Ding & Shuo Liu & Qiang Gao & Bili Zhang & Linli Zhou, 2022. "High-resolution silkworm pan-genome provides genetic insights into artificial selection and ecological adaptation," Nature Communications, Nature, vol. 13(1), pages 1-15, December.
    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.
    3. Joanna Hui Juan Tan & Zhihui Li & Mar Gonzalez Porta & Ramesh Rajaby & Weng Khong Lim & Ye An Tan & Rodrigo Toro Jimenez & Renyi Teo & Maxime Hebrard & Jack Ling Ow & Shimin Ang & Justin Jeyakani & Ya, 2024. "A Catalogue of Structural Variation across Ancestrally Diverse Asian Genomes," Nature Communications, Nature, vol. 15(1), pages 1-15, December.

    Most related items

    These are the items that most often cite the same works as this one and are cited by the same works as this one.
    1. Joanna Hui Juan Tan & Zhihui Li & Mar Gonzalez Porta & Ramesh Rajaby & Weng Khong Lim & Ye An Tan & Rodrigo Toro Jimenez & Renyi Teo & Maxime Hebrard & Jack Ling Ow & Shimin Ang & Justin Jeyakani & Ya, 2024. "A Catalogue of Structural Variation across Ancestrally Diverse Asian Genomes," Nature Communications, Nature, vol. 15(1), pages 1-15, December.
    2. Ramesh Rajaby & Dong-Xu Liu & Chun Hang Au & Yuen-Ting Cheung & Amy Yuet Ting Lau & Qing-Yong Yang & Wing-Kin Sung, 2023. "INSurVeyor: improving insertion calling from short read sequencing data," Nature Communications, Nature, vol. 14(1), pages 1-13, December.
    3. Xue Gao & Sheng Wang & Yan-Fen Wang & Shuang Li & Shi-Xin Wu & Rong-Ge Yan & Yi-Wen Zhang & Rui-Dong Wan & Zhen He & Ren-De Song & Xin-Quan Zhao & Dong-Dong Wu & Qi-En Yang, 2022. "Long read genome assemblies complemented by single cell RNA-sequencing reveal genetic and cellular mechanisms underlying the adaptive evolution of yak," Nature Communications, Nature, vol. 13(1), pages 1-14, December.
    4. Ludovica Montanucci & David Lewis-Smith & Ryan L. Collins & Lisa-Marie Niestroj & Shridhar Parthasarathy & Julie Xian & Shiva Ganesan & Marie Macnee & Tobias Brünger & Rhys H. Thomas & Michael Talkows, 2023. "Genome-wide identification and phenotypic characterization of seizure-associated copy number variations in 741,075 individuals," Nature Communications, Nature, vol. 14(1), pages 1-19, December.
    5. Yichen Henry Liu & Can Luo & Staunton G. Golding & Jacob B. Ioffe & Xin Maizie Zhou, 2024. "Tradeoffs in alignment and assembly-based methods for structural variant detection with long-read sequencing data," Nature Communications, Nature, vol. 15(1), pages 1-22, December.
    6. Kunpeng Li & Peng Xu & Jinpeng Wang & Xin Yi & Yuannian Jiao, 2023. "Identification of errors in draft genome assemblies at single-nucleotide resolution for quality assessment and improvement," Nature Communications, Nature, vol. 14(1), pages 1-12, December.
    7. Temitayo A. Olagunju & Benjamin D. Rosen & Holly L. Neibergs & Gabrielle M. Becker & Kimberly M. Davenport & Christine G. Elsik & Tracy S. Hadfield & Sergey Koren & Kristen L. Kuhn & Arang Rhie & Kati, 2024. "Telomere-to-telomere assemblies of cattle and sheep Y-chromosomes uncover divergent structure and gene content," Nature Communications, Nature, vol. 15(1), pages 1-12, December.
    8. Mohamed Awad & Xiangchao Gan, 2023. "GALA: a computational framework for de novo chromosome-by-chromosome assembly with long reads," Nature Communications, Nature, vol. 14(1), pages 1-11, December.
    9. Xiaoling Tong & Min-Jin Han & Kunpeng Lu & Shuaishuai Tai & Shubo Liang & Yucheng Liu & Hai Hu & Jianghong Shen & Anxing Long & Chengyu Zhan & Xin Ding & Shuo Liu & Qiang Gao & Bili Zhang & Linli Zhou, 2022. "High-resolution silkworm pan-genome provides genetic insights into artificial selection and ecological adaptation," Nature Communications, Nature, vol. 13(1), pages 1-15, December.
    10. Orshay Gabay & Yoav Shoshan & Eli Kopel & Udi Ben-Zvi & Tomer D. Mann & Noam Bressler & Roni Cohen‐Fultheim & Amos A. Schaffer & Shalom Hillel Roth & Ziv Tzur & Erez Y. Levanon & Eli Eisenberg, 2022. "Landscape of adenosine-to-inosine RNA recoding across human tissues," Nature Communications, Nature, vol. 13(1), pages 1-17, December.
    11. Yoshitaka Sakamoto & Shuhei Miyake & Miho Oka & Akinori Kanai & Yosuke Kawai & Satoi Nagasawa & Yuichi Shiraishi & Katsushi Tokunaga & Takashi Kohno & Masahide Seki & Yutaka Suzuki & Ayako Suzuki, 2022. "Phasing analysis of lung cancer genomes using a long read sequencer," Nature Communications, Nature, vol. 13(1), pages 1-17, December.
    12. Sook Wah Yee & Luis Ferrández-Peral & Pol Alentorn-Moron & Claudia Fontsere & Merve Ceylan & Megan L. Koleske & Niklas Handin & Virginia M. Artegoitia & Giovanni Lara & Huan-Chieh Chien & Xujia Zhou &, 2024. "Illuminating the function of the orphan transporter, SLC22A10, in humans and other primates," Nature Communications, Nature, vol. 15(1), pages 1-17, December.
    13. Sarah Morrison-Smith & Christina Boucher & Aleksandra Sarcevic & Noelle Noyes & Catherine O’Brien & Nazaret Cuadros & Jaime Ruiz, 2022. "Challenges in large-scale bioinformatics projects," Palgrave Communications, Palgrave Macmillan, vol. 9(1), pages 1-9, December.
    14. Zhuoran Xu & Quan Li & Luigi Marchionni & Kai Wang, 2023. "PhenoSV: interpretable phenotype-aware model for the prioritization of genes affected by structural variants," Nature Communications, Nature, vol. 14(1), pages 1-16, December.
    15. Cristian Groza & Carl Schwendinger-Schreck & Warren A. Cheung & Emily G. Farrow & Isabelle Thiffault & Juniper Lake & William B. Rizzo & Gilad Evrony & Tom Curran & Guillaume Bourque & Tomi Pastinen, 2024. "Pangenome graphs improve the analysis of structural variants in rare genetic diseases," Nature Communications, Nature, vol. 15(1), pages 1-12, December.
    16. Heyang Cui & Yong Zhou & Fang Wang & Caixia Cheng & Weimin Zhang & Ruifang Sun & Ling Zhang & Yanghui Bi & Min Guo & Yan Zhou & Xinhui Wang & Jiaxin Ren & Ruibing Bai & Ning Ding & Chen Cheng & Longlo, 2022. "Characterization of somatic structural variations in 528 Chinese individuals with Esophageal squamous cell carcinoma," Nature Communications, Nature, vol. 13(1), pages 1-18, December.
    17. Parithi Balachandran & Isha A. Walawalkar & Jacob I. Flores & Jacob N. Dayton & Peter A. Audano & Christine R. Beck, 2022. "Transposable element-mediated rearrangements are prevalent in human genomes," Nature Communications, Nature, vol. 13(1), pages 1-14, December.
    18. Tobias T. Schmidt & Carly Tyer & Preeyesh Rughani & Candy Haggblom & Jeffrey R. Jones & Xiaoguang Dai & Kelly A. Frazer & Fred H. Gage & Sissel Juul & Scott Hickey & Jan Karlseder, 2024. "High resolution long-read telomere sequencing reveals dynamic mechanisms in aging and cancer," Nature Communications, Nature, vol. 15(1), pages 1-11, December.
    19. Joanna Hård & Jeff E. Mold & Jesper Eisfeldt & Christian Tellgren-Roth & Susana Häggqvist & Ignas Bunikis & Orlando Contreras-Lopez & Chen-Shan Chin & Jessica Nordlund & Carl-Johan Rubin & Lars Feuk &, 2023. "Long-read whole-genome analysis of human single cells," Nature Communications, Nature, vol. 14(1), pages 1-12, December.
    20. Gabriel E. Rech & Santiago Radío & Sara Guirao-Rico & Laura Aguilera & Vivien Horvath & Llewellyn Green & Hannah Lindstadt & Véronique Jamilloux & Hadi Quesneville & Josefa González, 2022. "Population-scale long-read sequencing uncovers transposable elements associated with gene expression variation and adaptive signatures in Drosophila," Nature Communications, Nature, vol. 13(1), pages 1-16, December.

    More about this item

    Statistics

    Access and download statistics

    Corrections

    All material on this site has been provided by the respective publishers and authors. You can help correct errors and omissions. When requesting a correction, please mention this item's handle: RePEc:nat:natcom:v:12:y:2021:i:1:d:10.1038_s41467-021-26856-x. See general information about how to correct material in RePEc.

    If you have authored this item and are not yet registered with RePEc, we encourage you to do it here. This allows to link your profile to this item. It also allows you to accept potential citations to this item that we are uncertain about.

    If CitEc recognized a bibliographic reference but did not link an item in RePEc to it, you can help with this form .

    If you know of missing items citing this one, you can help us creating those links by adding the relevant references in the same way as above, for each refering item. If you are a registered author of this item, you may also want to check the "citations" tab in your RePEc Author Service profile, as there may be some citations waiting for confirmation.

    For technical questions regarding this item, or to correct its authors, title, abstract, bibliographic or download information, contact: Sonal Shukla or Springer Nature Abstracting and Indexing (email available below). General contact details of provider: http://www.nature.com .

    Please note that corrections may take a couple of weeks to filter through the various RePEc services.

    IDEAS is a RePEc service. RePEc uses bibliographic data supplied by the respective publishers.