IDEAS home Printed from https://ideas.repec.org/a/nat/natcom/v15y2024i1d10.1038_s41467-024-52027-9.html
   My bibliography  Save this article

Impact and characterization of serial structural variations across humans and great apes

Author

Listed:
  • Wolfram Höps

    (Genome Biology Unit, Meyerhofstr. 1)

  • Tobias Rausch

    (Genome Biology Unit, Meyerhofstr. 1
    University of Heidelberg)

  • Michael Jendrusch

    (Genome Biology Unit, Meyerhofstr. 1)

  • Jan O. Korbel

    (Genome Biology Unit, Meyerhofstr. 1
    European Bioinformatics Institute, Wellcome Genome Campus)

  • Fritz J. Sedlazeck

    (Baylor College of Medicine
    Rice University)

Abstract

Modern sequencing technology enables the systematic detection of complex structural variation (SV) across genomes. However, extensive DNA rearrangements arising through a series of mutations, a phenomenon we refer to as serial SV (sSV), remain underexplored, posing a challenge for SV discovery. Here, we present NAHRwhals ( https://github.com/WHops/NAHRwhals ), a method to infer repeat-mediated series of SVs in long-read genomic assemblies. Applying NAHRwhals to haplotype-resolved human genomes from 28 individuals reveals 37 sSV loci of various length and complexity. These sSVs explain otherwise cryptic variation in medically relevant regions such as the TPSAB1 gene, 8p23.1, 22q11 and Sotos syndrome regions. Comparisons with great ape assemblies indicate that most human sSVs formed recently, after the human-ape split, and involved non-repeat-mediated processes in addition to non-allelic homologous recombination. NAHRwhals reliably discovers and characterizes sSVs at scale and independent of species, uncovering their genomic abundance and suggesting broader implications for disease.

Suggested Citation

  • Wolfram Höps & Tobias Rausch & Michael Jendrusch & Jan O. Korbel & Fritz J. Sedlazeck, 2024. "Impact and characterization of serial structural variations across humans and great apes," Nature Communications, Nature, vol. 15(1), pages 1-15, December.
    • Handle: RePEc:nat:natcom:v:15:y:2024:i:1:d:10.1038_s41467-024-52027-9
    DOI: 10.1038/s41467-024-52027-9
    as

    Download full text from publisher

    File URL: https://www.nature.com/articles/s41467-024-52027-9
    File Function: Abstract
    Download Restriction: no
    File URL: https://libkey.io/10.1038/s41467-024-52027-9?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. 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.
    2. Wen-Wei Liao & Mobin Asri & Jana Ebler & Daniel Doerr & Marina Haukness & Glenn Hickey & Shuangjia Lu & Julian K. Lucas & Jean Monlong & Haley J. Abel & Silvia Buonaiuto & Xian H. Chang & Haoyu Cheng , 2023. "A draft human pangenome reference," Nature, Nature, vol. 617(7960), pages 312-324, May.
    3. Ting Wang & Lucinda Antonacci-Fulton & Kerstin Howe & Heather A. Lawson & Julian K. Lucas & Adam M. Phillippy & Alice B. Popejoy & Mobin Asri & Caryn Carson & Mark J. P. Chaisson & Xian Chang & Robert, 2022. "The Human Pangenome Project: a global resource to map genomic diversity," Nature, Nature, vol. 604(7906), pages 437-446, April.
    Full references (including those not matched with items on IDEAS)

    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. 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.
    2. Sean A. Misek & Aaron Fultineer & Jeremie Kalfon & Javad Noorbakhsh & Isabella Boyle & Priyanka Roy & Joshua Dempster & Lia Petronio & Katherine Huang & Alham Saadat & Thomas Green & Adam Brown & John, 2024. "Germline variation contributes to false negatives in CRISPR-based experiments with varying burden across ancestries," Nature Communications, Nature, vol. 15(1), pages 1-11, December.
    3. Robin Aguilar & Conor K. Camplisson & Qiaoyi Lin & Karen H. Miga & William S. Noble & Brian J. Beliveau, 2024. "Tigerfish designs oligonucleotide-based in situ hybridization probes targeting intervals of highly repetitive DNA at the scale of genomes," Nature Communications, Nature, vol. 15(1), pages 1-14, December.
    4. Tuomas Hämälä & Christopher Moore & Laura Cowan & Matthew Carlile & David Gopaulchan & Marie K. Brandrud & Siri Birkeland & Matthew Loose & Filip Kolář & Marcus A. Koch & Levi Yant, 2024. "Impact of whole-genome duplications on structural variant evolution in Cochlearia," Nature Communications, Nature, vol. 15(1), pages 1-13, December.
    5. Kang Hu & Peng Ni & Minghua Xu & You Zou & Jianye Chang & Xin Gao & Yaohang Li & Jue Ruan & Bin Hu & Jianxin Wang, 2024. "HiTE: a fast and accurate dynamic boundary adjustment approach for full-length transposable element detection and annotation," Nature Communications, Nature, vol. 15(1), pages 1-14, December.
    6. Can Luo & Yichen Henry Liu & Xin Maizie Zhou, 2024. "VolcanoSV enables accurate and robust structural variant calling in diploid genomes from single-molecule long read sequencing," Nature Communications, Nature, vol. 15(1), pages 1-20, December.
    7. Yilei Fu & Sergey Aganezov & Medhat Mahmoud & John Beaulaurier & Sissel Juul & Todd J. Treangen & Fritz J. Sedlazeck, 2024. "MethPhaser: methylation-based long-read haplotype phasing of human genomes," Nature Communications, Nature, vol. 15(1), pages 1-12, December.
    8. Marine Duhamel & Michael E. Hood & Ricardo C. Rodríguez de la Vega & Tatiana Giraud, 2023. "Dynamics of transposable element accumulation in the non-recombining regions of mating-type chromosomes in anther-smut fungi," Nature Communications, Nature, vol. 14(1), pages 1-18, December.
    9. Shuangying Jiang & Zhouqing Luo & Jie Wu & Kang Yu & Shijun Zhao & Zelin Cai & Wenfei Yu & Hui Wang & Li Cheng & Zhenzhen Liang & Hui Gao & Marco Monti & Daniel Schindler & Linsen Huang & Cheng Zeng &, 2023. "Building a eukaryotic chromosome arm by de novo design and synthesis," Nature Communications, Nature, vol. 14(1), pages 1-17, December.
    10. 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.
    11. Alessia Russo & Mattia Alessandrini & Moaine El Baidouri & Daniel Frei & Teresa Rosa Galise & Lara Gaidusch & Hannah F. Oertel & Sara E. Garcia Morales & Giacomo Potente & Qin Tian & Dmitry Smetanin &, 2024. "Genome of the early spider-orchid Ophrys sphegodes provides insights into sexual deception and pollinator adaptation," Nature Communications, Nature, vol. 15(1), pages 1-12, 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:15:y:2024:i:1:d:10.1038_s41467-024-52027-9. 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.