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Shotgun sequence assembly and recent segmental duplications within the human genome

Author

Listed:
  • Xinwei She

    (University of Washington School of Medicine)

  • Zhaoshi Jiang

    (University of Washington School of Medicine)

  • Royden A. Clark

    (Case Western Reserve University)

  • Ge Liu

    (Case Western Reserve University)

  • Ze Cheng

    (University of Washington School of Medicine)

  • Eray Tuzun

    (University of Washington School of Medicine)

  • Deanna M. Church

    (National Library of Medicine, National Institutes of Health)

  • Granger Sutton

    (Applied Biosystems)

  • Aaron L. Halpern

    (The Center for the Advancement of Genomics)

  • Evan E. Eichler

    (University of Washington School of Medicine)

Abstract

Complex eukaryotic genomes are now being sequenced at an accelerated pace primarily using whole-genome shotgun (WGS) sequence assembly approaches. WGS assembly was initially criticized because of its perceived inability to resolve repeat structures within genomes. Here, we quantify the effect of WGS sequence assembly on large, highly similar repeats by comparison of the segmental duplication content of two different human genome assemblies. Our analysis shows that large (> 15 kilobases) and highly identical (> 97%) duplications are not adequately resolved by WGS assembly. This leads to significant reduction in genome length and the loss of genes embedded within duplications. Comparable analyses of mouse genome assemblies confirm that strict WGS sequence assembly will oversimplify our understanding of mammalian genome structure and evolution; a hybrid strategy using a targeted clone-by-clone approach to resolve duplications is proposed.

Suggested Citation

  • Xinwei She & Zhaoshi Jiang & Royden A. Clark & Ge Liu & Ze Cheng & Eray Tuzun & Deanna M. Church & Granger Sutton & Aaron L. Halpern & Evan E. Eichler, 2004. "Shotgun sequence assembly and recent segmental duplications within the human genome," Nature, Nature, vol. 431(7011), pages 927-930, October.
    • Handle: RePEc:nat:nature:v:431:y:2004:i:7011:d:10.1038_nature03062
    DOI: 10.1038/nature03062
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    Cited by:

    1. Maëva Veyssiere & Javier Perea & Laetitia Michou & Anne Boland & Christophe Caloustian & Robert Olaso & Jean-François Deleuze & François Cornelis & Elisabeth Petit-Teixeira & Valérie Chaudru, 2019. "A novel nonsense variant in SUPT20H gene associated with Rheumatoid Arthritis identified by Whole Exome Sequencing of multiplex families," PLOS ONE, Public Library of Science, vol. 14(3), pages 1-17, March.

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