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Mapping and sequencing of structural variation from eight human genomes

Author

Listed:
  • Jeffrey M. Kidd

    (University of Washington, Seattle, Washington 98195, USA)

  • Gregory M. Cooper

    (University of Washington, Seattle, Washington 98195, USA)

  • William F. Donahue

    (Agencourt Bioscience Corporation, Beverly, Massachusetts 01915, USA)

  • Hillary S. Hayden

    (and University of Washington Genome Center, University of Washington, Seattle, Washington 98195, USA)

  • Nick Sampas

    (Agilent Technologies, Santa Clara, California 95051, USA)

  • Tina Graves

    (Washington University Genome Sequencing Center, School of Medicine, St Louis, Missouri 63108, USA)

  • Nancy Hansen

    (Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland 20892, USA)

  • Brian Teague

    (Laboratory of Genetics, University of Wisconsin, Madison, Wisconsin 53706, USA)

  • Can Alkan

    (University of Washington, Seattle, Washington 98195, USA)

  • Francesca Antonacci

    (University of Washington, Seattle, Washington 98195, USA)

  • Eric Haugen

    (and University of Washington Genome Center, University of Washington, Seattle, Washington 98195, USA)

  • Troy Zerr

    (University of Washington, Seattle, Washington 98195, USA)

  • N. Alice Yamada

    (Agilent Technologies, Santa Clara, California 95051, USA)

  • Peter Tsang

    (Agilent Technologies, Santa Clara, California 95051, USA)

  • Tera L. Newman

    (University of Washington, Seattle, Washington 98195, USA)

  • Eray Tüzün

    (University of Washington, Seattle, Washington 98195, USA)

  • Ze Cheng

    (University of Washington, Seattle, Washington 98195, USA)

  • Heather M. Ebling

    (Agencourt Bioscience Corporation, Beverly, Massachusetts 01915, USA)

  • Nadeem Tusneem

    (Agencourt Bioscience Corporation, Beverly, Massachusetts 01915, USA)

  • Robert David

    (Agencourt Bioscience Corporation, Beverly, Massachusetts 01915, USA)

  • Will Gillett

    (and University of Washington Genome Center, University of Washington, Seattle, Washington 98195, USA)

  • Karen A. Phelps

    (and University of Washington Genome Center, University of Washington, Seattle, Washington 98195, USA)

  • Molly Weaver

    (University of Washington, Seattle, Washington 98195, USA)

  • David Saranga

    (Agencourt Bioscience Corporation, Beverly, Massachusetts 01915, USA)

  • Adrianne Brand

    (Agencourt Bioscience Corporation, Beverly, Massachusetts 01915, USA)

  • Wei Tao

    (Agencourt Bioscience Corporation, Beverly, Massachusetts 01915, USA)

  • Erik Gustafson

    (Agencourt Bioscience Corporation, Beverly, Massachusetts 01915, USA)

  • Kevin McKernan

    (Agencourt Bioscience Corporation, Beverly, Massachusetts 01915, USA)

  • Lin Chen

    (University of Washington, Seattle, Washington 98195, USA)

  • Maika Malig

    (University of Washington, Seattle, Washington 98195, USA)

  • Joshua D. Smith

    (University of Washington, Seattle, Washington 98195, USA)

  • Joshua M. Korn

    (Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02114, USA)

  • Steven A. McCarroll

    (Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02114, USA)

  • David A. Altshuler

    (Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02114, USA)

  • Daniel A. Peiffer

    (Illumina, Inc., 9885 Towne Centre Drive, San Diego, California 92121, USA)

  • Michael Dorschner

    (University of Washington, Seattle, Washington 98195, USA)

  • John Stamatoyannopoulos

    (University of Washington, Seattle, Washington 98195, USA)

  • David Schwartz

    (Laboratory of Genetics, University of Wisconsin, Madison, Wisconsin 53706, USA)

  • Deborah A. Nickerson

    (University of Washington, Seattle, Washington 98195, USA)

  • James C. Mullikin

    (Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland 20892, USA)

  • Richard K. Wilson

    (Washington University Genome Sequencing Center, School of Medicine, St Louis, Missouri 63108, USA)

  • Laurakay Bruhn

    (Agilent Technologies, Santa Clara, California 95051, USA)

  • Maynard V. Olson

    (and University of Washington Genome Center, University of Washington, Seattle, Washington 98195, USA)

  • Rajinder Kaul

    (and University of Washington Genome Center, University of Washington, Seattle, Washington 98195, USA)

  • Douglas R. Smith

    (Agencourt Bioscience Corporation, Beverly, Massachusetts 01915, USA)

  • Evan E. Eichler

    (University of Washington, Seattle, Washington 98195, USA)

Abstract

Genetic variation among individual humans occurs on many different scales, ranging from gross alterations in the human karyotype to single nucleotide changes. Here we explore variation on an intermediate scale—particularly insertions, deletions and inversions affecting from a few thousand to a few million base pairs. We employed a clone-based method to interrogate this intermediate structural variation in eight individuals of diverse geographic ancestry. Our analysis provides a comprehensive overview of the normal pattern of structural variation present in these genomes, refining the location of 1,695 structural variants. We find that 50% were seen in more than one individual and that nearly half lay outside regions of the genome previously described as structurally variant. We discover 525 new insertion sequences that are not present in the human reference genome and show that many of these are variable in copy number between individuals. Complete sequencing of 261 structural variants reveals considerable locus complexity and provides insights into the different mutational processes that have shaped the human genome. These data provide the first high-resolution sequence map of human structural variation—a standard for genotyping platforms and a prelude to future individual genome sequencing projects.

Suggested Citation

  • Jeffrey M. Kidd & Gregory M. Cooper & William F. Donahue & Hillary S. Hayden & Nick Sampas & Tina Graves & Nancy Hansen & Brian Teague & Can Alkan & Francesca Antonacci & Eric Haugen & Troy Zerr & N. , 2008. "Mapping and sequencing of structural variation from eight human genomes," Nature, Nature, vol. 453(7191), pages 56-64, May.
    • Handle: RePEc:nat:nature:v:453:y:2008:i:7191:d:10.1038_nature06862
    DOI: 10.1038/nature06862
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    Cited by:

    1. Sandor Spisak & Viktoria Tisza & Pier Vitale Nuzzo & Ji-Heui Seo & Balint Pataki & Dezso Ribli & Zsofia Sztupinszki & Connor Bell & Mersedeh Rohanizadegan & David R. Stillman & Sarah Abou Alaiwi & Ala, 2023. "A biallelic multiple nucleotide length polymorphism explains functional causality at 5p15.33 prostate cancer risk locus," Nature Communications, Nature, vol. 14(1), pages 1-13, December.

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