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Multi-platform discovery of haplotype-resolved structural variation in human genomes

Author

Listed:
  • Mark J. P. Chaisson

    (University of Washington School of Medicine
    University of Southern California)

  • Ashley D. Sanders

    (Genome Biology Unit)

  • Xuefang Zhao

    (University of Michigan
    Harvard Medical School)

  • Ankit Malhotra

    (The Jackson Laboratory for Genomic Medicine)

  • David Porubsky

    (University of Groningen, University Medical Centre Groningen
    Saarland University and the Max Planck Institute for Informatics)

  • Tobias Rausch

    (Genome Biology Unit)

  • Eugene J. Gardner

    (University of Maryland School of Medicine)

  • Oscar L. Rodriguez

    (Icahn School of Medicine at Mount Sinai)

  • Li Guo

    (The School of Life Science and Technology of Xi’an Jiaotong University
    School of Electronics and Information Engineering, Xi’an Jiaotong University
    Xi’an Jiaotong University)

  • Ryan L. Collins

    (Harvard Medical School
    Harvard Medical School)

  • Xian Fan

    (The University of Texas MD Anderson Cancer Center)

  • Jia Wen

    (The University of North Carolina at Charlotte)

  • Robert E. Handsaker

    (Harvard Medical School
    Broad Institute of MIT and Harvard
    Broad Institute of MIT and Harvard)

  • Susan Fairley

    (Wellcome Genome Campus, Hinxton)

  • Zev N. Kronenberg

    (University of Washington School of Medicine)

  • Xiangmeng Kong

    (Yale University Medical School, Computational Biology and Bioinformatics Program
    Yale University)

  • Fereydoun Hormozdiari

    (University of California Davis
    University of California, Davis)

  • Dillon Lee

    (University of Utah School of Medicine)

  • Aaron M. Wenger

    (Pacific Biosciences)

  • Alex R. Hastie

    (Bionano Genomics)

  • Danny Antaki

    (Beyster Center for Genomics of Psychiatric Diseases, Department of Psychiatry University of California San Diego)

  • Thomas Anantharaman

    (Bionano Genomics)

  • Peter A. Audano

    (University of Washington School of Medicine)

  • Harrison Brand

    (Harvard Medical School)

  • Stuart Cantsilieris

    (University of Washington School of Medicine)

  • Han Cao

    (Bionano Genomics)

  • Eliza Cerveira

    (The Jackson Laboratory for Genomic Medicine)

  • Chong Chen

    (The University of Texas MD Anderson Cancer Center)

  • Xintong Chen

    (University of Maryland School of Medicine)

  • Chen-Shan Chin

    (Pacific Biosciences)

  • Zechen Chong

    (The University of Texas MD Anderson Cancer Center)

  • Nelson T. Chuang

    (University of Maryland School of Medicine)

  • Christine C. Lambert

    (Pacific Biosciences)

  • Deanna M. Church

    (10X Genomics)

  • Laura Clarke

    (Wellcome Genome Campus, Hinxton)

  • Andrew Farrell

    (University of Utah School of Medicine)

  • Joey Flores

    (Illumina, Inc.)

  • Timur Galeev

    (Yale University Medical School, Computational Biology and Bioinformatics Program
    Yale University)

  • David U. Gorkin

    (University of California San Diego
    Ludwig Institute for Cancer Research)

  • Madhusudan Gujral

    (Beyster Center for Genomics of Psychiatric Diseases, Department of Psychiatry University of California San Diego)

  • Victor Guryev

    (University of Groningen, University Medical Centre Groningen)

  • William Haynes Heaton

    (10X Genomics)

  • Jonas Korlach

    (Pacific Biosciences)

  • Sushant Kumar

    (Yale University Medical School, Computational Biology and Bioinformatics Program
    Yale University)

  • Jee Young Kwon

    (The Jackson Laboratory for Genomic Medicine
    Ewha Womans University)

  • Ernest T. Lam

    (Bionano Genomics)

  • Jong Eun Lee

    (DNA Link, Seodaemun-gu)

  • Joyce Lee

    (Bionano Genomics)

  • Wan-Ping Lee

    (The Jackson Laboratory for Genomic Medicine)

  • Sau Peng Lee

    (TreeCode Sdn Bhd, Bandar Botanic)

  • Shantao Li

    (Yale University Medical School, Computational Biology and Bioinformatics Program
    Yale University)

  • Patrick Marks

    (10X Genomics)

  • Karine Viaud-Martinez

    (Illumina, Inc.)

  • Sascha Meiers

    (Genome Biology Unit)

  • Katherine M. Munson

    (University of Washington School of Medicine)

  • Fabio C. P. Navarro

    (Yale University Medical School, Computational Biology and Bioinformatics Program
    Yale University)

  • Bradley J. Nelson

    (University of Washington School of Medicine)

  • Conor Nodzak

    (The University of North Carolina at Charlotte)

  • Amina Noor

    (Beyster Center for Genomics of Psychiatric Diseases, Department of Psychiatry University of California San Diego)

  • Sofia Kyriazopoulou-Panagiotopoulou

    (10X Genomics)

  • Andy W. C. Pang

    (Bionano Genomics)

  • Yunjiang Qiu

    (Ludwig Institute for Cancer Research
    University of California, San Diego)

  • Gabriel Rosanio

    (Beyster Center for Genomics of Psychiatric Diseases, Department of Psychiatry University of California San Diego)

  • Mallory Ryan

    (The Jackson Laboratory for Genomic Medicine)

  • Adrian Stütz

    (Genome Biology Unit)

  • Diana C. J. Spierings

    (University of Groningen, University Medical Centre Groningen)

  • Alistair Ward

    (University of Utah School of Medicine)

  • AnneMarie E. Welch

    (University of Washington School of Medicine)

  • Ming Xiao

    (Drexel University)

  • Wei Xu

    (10X Genomics)

  • Chengsheng Zhang

    (The Jackson Laboratory for Genomic Medicine)

  • Qihui Zhu

    (The Jackson Laboratory for Genomic Medicine)

  • Xiangqun Zheng-Bradley

    (Wellcome Genome Campus, Hinxton)

  • Ernesto Lowy

    (Wellcome Genome Campus, Hinxton)

  • Sergei Yakneen

    (Genome Biology Unit)

  • Steven McCarroll

    (Harvard Medical School
    Broad Institute of MIT and Harvard
    Broad Institute of MIT and Harvard)

  • Goo Jun

    (The University of Texas Health Science Center at Houston)

  • Li Ding

    (Washington University School of Medicine)

  • Chong Lek Koh

    (University of Malaya)

  • Bing Ren

    (University of California San Diego
    Ludwig Institute for Cancer Research)

  • Paul Flicek

    (Wellcome Genome Campus, Hinxton)

  • Ken Chen

    (The University of Texas MD Anderson Cancer Center)

  • Mark B. Gerstein

    (Yale University Medical School, Computational Biology and Bioinformatics Program
    Yale University
    Yale University
    Yale University)

  • Pui-Yan Kwok

    (University of California–San Francisco)

  • Peter M. Lansdorp

    (University of Groningen, University Medical Centre Groningen
    BC Cancer Agency
    University of British Columbia)

  • Gabor T. Marth

    (University of Utah School of Medicine)

  • Jonathan Sebat

    (Beyster Center for Genomics of Psychiatric Diseases, Department of Psychiatry University of California San Diego
    University of California San Diego
    University of California San Diego)

  • Xinghua Shi

    (The University of North Carolina at Charlotte)

  • Ali Bashir

    (Icahn School of Medicine at Mount Sinai)

  • Kai Ye

    (School of Electronics and Information Engineering, Xi’an Jiaotong University
    Xi’an Jiaotong University
    The First Affiliated Hospital of Xi’an Jiaotong University)

  • Scott E. Devine

    (University of Maryland School of Medicine)

  • Michael E. Talkowski

    (Harvard Medical School
    Broad Institute of MIT and Harvard
    Broad Institute of MIT and Harvard)

  • Ryan E. Mills

    (University of Michigan
    University of Michigan)

  • Tobias Marschall

    (Saarland University and the Max Planck Institute for Informatics)

  • Jan O. Korbel

    (Genome Biology Unit
    Wellcome Genome Campus, Hinxton)

  • Evan E. Eichler

    (University of Washington School of Medicine
    University of Washington)

  • Charles Lee

    (The Jackson Laboratory for Genomic Medicine
    Ewha Womans University)

Abstract

The incomplete identification of structural variants (SVs) from whole-genome sequencing data limits studies of human genetic diversity and disease association. Here, we apply a suite of long-read, short-read, strand-specific sequencing technologies, optical mapping, and variant discovery algorithms to comprehensively analyze three trios to define the full spectrum of human genetic variation in a haplotype-resolved manner. We identify 818,054 indel variants (

Suggested Citation

  • Mark J. P. Chaisson & Ashley D. Sanders & Xuefang Zhao & Ankit Malhotra & David Porubsky & Tobias Rausch & Eugene J. Gardner & Oscar L. Rodriguez & Li Guo & Ryan L. Collins & Xian Fan & Jia Wen & Robe, 2019. "Multi-platform discovery of haplotype-resolved structural variation in human genomes," Nature Communications, Nature, vol. 10(1), pages 1-16, December.
    • Handle: RePEc:nat:natcom:v:10:y:2019:i:1:d:10.1038_s41467-018-08148-z
    DOI: 10.1038/s41467-018-08148-z
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