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

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, Robert E. Handsaker, Susan Fairley, Zev N. Kronenberg, Xiangmeng Kong, Fereydoun Hormozdiari, Dillon Lee, Aaron M. Wenger, Alex R. Hastie, Danny Antaki, Thomas Anantharaman, Peter A. Audano, Harrison Brand, Stuart Cantsilieris, Han Cao, Eliza Cerveira, Chong Chen, Xintong Chen, Chen-Shan Chin, Zechen Chong, Nelson T. Chuang, Christine C. Lambert, Deanna M. Church, Laura Clarke, Andrew Farrell, Joey Flores, Timur Galeev, David U. Gorkin, Madhusudan Gujral, Victor Guryev, William Haynes Heaton, Jonas Korlach, Sushant Kumar, Jee Young Kwon, Ernest T. Lam, Jong Eun Lee, Joyce Lee, Wan-Ping Lee, Sau Peng Lee, Shantao Li, Patrick Marks, Karine Viaud-Martinez, Sascha Meiers, Katherine M. Munson, Fabio C. P. Navarro, Bradley J. Nelson, Conor Nodzak, Amina Noor, Sofia Kyriazopoulou-Panagiotopoulou, Andy W. C. Pang, Yunjiang Qiu, Gabriel Rosanio, Mallory Ryan, Adrian Stütz, Diana C. J. Spierings, Alistair Ward, AnneMarie E. Welch, Ming Xiao, Wei Xu, Chengsheng Zhang, Qihui Zhu, Xiangqun Zheng-Bradley, Ernesto Lowy, Sergei Yakneen, Steven McCarroll, Goo Jun, Li Ding, Chong Lek Koh, Bing Ren, Paul Flicek, Ken Chen, Mark B. Gerstein, Pui-Yan Kwok, Peter M. Lansdorp, Gabor T. Marth, Jonathan Sebat, Xinghua Shi, Ali Bashir, Kai Ye, Scott E. Devine, Michael E. Talkowski, Ryan E. Mills, Tobias Marschall, Jan O. Korbel (), Evan E. Eichler () and Charles Lee ()
Additional contact information
Mark J. P. Chaisson: University of Washington School of Medicine
Ashley D. Sanders: Genome Biology Unit
Xuefang Zhao: University of Michigan
Ankit Malhotra: The Jackson Laboratory for Genomic Medicine
David Porubsky: University of Groningen, University Medical Centre Groningen
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
Ryan L. Collins: 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
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
Fereydoun Hormozdiari: 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
David U. Gorkin: University of California San Diego
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
Jee Young Kwon: The Jackson Laboratory for Genomic Medicine
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
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
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
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
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
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
Pui-Yan Kwok: University of California–San Francisco
Peter M. Lansdorp: University of Groningen, University Medical Centre Groningen
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
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
Scott E. Devine: University of Maryland School of Medicine
Michael E. Talkowski: Harvard Medical School
Ryan E. Mills: University of Michigan
Tobias Marschall: Saarland University and the Max Planck Institute for Informatics
Jan O. Korbel: Genome Biology Unit
Evan E. Eichler: University of Washington School of Medicine
Charles Lee: The Jackson Laboratory for Genomic Medicine

Nature Communications, 2019, vol. 10, issue 1, 1-16

Abstract: 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 (

Date: 2019
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DOI: 10.1038/s41467-018-08148-z

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