Nature Communications (Apr 2019)
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,
- Charles Lee
Affiliations
- Mark J. P. Chaisson
- Department of Genome Sciences, University of Washington School of Medicine
- Ashley D. Sanders
- European Molecular Biology Laboratory, Genome Biology Unit
- Xuefang Zhao
- Department of Computational Medicine and Bioinformatics, University of Michigan
- Ankit Malhotra
- The Jackson Laboratory for Genomic Medicine
- David Porubsky
- European Research Institute for the Biology of Ageing, University of Groningen, University Medical Centre Groningen
- Tobias Rausch
- European Molecular Biology Laboratory, Genome Biology Unit
- Eugene J. Gardner
- Institute for Genome Sciences, University of Maryland School of Medicine
- Oscar L. Rodriguez
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai
- Li Guo
- The School of Life Science and Technology of Xi’an Jiaotong University
- Ryan L. Collins
- Center for Genomic Medicine, Massachusetts General Hospital, Department of Neurology, Harvard Medical School
- Xian Fan
- Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center
- Jia Wen
- Department of Bioinformatics and Genomics, College of Computing and Informatics, The University of North Carolina at Charlotte
- Robert E. Handsaker
- Department of Genetics, Harvard Medical School
- Susan Fairley
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton
- Zev N. Kronenberg
- Department of Genome Sciences, University of Washington School of Medicine
- Xiangmeng Kong
- Yale University Medical School, Computational Biology and Bioinformatics Program
- Fereydoun Hormozdiari
- Biochemistry and Molecular Medicine, University of California Davis
- Dillon Lee
- USTAR Center for Genetic Discovery and Department of Human Genetics, 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
- Department of Genome Sciences, University of Washington School of Medicine
- Harrison Brand
- Center for Genomic Medicine, Massachusetts General Hospital, Department of Neurology, Harvard Medical School
- Stuart Cantsilieris
- Department of Genome Sciences, University of Washington School of Medicine
- Han Cao
- Bionano Genomics
- Eliza Cerveira
- The Jackson Laboratory for Genomic Medicine
- Chong Chen
- Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center
- Xintong Chen
- Institute for Genome Sciences, University of Maryland School of Medicine
- Chen-Shan Chin
- Pacific Biosciences
- Zechen Chong
- Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center
- Nelson T. Chuang
- Institute for Genome Sciences, University of Maryland School of Medicine
- Christine C. Lambert
- Pacific Biosciences
- Deanna M. Church
- 10X Genomics
- Laura Clarke
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton
- Andrew Farrell
- USTAR Center for Genetic Discovery and Department of Human Genetics, University of Utah School of Medicine
- Joey Flores
- Illumina Clinical Services Laboratory, Illumina, Inc.
- Timur Galeev
- Yale University Medical School, Computational Biology and Bioinformatics Program
- David U. Gorkin
- Department of Cellular and Molecular Medicine, University of California San Diego
- Madhusudan Gujral
- Beyster Center for Genomics of Psychiatric Diseases, Department of Psychiatry University of California San Diego
- Victor Guryev
- European Research Institute for the Biology of Ageing, 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 Clinical Services Laboratory, Illumina, Inc.
- Sascha Meiers
- European Molecular Biology Laboratory, Genome Biology Unit
- Katherine M. Munson
- Department of Genome Sciences, University of Washington School of Medicine
- Fabio C. P. Navarro
- Yale University Medical School, Computational Biology and Bioinformatics Program
- Bradley J. Nelson
- Department of Genome Sciences, University of Washington School of Medicine
- Conor Nodzak
- Department of Bioinformatics and Genomics, College of Computing and Informatics, 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
- European Molecular Biology Laboratory, Genome Biology Unit
- Diana C. J. Spierings
- European Research Institute for the Biology of Ageing, University of Groningen, University Medical Centre Groningen
- Alistair Ward
- USTAR Center for Genetic Discovery and Department of Human Genetics, University of Utah School of Medicine
- AnneMarie E. Welch
- Department of Genome Sciences, University of Washington School of Medicine
- Ming Xiao
- School of Biomedical Engineering, 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
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton
- Ernesto Lowy
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton
- Sergei Yakneen
- European Molecular Biology Laboratory, Genome Biology Unit
- Steven McCarroll
- Department of Genetics, Harvard Medical School
- Goo Jun
- Human Genetics Center, School of Public Health, The University of Texas Health Science Center at Houston
- Li Ding
- Department of Medicine, McDonnell Genome Institute, Siteman Cancer Center, Washington University School of Medicine
- Chong Lek Koh
- High Impact Research, University of Malaya
- Bing Ren
- Department of Cellular and Molecular Medicine, University of California San Diego
- Paul Flicek
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton
- Ken Chen
- Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center
- Mark B. Gerstein
- Yale University Medical School, Computational Biology and Bioinformatics Program
- Pui-Yan Kwok
- Institute for Human Genetics, University of California–San Francisco
- Peter M. Lansdorp
- European Research Institute for the Biology of Ageing, University of Groningen, University Medical Centre Groningen
- Gabor T. Marth
- USTAR Center for Genetic Discovery and Department of Human Genetics, 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
- Department of Bioinformatics and Genomics, College of Computing and Informatics, The University of North Carolina at Charlotte
- Ali Bashir
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai
- Kai Ye
- MOE Key Lab for Intelligent Networks & Networks Security, School of Electronics and Information Engineering, Xi’an Jiaotong University
- Scott E. Devine
- Institute for Genome Sciences, University of Maryland School of Medicine
- Michael E. Talkowski
- Center for Genomic Medicine, Massachusetts General Hospital, Department of Neurology, Harvard Medical School
- Ryan E. Mills
- Department of Computational Medicine and Bioinformatics, University of Michigan
- Tobias Marschall
- Center for Bioinformatics, Saarland University and the Max Planck Institute for Informatics
- Jan O. Korbel
- European Molecular Biology Laboratory, Genome Biology Unit
- Evan E. Eichler
- Department of Genome Sciences, University of Washington School of Medicine
- Charles Lee
- The Jackson Laboratory for Genomic Medicine
- DOI
- https://doi.org/10.1038/s41467-018-08148-z
- Journal volume & issue
-
Vol. 10,
no. 1
pp. 1 – 16
Abstract
Structural variants (SVs) in human genomes contribute diversity and diseases. Here, the authors use a multi-platform strategy to generate haplotype-resolved SVs for three human parent–child trios.
