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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 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 Hastie, Danny Antaki, Peter Audano, Harrison Brand, Stuart Cantsilieris, Han Cao, Eliza Cerveira, Chong Chen, Xintong Chen, Chen-Shan Chin, Zechen Chong, Nelson T. Chuang, Deanna M. Church, Laura Clarke, Andrew Farrell, Joey Flores, Timur Galeev, David Gorkin, Madhusudan Gujral, Victor Guryev, William Haynes Heaton, Jonas Korlach, Sushant Kumar, Jee Young Kwon, Jong Eun Lee, Joyce Lee, Wan-Ping Lee, Sau Peng Lee, Patrick Marks, Karine Viaud-Martinez, Sascha Meiers, Katherine M. Munson, Fabio Navarro, Bradley J. Nelson, Conor Nodzak, Amina Noor, Sofia Kyriazopoulou-Panagiotopoulou, Andy 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, Goo Jun, Li Ding, Chong Lek Koh, Bing Ren, Paul Flicek, Ken Chen, Mark B. Gerstein, Pui-Yan Kwok, Peter M. Lansdorp, Gabor Marth, Jonathan Sebat, Xinghua Shi, Ali Bashir, Kai Ye, Scott E. Devine, Michael Talkowski, Ryan E. Mills, Tobias Marschall, Jan Korbel, Evan E. Eichler, Charles Lee
doi: https://doi.org/10.1101/193144
Mark J.P. Chaisson
1Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA 98195
2Molecular and Computational Biology, University of Southern California, Los Angeles, CA 90089
Ashley D. Sanders
3European Molecular Biology Laboratory, Genome Biology Unit, Heidelberg, Germany
Xuefang Zhao
4Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI 48109
5Center for Genomic Medicine, Massachusetts General Hospital, Department of Neurology, Harvard Medical School, Boston, MA 02114
Ankit Malhotra
6The Jackson Laboratory for Genomic Medicine, Farmington, CT 06032
David Porubsky
7European Research Institute for the Biology of Ageing, University of Groningen, University Medical Centre Groningen, NL-9713 AV Groningen, The Netherlands
8Center for Bioinformatics, Saarland University, Saarbrücken, Germany
Tobias Rausch
3European Molecular Biology Laboratory, Genome Biology Unit, Heidelberg, Germany
Eugene J. Gardner
9Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, Maryland 21201
Oscar Rodriguez
10Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York
Li Guo
11Xi’an Jiao Tong University, Shaanxi, China
Ryan L. Collins
5Center for Genomic Medicine, Massachusetts General Hospital, Department of Neurology, Harvard Medical School, Boston, MA 02114
12Program in Bioinformatics and Integrative Genomics, Harvard Medical School, Boston, MA
Xian Fan
13The University of Texas MD Anderson Cancer Center, Houston, TX 77030
Jia Wen
14Department of Bioinformatics and Genomics, College of Computing and Informatics, University of North Carolina, Charlotte, Charlotte, NC 28223
Robert E. Handsaker
15Stanley Center for Psychiatric Research; Harvard Medical School, Department of Genetics MA 02115
Susan Fairley
16European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD, United Kingdom
Zev N. Kronenberg
1Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA 98195
Xiangmeng Kong
17Yale University Medical School, Computational Biology and Bioinformatics Program, New Haven, Connecticut 06520
Fereydoun Hormozdiari
18Biochemistry and Molecular Medicine, University of California Davis, Davis, CA 95616
19UC Davis Genome Center, University of California, Davis, Davis, CA 95616
Dillon Lee
20USTAR Center for Genetic Discovery & Department of Human Genetics, University of Utah School of Medicine, Salt Lake City, Utah 84112
Aaron M. Wenger
21Pacific Biosciences, Menlo Park, CA 94025
Alex Hastie
22BioNano Genomics, San Diego, CA 92121
Danny Antaki
23Beyster Center for Genomics of Psychiatric Diseases, Department of Psychiatry University of California San Diego, La Jolla, CA 92093
Peter Audano
1Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA 98195
Harrison Brand
5Center for Genomic Medicine, Massachusetts General Hospital, Department of Neurology, Harvard Medical School, Boston, MA 02114
Stuart Cantsilieris
1Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA 98195
Han Cao
22BioNano Genomics, San Diego, CA 92121
Eliza Cerveira
6The Jackson Laboratory for Genomic Medicine, Farmington, CT 06032
Chong Chen
13The University of Texas MD Anderson Cancer Center, Houston, TX 77030
Xintong Chen
9Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, Maryland 21201
Chen-Shan Chin
21Pacific Biosciences, Menlo Park, CA 94025
Zechen Chong
13The University of Texas MD Anderson Cancer Center, Houston, TX 77030
Nelson T. Chuang
9Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, Maryland 21201
Deanna M. Church
2510X Genomics, Pleasanton, CA 94566
Laura Clarke
16European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD, United Kingdom
Andrew Farrell
20USTAR Center for Genetic Discovery & Department of Human Genetics, University of Utah School of Medicine, Salt Lake City, Utah 84112
Joey Flores
26Illumina Clinical Services Laboratory, Illumina, Inc., 5200 Illumina Way, San Diego CA 92122, USA
Timur Galeev
17Yale University Medical School, Computational Biology and Bioinformatics Program, New Haven, Connecticut 06520
David Gorkin
34Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA 92093
35Ludwig Institute for Cancer Research, 9500 Gilman Drive, La Jolla, CA 92093
Madhusudan Gujral
23Beyster Center for Genomics of Psychiatric Diseases, Department of Psychiatry University of California San Diego, La Jolla, CA 92093
Victor Guryev
7European Research Institute for the Biology of Ageing, University of Groningen, University Medical Centre Groningen, NL-9713 AV Groningen, The Netherlands
William Haynes Heaton
2510X Genomics, Pleasanton, CA 94566
Jonas Korlach
21Pacific Biosciences, Menlo Park, CA 94025
Sushant Kumar
17Yale University Medical School, Computational Biology and Bioinformatics Program, New Haven, Connecticut 06520
Jee Young Kwon
6The Jackson Laboratory for Genomic Medicine, Farmington, CT 06032
Jong Eun Lee
27DNA Link, Seodaemun-gu, Seoul, Korea
Joyce Lee
22BioNano Genomics, San Diego, CA 92121
Wan-Ping Lee
6The Jackson Laboratory for Genomic Medicine, Farmington, CT 06032
Sau Peng Lee
30TreeCode Sdn Bhd, Bandar Botanic, 41200 Klang, Malaysia
Patrick Marks
2510X Genomics, Pleasanton, CA 94566
Karine Viaud-Martinez
26Illumina Clinical Services Laboratory, Illumina, Inc., 5200 Illumina Way, San Diego CA 92122, USA
Sascha Meiers
3European Molecular Biology Laboratory, Genome Biology Unit, Heidelberg, Germany
Katherine M. Munson
1Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA 98195
Fabio Navarro
17Yale University Medical School, Computational Biology and Bioinformatics Program, New Haven, Connecticut 06520
Bradley J. Nelson
1Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA 98195
Conor Nodzak
14Department of Bioinformatics and Genomics, College of Computing and Informatics, University of North Carolina, Charlotte, Charlotte, NC 28223
Amina Noor
23Beyster Center for Genomics of Psychiatric Diseases, Department of Psychiatry University of California San Diego, La Jolla, CA 92093
Sofia Kyriazopoulou-Panagiotopoulou
2510X Genomics, Pleasanton, CA 94566
Andy Pang
2510X Genomics, Pleasanton, CA 94566
Yunjiang Qiu
24Bioinformatics and Systems Biology Graduate Program, University of California, San Diego, La Jolla, CA 92093
27DNA Link, Seodaemun-gu, Seoul, Korea
Gabriel Rosanio
23Beyster Center for Genomics of Psychiatric Diseases, Department of Psychiatry University of California San Diego, La Jolla, CA 92093
Mallory Ryan
6The Jackson Laboratory for Genomic Medicine, Farmington, CT 06032
Adrian Stütz
3European Molecular Biology Laboratory, Genome Biology Unit, Heidelberg, Germany
Diana C.J. Spierings
7European Research Institute for the Biology of Ageing, University of Groningen, University Medical Centre Groningen, NL-9713 AV Groningen, The Netherlands
Alistair Ward
20USTAR Center for Genetic Discovery & Department of Human Genetics, University of Utah School of Medicine, Salt Lake City, Utah 84112
AnneMarie E. Welch
1Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA 98195
Ming Xiao
31School of Biomedical Engineering, Drexel University, Philadelphia, PA 19104
Wei Xu
2510X Genomics, Pleasanton, CA 94566
Chengsheng Zhang
6The Jackson Laboratory for Genomic Medicine, Farmington, CT 06032
Qihui Zhu
6The Jackson Laboratory for Genomic Medicine, Farmington, CT 06032
Xiangqun Zheng-Bradley
16European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD, United Kingdom
Goo Jun
32Human Genetics Center, School of Public Health, The University of Texas Health Science Center at Houston, Houston, TX 77225
Li Ding
33Department of Medicine, McDonnell Genome Institute, Siteman Cancer Center, Washington University School of Medicine, St. Louis, Missouri 63108
Chong Lek Koh
29High Impact Research, University of Malaya, 50603 Kuala Lumpur, Malaysia
Bing Ren
34Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA 92093
35Ludwig Institute for Cancer Research, 9500 Gilman Drive, La Jolla, CA 92093
Paul Flicek
16European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD, United Kingdom
Ken Chen
13The University of Texas MD Anderson Cancer Center, Houston, TX 77030
Mark B. Gerstein
35Ludwig Institute for Cancer Research, 9500 Gilman Drive, La Jolla, CA 92093
36Department of Molecular Biophysics and Biochemistry, School of Medicine, Yale University, New Haven, CT 06520
Pui-Yan Kwok
37Department of Computer Science, Yale University, New Haven, CT 06511
Peter M. Lansdorp
7European Research Institute for the Biology of Ageing, University of Groningen, University Medical Centre Groningen, NL-9713 AV Groningen, The Netherlands
38Institute for Human Genetics, University of California–San Francisco, San Francisco, California
39Terry Fox Laboratory, BC Cancer Agency, Vancouver, BC V5Z 1L3, Canada
Gabor Marth
20USTAR Center for Genetic Discovery & Department of Human Genetics, University of Utah School of Medicine, Salt Lake City, Utah 84112
Jonathan Sebat
23Beyster Center for Genomics of Psychiatric Diseases, Department of Psychiatry University of California San Diego, La Jolla, CA 92093
28Department of Pediatrics, University of California San Diego, La Jolla, CA 92093, Ludwig Institute for Cancer Research, La Jolla, CA 92093
34Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA 92093
Xinghua Shi
14Department of Bioinformatics and Genomics, College of Computing and Informatics, University of North Carolina, Charlotte, Charlotte, NC 28223
Ali Bashir
10Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York
Kai Ye
13The University of Texas MD Anderson Cancer Center, Houston, TX 77030
Scott E. Devine
9Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, Maryland 21201
Michael Talkowski
5Center for Genomic Medicine, Massachusetts General Hospital, Department of Neurology, Harvard Medical School, Boston, MA 02114
41Molecular Neurogenetics Unit and Psychiatric and Neurodevelopmental Genetics Unit, Center for Human Genetic Research, Massachusetts General Hospital, Boston, MA 02114
42Department of Neurology, Massachusetts General Hospital and Harvard Medical School, Boston, MA 02114
43Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA 02142
44Center for Mendelian Genomics, Broad Institute of MIT and Harvard, Cambridge, MA 02142
Ryan E. Mills
4Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI 48109
45Department of Human Genetics, University of Michigan, Ann Arbor, MI 48109
Tobias Marschall
8Center for Bioinformatics, Saarland University, Saarbrücken, Germany
Jan Korbel
3European Molecular Biology Laboratory, Genome Biology Unit, Heidelberg, Germany
18Biochemistry and Molecular Medicine, University of California Davis, Davis, CA 95616
Evan E. Eichler
1Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA 98195
46Howard Hughes Medical Institute, University of Washington, Seattle, WA 98195
Charles Lee
6The Jackson Laboratory for Genomic Medicine, Farmington, CT 06032
47Department of Graduate Studies – Life Sciences, Ewha Womans University, Ewhayeodae-gil, Seodaemun-gu, Seoul, South Korea 120-750
Posted September 23, 2017.
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 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 Hastie, Danny Antaki, Peter Audano, Harrison Brand, Stuart Cantsilieris, Han Cao, Eliza Cerveira, Chong Chen, Xintong Chen, Chen-Shan Chin, Zechen Chong, Nelson T. Chuang, Deanna M. Church, Laura Clarke, Andrew Farrell, Joey Flores, Timur Galeev, David Gorkin, Madhusudan Gujral, Victor Guryev, William Haynes Heaton, Jonas Korlach, Sushant Kumar, Jee Young Kwon, Jong Eun Lee, Joyce Lee, Wan-Ping Lee, Sau Peng Lee, Patrick Marks, Karine Viaud-Martinez, Sascha Meiers, Katherine M. Munson, Fabio Navarro, Bradley J. Nelson, Conor Nodzak, Amina Noor, Sofia Kyriazopoulou-Panagiotopoulou, Andy 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, Goo Jun, Li Ding, Chong Lek Koh, Bing Ren, Paul Flicek, Ken Chen, Mark B. Gerstein, Pui-Yan Kwok, Peter M. Lansdorp, Gabor Marth, Jonathan Sebat, Xinghua Shi, Ali Bashir, Kai Ye, Scott E. Devine, Michael Talkowski, Ryan E. Mills, Tobias Marschall, Jan Korbel, Evan E. Eichler, Charles Lee
bioRxiv 193144; doi: https://doi.org/10.1101/193144
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 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 Hastie, Danny Antaki, Peter Audano, Harrison Brand, Stuart Cantsilieris, Han Cao, Eliza Cerveira, Chong Chen, Xintong Chen, Chen-Shan Chin, Zechen Chong, Nelson T. Chuang, Deanna M. Church, Laura Clarke, Andrew Farrell, Joey Flores, Timur Galeev, David Gorkin, Madhusudan Gujral, Victor Guryev, William Haynes Heaton, Jonas Korlach, Sushant Kumar, Jee Young Kwon, Jong Eun Lee, Joyce Lee, Wan-Ping Lee, Sau Peng Lee, Patrick Marks, Karine Viaud-Martinez, Sascha Meiers, Katherine M. Munson, Fabio Navarro, Bradley J. Nelson, Conor Nodzak, Amina Noor, Sofia Kyriazopoulou-Panagiotopoulou, Andy 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, Goo Jun, Li Ding, Chong Lek Koh, Bing Ren, Paul Flicek, Ken Chen, Mark B. Gerstein, Pui-Yan Kwok, Peter M. Lansdorp, Gabor Marth, Jonathan Sebat, Xinghua Shi, Ali Bashir, Kai Ye, Scott E. Devine, Michael Talkowski, Ryan E. Mills, Tobias Marschall, Jan Korbel, Evan E. Eichler, Charles Lee
bioRxiv 193144; doi: https://doi.org/10.1101/193144
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