Haplotype-resolved diverse human genomes and integrated analysis of structural variation

Peter Ebert; Peter A. Audano; Qihui Zhu; Bernardo Rodriguez-Martin; David Porubsky; Marc Jan Bonder; Arvis Sulovari; Jana Ebler; Weichen Zhou; Rebecca Serra Mari; Feyza Yilmaz; Xuefang Zhao; PingHsun Hsieh; Joyce Lee; Sushant Kumar; Jiadong Lin; Tobias Rausch; Yu Chen; Jingwen Ren; Martin Santamarina; Wolfram Höps; Hufsah Ashraf; Nelson T. Chuang; Xiaofei Yang; Katherine M. Munson; Alexandra P. Lewis; Susan Fairley; Luke J. Tallon; Wayne E. Clarke; Anna O. Basile; Marta Byrska-Bishop; André Corvelo; Uday S. Evani; Tsung-Yu Lu; Mark J. P. Chaisson; Junjie Chen; Chong Li; Harrison Brand; Aaron M. Wenger; Maryam Ghareghani; William T. Harvey; Benjamin Raeder; Patrick Hasenfeld; Allison A. Regier; Haley J. Abel; Ira M. Hall; Paul Flicek; Oliver Stegle; Mark B. Gerstein; Jose M. C. Tubio; Zepeng Mu; Yang I. Li; Xinghua Shi; Alex R. Hastie; Kai Ye; Zechen Chong; Ashley D. Sanders; Michael C. Zody; Michael E. Talkowski; Ryan E. Mills; Scott E. Devine; Charles Lee; Jan O. Korbel; Tobias Marschall; Evan E. Eichler

doi:10.1126/science.abf7117

Research Article

Haplotype-resolved diverse human genomes and integrated analysis of structural variation

View ORCID ProfilePeter Ebert¹,*,
View ORCID ProfilePeter A. Audano²,*,
View ORCID ProfileQihui Zhu³,*,
View ORCID ProfileBernardo Rodriguez-Martin⁴,*,
View ORCID ProfileDavid Porubsky²,
View ORCID ProfileMarc Jan Bonder⁴,⁵,
View ORCID ProfileArvis Sulovari²,
View ORCID ProfileJana Ebler¹,
View ORCID ProfileWeichen Zhou⁶,
View ORCID ProfileRebecca Serra Mari¹,
View ORCID ProfileFeyza Yilmaz³,
View ORCID ProfileXuefang Zhao⁷,⁸,
View ORCID ProfilePingHsun Hsieh ²,
View ORCID ProfileJoyce Lee⁹,
View ORCID ProfileSushant Kumar¹⁰,
View ORCID ProfileJiadong Lin¹¹,
View ORCID ProfileTobias Rausch⁴,
View ORCID ProfileYu Chen¹²,
Jingwen Ren¹³,
Martin Santamarina¹⁴,¹⁵,
Wolfram Höps⁴,
Hufsah Ashraf¹,
Nelson T. Chuang¹⁶,
View ORCID ProfileXiaofei Yang¹⁷,
View ORCID ProfileKatherine M. Munson²,
View ORCID ProfileAlexandra P. Lewis²,
View ORCID ProfileSusan Fairley¹⁸,
View ORCID ProfileLuke J. Tallon¹⁶,
Wayne E. Clarke ¹⁹,
View ORCID ProfileAnna O. Basile¹⁹,
View ORCID ProfileMarta Byrska-Bishop¹⁹,
View ORCID ProfileAndré Corvelo ¹⁹,
Uday S. Evani¹⁹,
View ORCID ProfileTsung-Yu Lu¹³,
Mark J. P. Chaisson ¹³,
View ORCID ProfileJunjie Chen²⁰,
Chong Li²⁰,
Harrison Brand⁷,⁸,
View ORCID ProfileAaron M. Wenger²¹,
Maryam Ghareghani²²,²³,¹,
View ORCID ProfileWilliam T. Harvey²,
View ORCID ProfileBenjamin Raeder⁴,
View ORCID ProfilePatrick Hasenfeld⁴,
View ORCID ProfileAllison A. Regier²⁴,
Haley J. Abel²⁴,
View ORCID ProfileIra M. Hall²⁵,
View ORCID ProfilePaul Flicek ¹⁸,
View ORCID ProfileOliver Stegle⁴,⁵,
View ORCID ProfileMark B. Gerstein ¹⁰,
View ORCID ProfileJose M. C. Tubio ¹⁴,¹⁵,
View ORCID ProfileZepeng Mu²⁶,
View ORCID ProfileYang I. Li ²⁷,
Xinghua Shi ²⁰,
View ORCID ProfileAlex R. Hastie⁹,
View ORCID ProfileKai Ye ¹¹,²⁸,
View ORCID ProfileZechen Chong ¹²,
View ORCID ProfileAshley D. Sanders⁴,
View ORCID ProfileMichael C. Zody ¹⁹,
View ORCID ProfileMichael E. Talkowski ⁷,⁸,
View ORCID ProfileRyan E. Mills ⁶,²⁸,
View ORCID ProfileScott E. Devine ¹⁶,
View ORCID ProfileCharles Lee ³,²⁹,³⁰,†,‡,
View ORCID ProfileJan O. Korbel ⁴,¹⁸,†,‡,
View ORCID ProfileTobias Marschall ¹,†,‡,
View ORCID ProfileEvan E. Eichler ²,³¹,†,‡

¹Heinrich Heine University, Medical Faculty, Institute for Medical Biometry and Bioinformatics, Moorenstraße 20, 40225 Düsseldorf, Germany.
²Department of Genome Sciences, University of Washington School of Medicine, 3720 15th Avenue NE, Seattle, WA 98195-5065, USA.
³The Jackson Laboratory for Genomic Medicine, 10 Discovery Drive, Farmington, CT 06032, USA.
⁴European Molecular Biology Laboratory (EMBL), Genome Biology Unit, Meyerhofstraße 1, 69117 Heidelberg, Germany.
⁵Division of Computational Genomics and Systems Genetics, German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany.
⁶Department of Computational Medicine and Bioinformatics, University of Michigan Medical School, 100 Washtenaw Avenue, Ann Arbor, MI 48109, USA.
⁷Center for Genomic Medicine, Massachusetts General Hospital, Department of Neurology, Harvard Medical School, Boston, MA 02114, USA.
⁸Program in Medical and Population Genetics and Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA.
⁹Bionano Genomics, San Diego, CA 92121, USA.
¹⁰Program in Computational Biology and Bioinformatics, Yale University, BASS 432 and 437, 266 Whitney Avenue, New Haven, CT 06520, USA.
¹¹School of Automation Science and Engineering, Faculty of Electronic and Information Engineering, Xi’an Jiaotong University, Xi’an, Shaanxi, 710049, China.
¹²Department of Genetics and Informatics Institute, School of Medicine, University of Alabama at Birmingham, Birmingham, AL 35294, USA.
¹³Department of Quantitative and Computational Biology, University of Southern California, Los Angeles, CA 90089, USA.
¹⁴Genomes and Disease, Centre for Research in Molecular Medicine and Chronic Diseases (CIMUS), Universidade de Santiago de Compostela, Santiago de Compostela, Spain.
¹⁵Department of Zoology, Genetics, and Physical Anthropology, Universidade de Santiago de Compostela, Santiago de Compostela, Spain.
¹⁶Institute for Genome Sciences, University of Maryland School of Medicine, 670 W Baltimore Street, Baltimore, MD 21201, USA.
¹⁷School of Computer Science and Technology, Faculty of Electronic and Information Engineering, Xi’an Jiaotong University, Xi’an, Shaanxi, 710049, China.
¹⁸European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK.
¹⁹New York Genome Center, New York, NY 10013, USA.
²⁰Department of Computer and Information Sciences, Temple University, Philadelphia, PA 19122, USA.
²¹Pacific Biosciences of California, Menlo Park, CA 94025, USA.
²²Max Planck Institute for Informatics, Saarland Informatics Campus E1.4, 66123 Saarbrücken, Germany.
²³Saarbrücken Graduate School of Computer Science, Saarland University, Saarland Informatics Campus E1.3, 66123 Saarbrücken, Germany.
²⁴Department of Medicine, Washington University, St. Louis, MO 63108, USA.
²⁵Department of Genetics, Yale School of Medicine, 333 Cedar Street, New Haven, CT 06510, USA.
²⁶Genetics, Genomics, and Systems Biology, University of Chicago, Chicago, IL 60637, USA.
²⁷Section of Genetic Medicine, Department of Medicine, University of Chicago, Chicago, IL 60637, USA.
²⁸Department of Human Genetics, University of Michigan, 1241 E. Catherine Street, Ann Arbor, MI 48109, USA.
²⁹Precision Medicine Center, The First Affiliated Hospital of Xi’an Jiaotong University, 277 West Yanta Road, Xi’an, 710061, Shaanxi, China.
³⁰Department of Graduate Studies–Life Sciences, Ewha Womans University, Ewhayeodae-gil, Seodaemun-gu, Seoul 120-750, South Korea.
³¹Howard Hughes Medical Institute, University of Washington, Seattle, WA 98195, USA.

↵‡Corresponding author. Email: eee{at}gs.washington.edu (E.E.E.); tobias.marschall{at}hhu.de (T.M.); jan.korbel{at}embl.org (J.O.K.); charles.lee{at}jax.org (C.L.)

↵* These authors contributed equally to this work.
↵† These authors contributed equally to this work.

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Science 02 Apr 2021:
Vol. 372, Issue 6537, eabf7117
DOI: 10.1126/science.abf7117

Peter Ebert

1Heinrich Heine University, Medical Faculty, Institute for Medical Biometry and Bioinformatics, Moorenstraße 20, 40225 Düsseldorf, Germany.

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Peter A. Audano

2Department of Genome Sciences, University of Washington School of Medicine, 3720 15th Avenue NE, Seattle, WA 98195-5065, USA.

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Qihui Zhu

3The Jackson Laboratory for Genomic Medicine, 10 Discovery Drive, Farmington, CT 06032, USA.

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Bernardo Rodriguez-Martin

4European Molecular Biology Laboratory (EMBL), Genome Biology Unit, Meyerhofstraße 1, 69117 Heidelberg, Germany.

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David Porubsky

2Department of Genome Sciences, University of Washington School of Medicine, 3720 15th Avenue NE, Seattle, WA 98195-5065, USA.

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Marc Jan Bonder

4European Molecular Biology Laboratory (EMBL), Genome Biology Unit, Meyerhofstraße 1, 69117 Heidelberg, Germany.

5Division of Computational Genomics and Systems Genetics, German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany.

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Arvis Sulovari

2Department of Genome Sciences, University of Washington School of Medicine, 3720 15th Avenue NE, Seattle, WA 98195-5065, USA.

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Jana Ebler

1Heinrich Heine University, Medical Faculty, Institute for Medical Biometry and Bioinformatics, Moorenstraße 20, 40225 Düsseldorf, Germany.

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Weichen Zhou

6Department of Computational Medicine and Bioinformatics, University of Michigan Medical School, 100 Washtenaw Avenue, Ann Arbor, MI 48109, USA.

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Rebecca Serra Mari

1Heinrich Heine University, Medical Faculty, Institute for Medical Biometry and Bioinformatics, Moorenstraße 20, 40225 Düsseldorf, Germany.

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Feyza Yilmaz

3The Jackson Laboratory for Genomic Medicine, 10 Discovery Drive, Farmington, CT 06032, USA.

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Xuefang Zhao

7Center for Genomic Medicine, Massachusetts General Hospital, Department of Neurology, Harvard Medical School, Boston, MA 02114, USA.

8Program in Medical and Population Genetics and Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA.

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PingHsun Hsieh

2Department of Genome Sciences, University of Washington School of Medicine, 3720 15th Avenue NE, Seattle, WA 98195-5065, USA.

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Joyce Lee

9Bionano Genomics, San Diego, CA 92121, USA.

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Sushant Kumar

10Program in Computational Biology and Bioinformatics, Yale University, BASS 432 and 437, 266 Whitney Avenue, New Haven, CT 06520, USA.

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Jiadong Lin

11School of Automation Science and Engineering, Faculty of Electronic and Information Engineering, Xi’an Jiaotong University, Xi’an, Shaanxi, 710049, China.

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Tobias Rausch

4European Molecular Biology Laboratory (EMBL), Genome Biology Unit, Meyerhofstraße 1, 69117 Heidelberg, Germany.

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Yu Chen

12Department of Genetics and Informatics Institute, School of Medicine, University of Alabama at Birmingham, Birmingham, AL 35294, USA.

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Jingwen Ren

13Department of Quantitative and Computational Biology, University of Southern California, Los Angeles, CA 90089, USA.

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Martin Santamarina

14Genomes and Disease, Centre for Research in Molecular Medicine and Chronic Diseases (CIMUS), Universidade de Santiago de Compostela, Santiago de Compostela, Spain.

15Department of Zoology, Genetics, and Physical Anthropology, Universidade de Santiago de Compostela, Santiago de Compostela, Spain.

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Wolfram Höps

4European Molecular Biology Laboratory (EMBL), Genome Biology Unit, Meyerhofstraße 1, 69117 Heidelberg, Germany.

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Hufsah Ashraf

1Heinrich Heine University, Medical Faculty, Institute for Medical Biometry and Bioinformatics, Moorenstraße 20, 40225 Düsseldorf, Germany.

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Nelson T. Chuang

16Institute for Genome Sciences, University of Maryland School of Medicine, 670 W Baltimore Street, Baltimore, MD 21201, USA.

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Xiaofei Yang

17School of Computer Science and Technology, Faculty of Electronic and Information Engineering, Xi’an Jiaotong University, Xi’an, Shaanxi, 710049, China.

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Katherine M. Munson

2Department of Genome Sciences, University of Washington School of Medicine, 3720 15th Avenue NE, Seattle, WA 98195-5065, USA.

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Alexandra P. Lewis

2Department of Genome Sciences, University of Washington School of Medicine, 3720 15th Avenue NE, Seattle, WA 98195-5065, USA.

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Susan Fairley

18European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK.

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Luke J. Tallon

16Institute for Genome Sciences, University of Maryland School of Medicine, 670 W Baltimore Street, Baltimore, MD 21201, USA.

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Wayne E. Clarke

19New York Genome Center, New York, NY 10013, USA.

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Anna O. Basile

19New York Genome Center, New York, NY 10013, USA.

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Marta Byrska-Bishop

19New York Genome Center, New York, NY 10013, USA.

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André Corvelo

19New York Genome Center, New York, NY 10013, USA.

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Uday S. Evani

19New York Genome Center, New York, NY 10013, USA.

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Tsung-Yu Lu

13Department of Quantitative and Computational Biology, University of Southern California, Los Angeles, CA 90089, USA.

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Mark J. P. Chaisson

13Department of Quantitative and Computational Biology, University of Southern California, Los Angeles, CA 90089, USA.

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Junjie Chen

20Department of Computer and Information Sciences, Temple University, Philadelphia, PA 19122, USA.

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Chong Li

20Department of Computer and Information Sciences, Temple University, Philadelphia, PA 19122, USA.

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Harrison Brand

7Center for Genomic Medicine, Massachusetts General Hospital, Department of Neurology, Harvard Medical School, Boston, MA 02114, USA.

8Program in Medical and Population Genetics and Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA.

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Aaron M. Wenger

21Pacific Biosciences of California, Menlo Park, CA 94025, USA.

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Maryam Ghareghani

22Max Planck Institute for Informatics, Saarland Informatics Campus E1.4, 66123 Saarbrücken, Germany.

23Saarbrücken Graduate School of Computer Science, Saarland University, Saarland Informatics Campus E1.3, 66123 Saarbrücken, Germany.

1Heinrich Heine University, Medical Faculty, Institute for Medical Biometry and Bioinformatics, Moorenstraße 20, 40225 Düsseldorf, Germany.

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William T. Harvey

2Department of Genome Sciences, University of Washington School of Medicine, 3720 15th Avenue NE, Seattle, WA 98195-5065, USA.

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Benjamin Raeder

4European Molecular Biology Laboratory (EMBL), Genome Biology Unit, Meyerhofstraße 1, 69117 Heidelberg, Germany.

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Patrick Hasenfeld

4European Molecular Biology Laboratory (EMBL), Genome Biology Unit, Meyerhofstraße 1, 69117 Heidelberg, Germany.

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Allison A. Regier

24Department of Medicine, Washington University, St. Louis, MO 63108, USA.

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Haley J. Abel

24Department of Medicine, Washington University, St. Louis, MO 63108, USA.

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Ira M. Hall

25Department of Genetics, Yale School of Medicine, 333 Cedar Street, New Haven, CT 06510, USA.

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Paul Flicek

18European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK.

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Oliver Stegle

4European Molecular Biology Laboratory (EMBL), Genome Biology Unit, Meyerhofstraße 1, 69117 Heidelberg, Germany.

5Division of Computational Genomics and Systems Genetics, German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany.

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Mark B. Gerstein

10Program in Computational Biology and Bioinformatics, Yale University, BASS 432 and 437, 266 Whitney Avenue, New Haven, CT 06520, USA.

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Jose M. C. Tubio

14Genomes and Disease, Centre for Research in Molecular Medicine and Chronic Diseases (CIMUS), Universidade de Santiago de Compostela, Santiago de Compostela, Spain.

15Department of Zoology, Genetics, and Physical Anthropology, Universidade de Santiago de Compostela, Santiago de Compostela, Spain.

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Zepeng Mu

26Genetics, Genomics, and Systems Biology, University of Chicago, Chicago, IL 60637, USA.

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Yang I. Li

27Section of Genetic Medicine, Department of Medicine, University of Chicago, Chicago, IL 60637, USA.

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Xinghua Shi

20Department of Computer and Information Sciences, Temple University, Philadelphia, PA 19122, USA.

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Alex R. Hastie

9Bionano Genomics, San Diego, CA 92121, USA.

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Kai Ye

11School of Automation Science and Engineering, Faculty of Electronic and Information Engineering, Xi’an Jiaotong University, Xi’an, Shaanxi, 710049, China.

28Department of Human Genetics, University of Michigan, 1241 E. Catherine Street, Ann Arbor, MI 48109, USA.

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Zechen Chong

12Department of Genetics and Informatics Institute, School of Medicine, University of Alabama at Birmingham, Birmingham, AL 35294, USA.

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Ashley D. Sanders

4European Molecular Biology Laboratory (EMBL), Genome Biology Unit, Meyerhofstraße 1, 69117 Heidelberg, Germany.

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Michael C. Zody

19New York Genome Center, New York, NY 10013, USA.

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Michael E. Talkowski

7Center for Genomic Medicine, Massachusetts General Hospital, Department of Neurology, Harvard Medical School, Boston, MA 02114, USA.

8Program in Medical and Population Genetics and Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA.

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Ryan E. Mills

6Department of Computational Medicine and Bioinformatics, University of Michigan Medical School, 100 Washtenaw Avenue, Ann Arbor, MI 48109, USA.

28Department of Human Genetics, University of Michigan, 1241 E. Catherine Street, Ann Arbor, MI 48109, USA.

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Scott E. Devine

16Institute for Genome Sciences, University of Maryland School of Medicine, 670 W Baltimore Street, Baltimore, MD 21201, USA.

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Charles Lee

3The Jackson Laboratory for Genomic Medicine, 10 Discovery Drive, Farmington, CT 06032, USA.

29Precision Medicine Center, The First Affiliated Hospital of Xi’an Jiaotong University, 277 West Yanta Road, Xi’an, 710061, Shaanxi, China.

30Department of Graduate Studies–Life Sciences, Ewha Womans University, Ewhayeodae-gil, Seodaemun-gu, Seoul 120-750, South Korea.

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For correspondence: eee@gs.washington.edu tobias.marschall@hhu.de jan.korbel@embl.org charles.lee@jax.org

Jan O. Korbel

4European Molecular Biology Laboratory (EMBL), Genome Biology Unit, Meyerhofstraße 1, 69117 Heidelberg, Germany.

18European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK.

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For correspondence: eee@gs.washington.edu tobias.marschall@hhu.de jan.korbel@embl.org charles.lee@jax.org

Tobias Marschall

1Heinrich Heine University, Medical Faculty, Institute for Medical Biometry and Bioinformatics, Moorenstraße 20, 40225 Düsseldorf, Germany.

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For correspondence: eee@gs.washington.edu tobias.marschall@hhu.de jan.korbel@embl.org charles.lee@jax.org

Evan E. Eichler

2Department of Genome Sciences, University of Washington School of Medicine, 3720 15th Avenue NE, Seattle, WA 98195-5065, USA.

31Howard Hughes Medical Institute, University of Washington, Seattle, WA 98195, USA.

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For correspondence: eee@gs.washington.edu tobias.marschall@hhu.de jan.korbel@embl.org charles.lee@jax.org

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