About the Authors
- Malachi Griffith
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* E-mail: mgriffit@genome.wustl.edu (MG); ogriffit@genome.wustl.edu (OLG)
¶‡ These authors contributed equally and are listed in alphabetical order.
Affiliations The Genome Institute, Washington University in St. Louis, St. Louis, Missouri, United States of America, Department of Genetics, Washington University School of Medicine, St. Louis, Missouri, United States of America
- Obi L. Griffith
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* E-mail: mgriffit@genome.wustl.edu (MG); ogriffit@genome.wustl.edu (OLG)
¶‡ These authors contributed equally and are listed in alphabetical order.
Affiliations The Genome Institute, Washington University in St. Louis, St. Louis, Missouri, United States of America, Department of Medicine, Washington University School of Medicine, St. Louis, Missouri, United States of America
- Scott M. Smith
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Current address: Counsyl Inc., South San Francisco, United States of America
¶‡ These authors contributed equally and are listed in alphabetical order.
Affiliation The Genome Institute, Washington University in St. Louis, St. Louis, Missouri, United States of America
- Avinash Ramu
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Affiliation The Genome Institute, Washington University in St. Louis, St. Louis, Missouri, United States of America
- Matthew B. Callaway
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Affiliation The Genome Institute, Washington University in St. Louis, St. Louis, Missouri, United States of America
- Anthony M. Brummett
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Affiliation The Genome Institute, Washington University in St. Louis, St. Louis, Missouri, United States of America
- Michael J. Kiwala
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Affiliation The Genome Institute, Washington University in St. Louis, St. Louis, Missouri, United States of America
- Adam C. Coffman
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Affiliation The Genome Institute, Washington University in St. Louis, St. Louis, Missouri, United States of America
- Allison A. Regier
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Affiliation The Genome Institute, Washington University in St. Louis, St. Louis, Missouri, United States of America
- Ben J. Oberkfell
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Affiliation The Genome Institute, Washington University in St. Louis, St. Louis, Missouri, United States of America
- Gabriel E. Sanderson
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Affiliation The Genome Institute, Washington University in St. Louis, St. Louis, Missouri, United States of America
- Thomas P. Mooney
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Affiliation The Genome Institute, Washington University in St. Louis, St. Louis, Missouri, United States of America
- Nathaniel G. Nutter
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Affiliation The Genome Institute, Washington University in St. Louis, St. Louis, Missouri, United States of America
- Edward A. Belter
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Affiliation The Genome Institute, Washington University in St. Louis, St. Louis, Missouri, United States of America
- Feiyu Du
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Affiliation The Genome Institute, Washington University in St. Louis, St. Louis, Missouri, United States of America
- Robert L. Long
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Affiliation The Genome Institute, Washington University in St. Louis, St. Louis, Missouri, United States of America
- Travis E. Abbott
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Affiliation The Genome Institute, Washington University in St. Louis, St. Louis, Missouri, United States of America
- Ian T. Ferguson
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Affiliation The Genome Institute, Washington University in St. Louis, St. Louis, Missouri, United States of America
- David L. Morton
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Affiliation The Genome Institute, Washington University in St. Louis, St. Louis, Missouri, United States of America
- Mark M. Burnett
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Affiliation The Genome Institute, Washington University in St. Louis, St. Louis, Missouri, United States of America
- James V. Weible
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Affiliation The Genome Institute, Washington University in St. Louis, St. Louis, Missouri, United States of America
- Joshua B. Peck
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Affiliation The Genome Institute, Washington University in St. Louis, St. Louis, Missouri, United States of America
- Adam Dukes
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Affiliation The Genome Institute, Washington University in St. Louis, St. Louis, Missouri, United States of America
- Joshua F. McMichael
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Affiliation The Genome Institute, Washington University in St. Louis, St. Louis, Missouri, United States of America
- Justin T. Lolofie
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Current address: University of Hawaii at Manoa, Honolulu, Hawaii, United States of America
Affiliation The Genome Institute, Washington University in St. Louis, St. Louis, Missouri, United States of America
- Brian R. Derickson
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Affiliation The Genome Institute, Washington University in St. Louis, St. Louis, Missouri, United States of America
- Jasreet Hundal
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Affiliation The Genome Institute, Washington University in St. Louis, St. Louis, Missouri, United States of America
- Zachary L. Skidmore
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Affiliation The Genome Institute, Washington University in St. Louis, St. Louis, Missouri, United States of America
- Benjamin J. Ainscough
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Affiliation The Genome Institute, Washington University in St. Louis, St. Louis, Missouri, United States of America
- Nathan D. Dees
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Affiliation The Genome Institute, Washington University in St. Louis, St. Louis, Missouri, United States of America
- William S. Schierding
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Current address: Liggins Institute, Auckland University, Auckland, New Zealand
Affiliation The Genome Institute, Washington University in St. Louis, St. Louis, Missouri, United States of America
- Cyriac Kandoth
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Current address: Memorial Sloan-Kettering Cancer Center, New York, New York, United States of America
Affiliation The Genome Institute, Washington University in St. Louis, St. Louis, Missouri, United States of America
- Kyung H. Kim
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Affiliation The Genome Institute, Washington University in St. Louis, St. Louis, Missouri, United States of America
- Charles Lu
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Affiliation The Genome Institute, Washington University in St. Louis, St. Louis, Missouri, United States of America
- Christopher C. Harris
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Affiliation The Genome Institute, Washington University in St. Louis, St. Louis, Missouri, United States of America
- Nicole Maher
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Affiliation Department of Medicine, Washington University School of Medicine, St. Louis, Missouri, United States of America
- Christopher A. Maher
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Affiliations The Genome Institute, Washington University in St. Louis, St. Louis, Missouri, United States of America, Department of Medicine, Washington University School of Medicine, St. Louis, Missouri, United States of America, Siteman Cancer Center, Washington University School of Medicine, St. Louis, Missouri, United States of America
- Vincent J. Magrini
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Affiliations The Genome Institute, Washington University in St. Louis, St. Louis, Missouri, United States of America, Department of Genetics, Washington University School of Medicine, St. Louis, Missouri, United States of America
- Benjamin S. Abbott
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Affiliation The Genome Institute, Washington University in St. Louis, St. Louis, Missouri, United States of America
- Ken Chen
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Current address: Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, Texas, United States of America
Affiliation The Genome Institute, Washington University in St. Louis, St. Louis, Missouri, United States of America
- Eric Clark
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Current address: University of Illinois at Urbana-Champaign, Champaign, Illinois, United States of America
Affiliation The Genome Institute, Washington University in St. Louis, St. Louis, Missouri, United States of America
- Indraniel Das
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Affiliation The Genome Institute, Washington University in St. Louis, St. Louis, Missouri, United States of America
- Xian Fan
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Current address: Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, Texas, United States of America
Affiliation The Genome Institute, Washington University in St. Louis, St. Louis, Missouri, United States of America
- Amy E. Hawkins
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Affiliation The Genome Institute, Washington University in St. Louis, St. Louis, Missouri, United States of America
- Todd G. Hepler
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Affiliation The Genome Institute, Washington University in St. Louis, St. Louis, Missouri, United States of America
- Todd N. Wylie
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Affiliation The Genome Institute, Washington University in St. Louis, St. Louis, Missouri, United States of America
- Shawn M. Leonard
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Affiliation The Genome Institute, Washington University in St. Louis, St. Louis, Missouri, United States of America
- William E. Schroeder
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Affiliation The Genome Institute, Washington University in St. Louis, St. Louis, Missouri, United States of America
- Xiaoqi Shi
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Affiliation The Genome Institute, Washington University in St. Louis, St. Louis, Missouri, United States of America
- Lynn K. Carmichael
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Affiliation The Genome Institute, Washington University in St. Louis, St. Louis, Missouri, United States of America
- Matthew R. Weil
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Affiliation The Genome Institute, Washington University in St. Louis, St. Louis, Missouri, United States of America
- Richard W. Wohlstadter
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Affiliation The Genome Institute, Washington University in St. Louis, St. Louis, Missouri, United States of America
- Gary Stiehr
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Affiliation The Genome Institute, Washington University in St. Louis, St. Louis, Missouri, United States of America
- Michael D. McLellan
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Affiliation The Genome Institute, Washington University in St. Louis, St. Louis, Missouri, United States of America
- Craig S. Pohl
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Affiliation The Genome Institute, Washington University in St. Louis, St. Louis, Missouri, United States of America
- Christopher A. Miller
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Affiliation The Genome Institute, Washington University in St. Louis, St. Louis, Missouri, United States of America
- Daniel C. Koboldt
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Affiliation The Genome Institute, Washington University in St. Louis, St. Louis, Missouri, United States of America
- Jason R. Walker
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Affiliation The Genome Institute, Washington University in St. Louis, St. Louis, Missouri, United States of America
- James M. Eldred
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Affiliation The Genome Institute, Washington University in St. Louis, St. Louis, Missouri, United States of America
- David E. Larson
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Affiliations The Genome Institute, Washington University in St. Louis, St. Louis, Missouri, United States of America, Department of Genetics, Washington University School of Medicine, St. Louis, Missouri, United States of America
- David J. Dooling
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Current address: Monsanto Company, St. Louis, Missouri, United States of America
Affiliation The Genome Institute, Washington University in St. Louis, St. Louis, Missouri, United States of America
- Li Ding
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Affiliations The Genome Institute, Washington University in St. Louis, St. Louis, Missouri, United States of America, Department of Genetics, Washington University School of Medicine, St. Louis, Missouri, United States of America, Siteman Cancer Center, Washington University School of Medicine, St. Louis, Missouri, United States of America
- Elaine R. Mardis
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Affiliations The Genome Institute, Washington University in St. Louis, St. Louis, Missouri, United States of America, Department of Genetics, Washington University School of Medicine, St. Louis, Missouri, United States of America, Department of Medicine, Washington University School of Medicine, St. Louis, Missouri, United States of America, Siteman Cancer Center, Washington University School of Medicine, St. Louis, Missouri, United States of America, Department of Molecular Microbiology, Washington University School of Medicine, St. Louis, Missouri, United States of America
- Richard K. Wilson
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Affiliations The Genome Institute, Washington University in St. Louis, St. Louis, Missouri, United States of America, Department of Genetics, Washington University School of Medicine, St. Louis, Missouri, United States of America, Department of Medicine, Washington University School of Medicine, St. Louis, Missouri, United States of America, Siteman Cancer Center, Washington University School of Medicine, St. Louis, Missouri, United States of America, Department of Molecular Microbiology, Washington University School of Medicine, St. Louis, Missouri, United States of America
Competing Interests
The authors have declared that no competing interests exist.
Author Contributions
Conceived and designed the experiments: MG OLG SMS AMB BJO JRW JME DEL DJD LD ERM RKW. Performed the experiments: NM CAMa VJM. Analyzed the data: MG OLG SMS AAR ZLS BJA. Contributed reagents/materials/analysis tools: MG OLG SMS MBC AMB MJK ACC AAR BJO GES TPM NGN EAB FD RLL TEA ITF DLM MMB JVW JBP AD JFM JTL BRD JH NDD WSS CK KHK CL CCH NM CAMa BSA KC EC ID XF AEH TGH TNW SML WES XS LKC MRW RWW GS MDM CSP CAMi DCK JRW JME DEL DJD. Wrote the paper: SMS MG OLG DJD. SMS, JME, AMB, and BJO conceived of the original architecture, with input from DJD. JRW, GES, CCH, AD and EAB scaled the system up and TPM, NGN, AAR and BRD brought the core system to its current state. GS implemented processing profiles. CCH added the build tracking. The alignment API was developed by JRW, CCH, BJO, SMS, TPM, AD, ACC, GES and EAB. The variant detection API was designed by GS, RLL, TEA, AMB and SMS. Sequence transformation APIs were implemented by EAB, KHK, and FD. The workflow system was developed by EC, LKC, JRW, AMB, EAB, SMS, TEA, MMB, DLM, ACC and DEL. The annotation system was developed by XS, LD, MDM, GS, AD, EAB, JVW, AAR, SMS. The original somatic pipeline workflow was developed by DEL, DCK, NDD, CCH, GES, RLL, FD, BRD, MG, DEL, JVW, CAMi, and SMS. The validation system was developed by NDD, DCK, DEL, TPM and JVW. The GMS software was developed by TPM, GES, NGN, AAR, TEA, ITF, ACC, JVW, DLM, AD, DEL, MMB, CCH, XS, RLL, JBP, JFM, AMB, BJO, CAMi, EAB, TNW, BSA, CK, NDD, BJA, JRW, NGN, DCK, WSS, CAMa, KHK, KC, XF, FD, MBC, JME, JH, BRD, JTL, EC, AAR, MG, OLG and SMS, with contributions of LIMS integration from SML, CSP, TGH, ID, BSA and AEH. Cancer analysis processing profiles and tools were developed by MG, OLG, DEL, LD, MDM, JRW, DCK, NDD, CL, CAMi, CAMa, CCH, WSS, XS, JH, TNW, CK, MBC, KC, XF, GES, AAR, FD, SMS and BSA. Germline analysis processing profiles were developed by DEL, DCK, CL, WSS, TEA, CCH, RLL, and GES. Reference sequence code was written by EAB, KHK, TEA, and AAR. UR and App API were the work of SMS, AMB, TGH, DJD, CSP, JME, EC, NGN, BRD, TEA, BJO, ID, JRW and MBC. The sample and patient tracking was designed by SMS, CSP, LKC and BRD. The disk allocation system was developed by WES, MJK, TGH, AEH, BSA, ID, JTL, CSP, BRD, NGN, BJO, JVW and AMB. The web interface was developed by BJO, JTL, EC, JFM, ACC and BJO. The computational platform behind the GMS was developed by DJD, RWW, MBC, GS, MRW, NGN, EC, CSP, JFM, AMB, ACC, BRD and SMS. The system federation was developed by SMS. Installation testing and debugging was done by SMS, MG, OLG, ARa, ZLS, ARa and MJK.