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Good laboratory practice for clinical next-generation sequencing informatics pipelines

Nature Biotechnology volume 33, pages 689–693 (2015)Cite this article

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Figure 1: Model for tertiary analysis of sequence variants.

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Acknowledgements

This work was supported in part by an appointment to A.S.G. to the Research Participation Program at the Centers for Disease Control and Prevention, administered by the Oak Ridge Institute for Science and Education through an interagency agreement between the US Department of Energy and the CDC. H.L.R. was supported in part by National Institutes of Health grants U01HG006500 and U41HG006834. The findings and conclusions in this report are those of the authors and do not necessarily represent the views of the CDC, the Agency for Toxic Substances and Disease Registry or the FDA. Certain commercial equipment, instruments or materials are identified in this document. Such identification does not imply recommendation or endorsement by the CDC, the Agency for Toxic Substances and Disease Registry, the FDA or NIST, nor does it imply that the products identified are necessarily the best available for the purpose.

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Author notes

  1. Amy S Gargis, Sivakumar Gowrisankar, Nazneen Aziz, Deanna M Church, Nabil Hafez, Tobias Mann, Jeffrey Reid & Perry G Ridge

    Present address: Present addresses: Division of Preparedness and Emerging Infections, Center for Disease Control and Prevention, Atlanta, Georgia, USA (A.S.G.); Novartis Institutes for Biomedical Research, Cambridge, Massachusetts, USA (S.G.); Phoenix Children's Hospital, Phoenix, Arizona, USA (N.A.); Personalis, Menlo Park, California, USA (D.M.C.); Quest Diagnostics, Marlborough, Massachusetts, USA (N.H.); Progenity, Ann Arbor, Michigan, USA (T.M.); Regeneron Pharmaceuticals, Tarrytown, New York, USA (J.R.); and Brigham Young University, Provo, Utah, USA (P.G.R.).,

Authors and Affiliations

  1. Division of Laboratory Systems, Centers for Disease Control and Prevention, Atlanta, Georgia, USA

    Amy S Gargis, Lisa Kalman, Barbara A Zehnbauer & Ira M Lubin

  2. Department of Pediatrics, Medical College of Wisconsin, Milwaukee, Wisconsin, USA

    David P Bick, David P Dimmock & Elizabeth A Worthey

  3. Department of Human Genetics, Emory University School of Medicine, Atlanta, Georgia, USA

    Cristina da Silva & Madhuri R Hegde

  4. Laboratory for Molecular Medicine, Partners Healthcare Personalized Medicine, Cambridge, Massachusetts, USA

    Birgit H Funke, Sivakumar Gowrisankar & Heidi L Rehm

  5. Department of Pathology, Harvard Medical School, Boston, Massachusetts, USA

    Birgit H Funke, Sivakumar Gowrisankar & Heidi L Rehm

  6. Department of Genetics, Washington University School of Medicine, St. Louis, Missouri, USA

    Shashikant Kulkarni

  7. Department of Pediatrics, Washington University School of Medicine, St. Louis, Missouri, USA

    Shashikant Kulkarni

  8. Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, Missouri, USA

    Shashikant Kulkarni & Rakesh Nagarajan

  9. Department of Physiology and Biophysics, Cornell University, New York, New York, USA

    Christopher E Mason

  10. Department of Pathology, University of Utah, Salt Lake City, Utah, USA

    Karl V Voelkerding & Perry G Ridge

  11. Institute for Clinical and Experimental Pathology, Associated Regional and University Pathologists (ARUP) Laboratories, Salt Lake City, Utah, USA

    Karl V Voelkerding

  12. College of American Pathologists, Northfield, Illinois, USA

    Nazneen Aziz

  13. National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, USA

    John Barnes

  14. Division of Laboratory Services, Centers for Medicare and Medicaid Services, Baltimore, Maryland, USA

    Sarah F Bennett

  15. Center for Devices and Radiological Health, Food and Drug Administration, Silver Spring, Maryland, USA

    Himani Bisht

  16. National Center for Biotechnology Information, National Institutes of Health, Bethesda, Maryland, USA

    Deanna M Church

  17. Division of Viral Hepatitis, Centers for Disease Control and Prevention, Atlanta, Georgia, USA

    Zoya Dimitrova, Lilia M Ganova-Raeva, David S Campo & Pavel Skums

  18. Division of Select Agents and Toxins, Centers for Disease Control and Prevention, Atlanta, Georgia, USA

    Shaw R Gargis

  19. GenomeQuest, Westborough, Massachusetts, USA

    Nabil Hafez & Richard B Resnick

  20. Clinical Services, Illumina, San Diego, California, USA

    Tina Hambuch

  21. Thermo Fisher Scientific, South San Francisco, California, USA

    Fiona C L Hyland

  22. Texas Children's Hospital and Department of Pathology & Immunology, Texas Children's Microbiome Center, Baylor College of Medicine, Houston, Texas, USA

    Ruth Ann Luna

  23. National Center for Emerging and Zoonotic Infectious Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, USA

    Duncan MacCannell

  24. Illumina, San Diego, California, USA

    Tobias Mann

  25. SoftGenetics, State College, Pennsylvania, USA

    Megan R McCluskey

  26. Oncology, Illumina, San Diego, California, USA

    Timothy K McDaniel

  27. Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, USA

    Jeffrey Reid & Lee-Jun C Wong

  28. Material Measurement Laboratory, National Institute of Standards and Technology, Gaithersburg, Maryland, USA

    Marc L Salit & Justin M Zook

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  1. Amy S Gargis
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  36. Pavel Skums
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  37. Lee-Jun C Wong
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  38. Barbara A Zehnbauer
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  39. Justin M Zook
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  40. Ira M Lubin
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Corresponding author

Correspondence to Ira M Lubin.

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Competing interests

D.P.D. is at Children's Hospital of Wisconsin/Medical College of Wisconsin, offering fee-for-service genetic counseling and whole-genome and whole-exome sequencing services; has a consulting agreement with Illumina and Complete Genomics; and is founder and shareholder of Genomic Health Innovations, which provides fee-for-service genomic interpretation and consultation services. B.H.F. is at the Partners Healthcare Personalized Medicine fee-for-service laboratory performing next-generation sequencing, is on the advisory board at InVitae and is a consultant for InVitae and Phoenix Children's Hospital. S.G. is at Novartis Institutes for BioMedical Research. R.N. helped to start up commercialization of the Clinical Genomicist Workstation, developed at Washington University. E.A.W. is at the Medical College of Wisconsin, offering fee-for-service genetic counseling and whole-genome and whole-exome sequencing services, and is founder of and a shareholder in Genomic Health Innovations, which provides fee-for-service genomic interpretation and consultation services. D.M.C. is at Personalis Inc., a company that provides whole-genome and whole-exome sequencing, analysis and interpretation services. N.H. is at Quest Diagnostics. T.H. is employed by and a stockholder of Illumina, Inc. F.C.L.H. is at Thermo Fisher Scientific. M.R.M. is at SoftGenetics. T.K.M. is at Illumina. H.L.R. is at Partners Healthcare Personalized Medicine and is an advisory board member for Complete Genomics, Curovese, Knome, Omicia and Ingenuity/Qiagen. J.R. is at Regeneron Pharmaceuticals. R.B.R. is at GenomeQuest. L.-J.C.W. is vice president and senior laboratory director of Baylor-Miraca Genetics Laboratories, which offers next-generation sequencing–based fee-for-service genetic tests. T.M. is at Progenity Inc., a company that provides carrier screening services, and is a stockholder of Illumina.

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Gargis, A., Kalman, L., Bick, D. et al. Good laboratory practice for clinical next-generation sequencing informatics pipelines. Nat Biotechnol 33, 689–693 (2015). https://doi.org/10.1038/nbt.3237

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