Good laboratory practice for clinical next-generation sequencing informatics pipelines (original) (raw)

To the Editor:

We report principles and guidelines (Supplementary Note) that were developed by the Next-Generation Sequencing: Standardization of Clinical Testing II (Nex-StoCT II) informatics workgroup, which was first convened on October 11–12, 2012, in Atlanta, Georgia, by the US Centers for Disease Control and Prevention (CDC; Atlanta, GA). We present here recommendations for the design, optimization and implementation of an informatics pipeline for clinical next-generation sequencing (NGS) to detect germline sequence variants in compliance with existing regulatory and professional quality standards1. The workgroup, which included informatics experts, clinical and research laboratory professionals, physicians with experience in interpreting NGS results, NGS test platform and software developers and participants from US government agencies and professional organizations, also discussed the use of NGS in testing for cancer and infectious disease. A typical NGS analytical process and selected workgroup recommendations are summarized in Table 1, and detailed in the guidelines presented in the Supplementary Note.

Table 1 Nex-StoCT II workgroup recommendations

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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

Authors

  1. Amy S Gargis
  2. Lisa Kalman
  3. David P Bick
  4. Cristina da Silva
  5. David P Dimmock
  6. Birgit H Funke
  7. Sivakumar Gowrisankar
  8. Madhuri R Hegde
  9. Shashikant Kulkarni
  10. Christopher E Mason
  11. Rakesh Nagarajan
  12. Karl V Voelkerding
  13. Elizabeth A Worthey
  14. Nazneen Aziz
  15. John Barnes
  16. Sarah F Bennett
  17. Himani Bisht
  18. Deanna M Church
  19. Zoya Dimitrova
  20. Shaw R Gargis
  21. Nabil Hafez
  22. Tina Hambuch
  23. Fiona C L Hyland
  24. Ruth Ann Luna
  25. Duncan MacCannell
  26. Tobias Mann
  27. Megan R McCluskey
  28. Timothy K McDaniel
  29. Lilia M Ganova-Raeva
  30. Heidi L Rehm
  31. Jeffrey Reid
  32. David S Campo
  33. Richard B Resnick
  34. Perry G Ridge
  35. Marc L Salit
  36. Pavel Skums
  37. Lee-Jun C Wong
  38. Barbara A Zehnbauer
  39. Justin M Zook
  40. Ira M Lubin

Corresponding author

Correspondence toIra 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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