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Position statement
CCMG practice guideline: laboratory guidelines for next-generation sequencing
  1. Stacey Hume1,
  2. Tanya N Nelson2,3,4,
  3. Marsha Speevak5,
  4. Elizabeth McCready6,
  5. Ron Agatep7,8,
  6. Harriet Feilotter9,
  7. Jillian Parboosingh10,11,
  8. Dimitri J Stavropoulos12,13,
  9. Sherryl Taylor1,
  10. Tracy L Stockley13,14
  11. On behalf of Canadian College of Medical Geneticists (CCMG)
  1. 1Department of Medical Genetics, University of Alberta, Edmonton, Alberta, Canada
  2. 2Department of Pathology and Laboratory Medicine, BC Children's Hospital, Vancouver, British Columbia, Canada
  3. 3Department of Pathology and Laboratory Medicine, The University of British Columbia, Vancouver, British Columbia, Canada
  4. 4Department of Medical Genetics, University of British Columbia, Vancouver, British Columbia, Canada
  5. 5Department of Laboratory Medicine and Genetics, Trillium Health Partners, Mississauga, Ontario, Canada
  6. 6Department of Pathology and Molecular Medicine, McMaster University, Hamilton, Ontario, Canada
  7. 7Department of Biochemistry and Molecular Genetics, University of Manitoba, Winnipeg, Manitoba, Canada
  8. 8Genomics Laboratory, Shared Health Diagnostic Services, Winnipeg, Manitoba, Canada
  9. 9Department of Pathology and Molecular Medicine, Queen’s University, Kingston, Ontario, Canada
  10. 10Department of Medical Genetics, University of Calgary Cumming School of Medicine, Calgary, Alberta, Canada
  11. 11Research Institute, Alberta Children’s Hospital, Calgary, Alberta, Canada
  12. 12Department of Paediatric Laboratory Medicine, Genome Diagnostics, Hospital for Sick Children, Toronto, Ontario, Canada
  13. 13Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Ontario, Canada
  14. 14Department of Clinical Laboratory Genetics, Laboratory Medicine Program, University Health Network, Toronto, Ontario, Canada
  1. Correspondence to Dr Tracy L Stockley, Department of Clinical Laboratory Genetics, Laboratory Medicine Program, University Health Network, Toronto, ON M5G 2C4, Canada; tracy.stockley{at}uhn.ca

Purpose

The purpose of this document is to provide guidance for the use of next-generation sequencing (NGS, also known as massively parallel sequencing or MPS) in Canadian clinical genetic laboratories for detection of genetic variants in genomic DNA and mitochondrial DNA for inherited disorders, as well as somatic variants in tumour DNA for acquired cancers. They are intended for Canadian clinical laboratories engaged in developing, validating and using NGS methods.

Methods of statement development The document was drafted by the Canadian College of Medical Geneticists (CCMG) Ad Hoc Working Group on NGS Guidelines to make recommendations relevant to NGS. The statement was circulated for comment to the CCMG Laboratory Practice and Clinical Practice committees, and to the CCMG membership. Following incorporation of feedback, the document was approved by the CCMG Board of Directors.

Disclaimer The CCMG is a Canadian organisation responsible for certifying medical geneticists and clinical laboratory geneticists, and for establishing professional and ethical standards for clinical genetics services in Canada. The current CCMG Practice Guidelines were developed as a resource for clinical laboratories in Canada and should not be considered to be inclusive of all information laboratories should consider in the validation and use of NGS for a clinical laboratory service.

  • diagnostics tests
  • genetics
  • guidelines
  • molecular genetics

This is an open access article distributed in accordance with the Creative Commons Attribution Non Commercial (CC BY-NC 4.0) license, which permits others to distribute, remix, adapt, build upon this work non-commercially, and license their derivative works on different terms, provided the original work is properly cited, appropriate credit is given, any changes made indicated, and the use is non-commercial. See: http://creativecommons.org/licenses/by-nc/4.0/.

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Footnotes

  • SH and TNN contributed equally.

  • Contributors TLS conceived the project, assembled the Ad Hoc Working Group and coordinated the group activities. SH, TNN, MS, EM, RA, HF, JP, DJS, ST and TLS contributed to document planning, participated in discussions, and wrote and reviewed document content. SH, TNN and TLS also reviewed comments from the CCMG membership, made revisions based on comments and performed an overall edit of the final document. All authors provided approval of the final version of the document.

  • Funding The authors would like to thank the Canadian College of Medical Geneticists for providing administrative support for document circulation among the membership.

  • Competing interests None declared.

  • Patient consent for publication Not required.

  • Ethics approval Approved by the CCMG Board of Directors: 16 January 2019.

  • Provenance and peer review Not commissioned; externally peer reviewed.

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