The Somatic Curation and Interpretation Across Laboratories (SOCIAL) project— current state of solid-tumour variant interpretation for molecular pathology in Canada

  • T. Spence Advanced Molecular Diagnostics Laboratory, Princess Margaret Cancer Centre, University Health Network, University Health Network
  • M. A. Sukhai Advanced Molecular Diagnostics Laboratory, Princess Margaret Cancer Centre, University Health Network, University Health Network
  • S. Kamel-Reid Advanced Molecular Diagnostics Laboratory, Princess Margaret Cancer Centre, University Health Network, Laboratory Medicine Program, University Health Network, University of Toronto
  • T. L. Stockley Advanced Molecular Diagnostics Laboratory, Princess Margaret Cancer Centre, University Health Network, Laboratory Medicine Program, University Health Network, University of Toronto
Keywords: Classification guidelines, classification schemes, national surveys, solid tumours, somatic variant interpretation, variant annotation

Abstract

Background Practices in somatic variant interpretation and classification vary between Canadian clinical molecular diagnostic laboratories, and understanding of current practices and perspectives is limited. To define gaps and future directions, including consensus guideline development, the Somatic Curation and Interpretation Across Laboratories (social) project examined the present state of somatic variant interpretation in Canadian molecular laboratories, including testing volumes and methods, data sources and evidence criteria, and application of published classification guidelines.

Methods Individuals who perform somatic variant interpretation in Canadian centres were invited to participate in an online survey. Invitees included laboratory directors (certified as Fellows of the Canadian College of Medical Geneticists or the American College of Medical Geneticists), md or md and phd molecular pathologists, and other phd experts, including phd specialists in variant annotation or bioinformatics. Current testing methods, volumes, and platforms in next-generation sequencing, use of variant annotation resources and evidence criteria, and preference for variant classification schemes were evaluated.

Results Responses were received from 37 participants in 8 provinces. A somatic variant classification scheme jointly supported by the Association for Molecular Pathology (amp), the American Society of Clinical Oncology (asco), and the College of American Pathologists (cap) was used by 47% of respondents; an alternative guideline or a combination of published guidelines was used by 35% of respondents. The remaining 18% did not use a published scheme. Only 41% of respondents used a published scheme without alteration. Although all respondents indicated that there is a need for Canadian laboratories to adopt a somatic variant classification guideline, only 38% of respondents felt that it should be mandatory to adopt the amp/asco/cap–endorsed guideline.

Conclusions Data from the social project identified high variability in current practice, yet strong support for standardization of solid-tumour somatic variant interpretation across Canadian institutions. Aligning classification methods will reduce variation in cross-institutional classification and reporting practices, aiding in consistent practice nationwide.


Author Biographies

T. Spence, Advanced Molecular Diagnostics Laboratory, Princess Margaret Cancer Centre, University Health Network, University Health Network

Department of Clinical Laboratory Genetics, Laboratory Medicine Program

M. A. Sukhai, Advanced Molecular Diagnostics Laboratory, Princess Margaret Cancer Centre, University Health Network, University Health Network
Department of Clinical Laboratory Genetics, Laboratory Medicine Program
S. Kamel-Reid, Advanced Molecular Diagnostics Laboratory, Princess Margaret Cancer Centre, University Health Network, Laboratory Medicine Program, University Health Network, University of Toronto

Department of Clinical Laboratory Genetics, Department of Laboratory Medicine and Pathobiology

T. L. Stockley, Advanced Molecular Diagnostics Laboratory, Princess Margaret Cancer Centre, University Health Network, Laboratory Medicine Program, University Health Network, University of Toronto
Department of Clinical Laboratory Genetics, Department of Laboratory Medicine and Pathobiology
Published
2019-12-20
How to Cite
Spence, T., Sukhai, M. A., Kamel-Reid, S., & Stockley, T. L. (2019). The Somatic Curation and Interpretation Across Laboratories (SOCIAL) project— current state of solid-tumour variant interpretation for molecular pathology in Canada. Current Oncology, 26(6). https://doi.org/10.3747/co.26.5281
Section
Cancer Genetics