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Published on: April 11, 2016
Inter-laboratory proficiency testing scheme for tumour next-generation sequencing in Ontario: a pilot study
1Toronto, ON: Advanced Molecular Diagnostics Laboratory, Princess Margaret Cancer Centre, University Health Network (Spence, Stockley); Bioinformatics and HPC Core, Princess Margaret Cancer Centre, University Health Network (Stickle); Cancer Genomics Program, Princess Margaret Cancer Centre, University Health Network (Yu, Chow, Siu); Division of Medical Oncology and Hematology, Princess Margaret Cancer Centre, University Health Network (Siu, Bedard); Department of Medicine, University of Toronto (Siu, Bedard); Department of Clinical Laboratory Genetics, University Health Network (Stockley); Department of Laboratory Medicine and Pathobiology, University of Toronto (Stockley).
This study assessed next-generation sequencing (NGS) proficiency in Ontario labs for solid tumor testing. While technical accuracy was high, significant differences in reporting clinically relevant variants highlight a need for consensus.
Area of Science:
- Oncology
- Genomics
- Clinical Pathology
Background:
- Pilot proficiency testing for 5 Ontario clinical labs focused on solid tumor next-generation sequencing (NGS).
- Assessed identification and reporting of NGS test results from archival formalin-fixed, paraffin-embedded (FFPE) tissue for the Ontario-wide Cancer Targeted Nucleic Acid Evaluation (OCTANE) study.
Purpose of the Study:
- To evaluate laboratory proficiency in identifying and reporting NGS results for solid tumors.
- To identify areas for improvement in NGS testing and reporting practices within Ontario clinical laboratories.
Main Methods:
- A reference laboratory provided 10 FFPE tissue specimens to 4 participating laboratories.
- Laboratories performed NGS testing using their standard protocols, returning identified genes, variants, and variant call format (VCF) files for assessment.
Main Results:
- Excellent 100% technical concordance was achieved in identifying 98 exonic variants across all participating sites.
- Significant variability was observed in the reporting of clinically relevant variants; only 3 of 38 variants were concordantly reported by all centers.
Conclusions:
- High technical accuracy in NGS tumor profiling was demonstrated across laboratories.
- Discrepancies in reporting clinically relevant variants indicate a need for consensus among Ontario laboratories to standardize reporting practices.
