Inter-laboratory proficiency testing scheme for tumour next-generation sequencing in Ontario: a pilot study

T Spence¹, N Stickle¹, C Yu¹, H Chow¹, H Feilotter², B Lo³, E McCready⁴, B Sadikovic⁵, L L Siu¹, P L Bedard¹, T L Stockley¹

Affiliations

¹ Toronto, 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).
² Kingston, ON: Molecular Diagnostics, Kingston Health Sciences Centre (Feilotter); Department of Pathology and Molecular Medicine, Queen's University (Feilotter).
³ Ottawa, ON: Molecular Oncology Diagnostics Laboratory, The Ottawa Hospital (Lo); Department of Pathology and Laboratory Medicine, University of Ottawa (Lo).
⁴ Hamilton, ON: Hamilton Health Sciences and St. Joseph's Healthcare (McCready); Department of Pathology and Molecular Medicine, McMaster University (McCready).
⁵ London, ON: Pathology and Laboratory Medicine Program, London Health Sciences Centre (Sadikovic); Department of Pathology and Laboratory Medicine, Western University (Sadikovic).

PMID: 31896942
PMCID: PMC6927773
DOI: 10.3747/co.26.5379

Inter-laboratory proficiency testing scheme for tumour next-generation sequencing in Ontario: a pilot study

T Spence et al. Curr Oncol. 2019 Dec.

. 2019 Dec;26(6):e717-e732.

doi: 10.3747/co.26.5379. Epub 2019 Dec 1.

Authors

T Spence¹, N Stickle¹, C Yu¹, H Chow¹, H Feilotter², B Lo³, E McCready⁴, B Sadikovic⁵, L L Siu¹, P L Bedard¹, T L Stockley¹

Affiliations

¹ Toronto, 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).
² Kingston, ON: Molecular Diagnostics, Kingston Health Sciences Centre (Feilotter); Department of Pathology and Molecular Medicine, Queen's University (Feilotter).
³ Ottawa, ON: Molecular Oncology Diagnostics Laboratory, The Ottawa Hospital (Lo); Department of Pathology and Laboratory Medicine, University of Ottawa (Lo).
⁴ Hamilton, ON: Hamilton Health Sciences and St. Joseph's Healthcare (McCready); Department of Pathology and Molecular Medicine, McMaster University (McCready).
⁵ London, ON: Pathology and Laboratory Medicine Program, London Health Sciences Centre (Sadikovic); Department of Pathology and Laboratory Medicine, Western University (Sadikovic).

PMID: 31896942
PMCID: PMC6927773
DOI: 10.3747/co.26.5379

Abstract

Background: A pilot inter-laboratory proficiency scheme for 5 Ontario clinical laboratories testing tumour samples for the Ontario-wide Cancer Targeted Nucleic Acid Evaluation (octane) study was undertaken to assess proficiency in the identification and reporting of next-generation sequencing (ngs) test results in solid tumour testing from archival formalin-fixed, paraffin-embedded (ffpe) tissue.

Methods: One laboratory served as the reference centre and provided samples to 4 participating laboratories. An analyte-based approach was applied: each participating laboratory received 10 ffpe tissue specimens profiled at the reference centre, with tumour site and histology provided. Laboratories performed testing per their standard ngs tumour test protocols. Items returned for assessment included genes and variants that would be typically reported in routine clinical testing and variant call format (vcf) files to allow for assessment of ngs technical quality.

Results: Two main aspects were assessed:■ Technical quality and accuracy of identification of exonic variants■ Site-specific reporting practicesTechnical assessment included evaluation of exonic variant identification, quality assessment of the vcf files to evaluate base calling, variant allele frequency, and depth of coverage for all exonic variants. Concordance at 100% was observed from all sites in the technical identification of 98 exonic variants across the 10 cases. Variability between laboratories in the choice of variants considered clinically reportable was significant. Of the 38 variants reported as clinically relevant by at least 1 site, only 3 variants were concordantly reported by all participating centres as clinically relevant.

Conclusions: Although excellent technical concordance for ngs tumour profiling was observed across participating institutions, differences in the reporting of clinically relevant variants were observed, highlighting reporting as a gap where consensus on the part of Ontario laboratories is needed.

Keywords: External quality assessment; inter-laboratory comparison; next-generation sequencing; tumour molecular profiling.

2019 Multimed Inc.

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Conflict of interest statement

CONFLICT OF INTEREST DISCLOSURES We have read and understood Current Oncology’s policy on disclosing conflicts of interest, and we declare the following interests: HC reports grants from the Ontario Institute for Cancer Research during the conduct of the study. HF reports nonfinancial support from Thermo Fisher outside the submitted work. BL reports personal fees from Novartis, Bayer, Roche, and AstraZeneca outside the submitted work. BS reports fees from the Ontario Institute for Cancer Research during the conduct of the study. LLS reports other consideration from Merck (compensated), Pfizer (compensated), Celgene (compensated), AstraZeneca/Medimmune (compensated), MorphoSys (compensated), Roche (compensated), Geneseeq Technology (compensated), Loxo Oncology (compensated), Oncorus (compensated), Symphogen (compensated), Seattle Genetics (compensated); grants from Novartis, Bristol–Myers Squibb, Pfizer, Boehringer Ingelheim, GlaxoSmithKline, Roche/Genentech, Karyopharm, AstraZeneca/Medimmune, Merck, Celgene, Astellas, Bayer, AbbVie, Amgen, Symphogen, Intensity Therapeutics, Mirati Therapeutics, and Shattuck Labs; and other consideration from Agios Pharmaceuticals (spouse) outside the submitted work. PLB is a member of the steering committee for the American Association for Cancer Research Project genie, past chair of the Canadian Cancer Trials Group Investigational New Drug Committee, a member of the executive board for the Breast International Group, a section editor for The Oncologist and for JNCI Cancer Spectrum outside the submitted work. The remaining authors have no conflicts of interest to disclose.

Figures

**FIGURE 1**
Flow-chart depicting the pilot proficiency-testing workflow. Ten formalin-fixed, paraffin-embedded (FFPE) tumour proficiency testing cases with known variants from prior testing at the reference centre were distributed to each of the 4 participating laboratories, with tumour site and histology indicated. Cases were processed at participating centres per routine clinical testing for the Ontario-wide Cancer Targeted Nucleic Acid Evaluation (OCTANE) study. Participating centres were requested to provide a list of the genes reported for each tumour site, clinically reportable variants, and variant call format (VCF) files. Comparative assessment was performed to evaluate concordance in the technical identification of variants and concordance in the clinically reported and annotated variants. H/E = hematoxylin and eosin stained; HGVS = Human Genome Variation Society.

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Inter-laboratory proficiency testing scheme for tumour next-generation sequencing in Ontario: a pilot study

Affiliations

Inter-laboratory proficiency testing scheme for tumour next-generation sequencing in Ontario: a pilot study

Authors

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Abstract

Conflict of interest statement

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