安大略省肿瘤下一代测序的实验室间能力验证计划：一项试点研究。
Inter-laboratory proficiency testing scheme for tumour next-generation sequencing in Ontario: a pilot study.
机构信息
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).
Kingston, ON: Molecular Diagnostics, Kingston Health Sciences Centre (Feilotter); Department of Pathology and Molecular Medicine, Queen's University (Feilotter).
出版信息
Curr Oncol. 2019 Dec;26(6):e717-e732. doi: 10.3747/co.26.5379. Epub 2019 Dec 1.
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.
背景
为了评估安大略省肿瘤靶向核酸评估（octane）研究中对存档福尔马林固定、石蜡包埋（ffpe）组织中下一代测序（ngs）检测结果进行识别和报告的能力，对 5 个安大略省临床实验室进行了一项试点实验室间能力验证计划，这些实验室正在测试肿瘤样本。
方法
一个实验室作为参考中心，向 4 个参与实验室提供样本。采用基于分析物的方法：每个参与实验室收到了在参考中心进行分析的 10 个 ffpe 组织样本，提供了肿瘤部位和组织学信息。实验室按照其标准的 ngs 肿瘤测试协议进行测试。评估的项目包括通常在常规临床测试中报告的基因和变体，以及变体调用格式（vcf）文件，以允许评估 ngs 技术质量。
结果
评估了两个主要方面：
外显子变异识别的技术质量和准确性
特定部位的报告实践
技术评估包括外显子变异识别的评估、vcf 文件的质量评估，以评估碱基调用、变体等位基因频率和所有外显子变异的覆盖深度。在 10 个病例中，所有位点在外显子变异的技术识别中都观察到了 100%的一致性。在考虑报告的临床相关变异的选择方面，实验室之间存在显著的变异性。在至少 1 个站点报告为临床相关的 38 个变异中，只有 3 个变异被所有参与中心一致报告为临床相关。
结论
尽管在参与机构中观察到了出色的 ngs 肿瘤分析技术一致性，但在报告临床相关变异方面存在差异，这突出了报告是一个需要安大略省实验室达成共识的差距。
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