Multisite verification of the accuracy of a multi-gene next generation sequencing panel for detection of mutations and copy number alterations in solid tumours

• Published in: PloS one Vol. 16; no. 10; p. e0258188
• Main Authors: Bartlett, John, Amemiya, Yutaka, Arts, Heleen, Bayani, Jane, Eng, Barry, Grafodatskaya, Daria, Kamel Reid, Suzanne, Lariviere, Mathieu, Lo, Bryan, McClure, Rebecca, Mittal, Vinay, Sadikovic, Bekim, Sadis, Seth, Seth, Arun, Smith, Jeff, Zhang, Xiao, Feilotter, Harriet
• Format: Journal Article
• Language: English
• Published: San Francisco Public Library of Science 01.10.2021; Public Library of Science (PLoS)
• Subjects: Analysis; Assaying; Biology and life sciences; Cancer; Copy number; Deoxyribonucleic acid; DNA; Gene expression; Gene sequencing; Genes; Genetic aspects; Genetic testing; Genomics; Health sciences; Laboratories; Medical research; Medicine; Medicine and health sciences; Metastasis; Mutation; Next-generation sequencing; Nucleotides; Pathology; Research and analysis methods; Ribonucleic acid; RNA; Solid tumors; Tumors; Workflow; Canada; Ontario Canada; South San Francisco California; Toronto Ontario Canada; United States > US
• ISSN: 1932-6203; 1932-6203
• DOI: 10.1371/journal.pone.0258188

Molecular variants including single nucleotide variants (SNVs), copy number variants (CNVs) and fusions can be detected in the clinical setting using deep targeted sequencing. These assays support low limits of detection using little genomic input material. They are gaining in popularity in clinical laboratories, where sample volumes are limited, and low variant allele fractions may be present. However, data on reproducibility between laboratories is limited. Using a ring study, we evaluated the performance of 7 Ontario laboratories using targeted sequencing panels. All laboratories analysed a series of control and clinical samples for SNVs/CNVs and gene fusions. High concordance was observed across laboratories for measured CNVs and SNVs. Over 97% of SNV calls in clinical samples were detected by all laboratories. Whilst only a single CNV was detected in the clinical samples tested, all laboratories were able to reproducibly report both the variant and copy number. Concordance for information derived from RNA was lower than observed for DNA, due largely to decreased quality metrics associated with the RNA components of the assay, suggesting that the RNA portions of comprehensive NGS assays may be more vulnerable to variations in approach and workflow. Overall the results of this study support the use of the OFA for targeted sequencing for testing of clinical samples and suggest specific internal quality metrics that can be reliable indicators of assay failure. While we believe this evidence can be interpreted to support deep targeted sequencing in general, additional studies should be performed to confirm this.