Comparison of Large, Medium, and Small Solid Tumor Gene Panels for Detection of Clinically Actionable Mutations in Cance
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ORIGINAL RESEARCH ARTICLE
Comparison of Large, Medium, and Small Solid Tumor Gene Panels for Detection of Clinically Actionable Mutations in Cancer Eric Vail1,3 · Jianbo Song1 · Jing Xu1 · Joseph S. Frye1 · Jong Taek Kim1 · Andy Pao1 · Rhona Schreck1 · Angela S. Aguiluz1 · Wenjuan Zhang1 · Serhan Alkan1,3 · Alain Mita2,3 · Monica Mita2,3 · Robert A. Figlin2,3 · David M. Engman1,3 · Jean R. Lopategui1,3
© Springer Nature Switzerland AG 2020
Abstract Background Next-generation sequencing of gene panels has supplanted single-gene testing for cancer molecular diagnostics in many laboratories. Considerations for the optimal number of genes to assess in a panel depend on the purpose of the testing. Objective To address the optimal size for the identification of clinically actionable variants in different-sized solid tumor sequencing panels. Patients and methods Sequencing results from 480 patients with a large, 315 gene, panel were compared against coverage of a medium, 161 gene, and small, 50 gene, panel. Results The large panel detected a total of 2072 sequence variants in 480 patient specimens; 61 (12.7%) contained variants for which there is therapy approved by the US Food and Drug Administration, 89 (18.5%) had variants associated with an offlabel therapy, and 312 (65.0%) contained variants eligible for a genomically matched clinical trial. The small panel covered only 737 of the 2072 variants (35.5%) and somewhat fewer therapy-related variants (on-label 88.5%, off-label 60.7%). The medium-size panel included 1354 of the 2072 (65.3%) variants reported by the large panel. All 318 patients with a clinically actionable variant would have been identified by the medium panel. Conclusions The results demonstrate that a carefully designed medium size gene panel is as effective as a large panel for the detection of clinically actionable variants and can be run by most molecular pathology laboratories.
1 Introduction Genomic analysis of solid tumor tissue is the standard of care for several of the most common types of human malignancies, including non-small-cell lung carcinoma (NSCLC), Electronic supplementary material The online version of this article (https://doi.org/10.1007/s11523-020-00743-9) contains supplementary material, which is available to authorized users. * Eric Vail [email protected] * Jean R. Lopategui [email protected] 1
Department of Pathology and Laboratory Medicine, CedarsSinai Medical Center, Los Angeles, CA, USA
2
Division of Hematology‑Oncology, Cedars-Sinai Medical Center, Los Angeles, CA, USA
3
Samuel Oschin Comprehensive Cancer Institute, Cedars-Sinai Medical Center, Los Angeles, CA, USA
Key Points In solid tumor profiling the optimal size of sequencing panel for the detection of actionable mutations is not defined. We compared the clinical results from a large panel (315 genes) to the coverage of a medium (161 genes) and a small (50 genes) panel. Our results indicate that the gene content of the mediumsized panel encompassed all actionable mutations of the larg
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