Assessment of Two Commercial Comprehensive Gene Panels for Personalized Cancer Treatment

Ottestad, Anine Larsen; Huang, Mo; Emdal, Elisabeth Fritzke; Mjelle, Robin; Skarpeteig, Veronica; Dai, Hong Yan

doi:10.3390/jpm13010042

Open AccessArticle

Assessment of Two Commercial Comprehensive Gene Panels for Personalized Cancer Treatment

by

Anine Larsen Ottestad

^1,2,*

,

Mo Huang

^1,2,3,

Elisabeth Fritzke Emdal

⁴

,

Robin Mjelle

^1,4,

Veronica Skarpeteig

⁴ and

Hong Yan Dai

^1,4

¹

Department of Clinical and Molecular Medicine, Faculty of Medicine and Health Sciences, Norwegian University of Science and Technology (NTNU), 7030 Trondheim, Norway

²

Department of Oncology, St. Olavs Hospital, Trondheim University Hospital, 7030 Trondheim, Norway

³

Department of Biosciences and Nutrition, Karolinska Institute, 17177 Stockholm, Sweden

⁴

Department of Pathology, Clinic of Laboratory Medicine, St. Olavs Hospital, Trondheim University Hospital, 7030 Trondheim, Norway

^*

Author to whom correspondence should be addressed.

J. Pers. Med. 2023, 13(1), 42; https://doi.org/10.3390/jpm13010042

Submission received: 28 November 2022 / Revised: 20 December 2022 / Accepted: 22 December 2022 / Published: 26 December 2022

Download

Browse Figures

Review Reports Versions Notes

Abstract

(1) Background: Analysis of tumor DNA by next-generation sequencing (NGS) plays various roles in the classification and management of cancer. This study aimed to assess the performance of two similar and large, comprehensive gene panels with a focus on clinically relevant variant detection and tumor mutation burden (TMB) assessment; (2) Methods: DNA from 19 diagnostic small cell lung cancer biopsies and an AcroMetrix™ assessment sample with >500 mutations were sequenced using Oncomine^™ Comprehensive Assay Plus (OCAP) on the Ion Torrent platform and TruSight Oncology 500 Assay (TSO500) on the Illumina platform; (3) Results: OCAP and TSO500 achieved comparable NGS quality, such as mean read coverage and mean coverage uniformity. A total of 100% of the variants in the diagnostic samples and 80% of the variants in the AcroMetrix™ assessment sample were detected by both panels, and the panels reported highly similar variant allele frequency. A proportion of 14/19 (74%) samples were classified in the same TMB category; (4) Conclusions: Comparable results were obtained using OCAP and TSO500, suggesting that both panels could be applied to screen patients for enrolment in personalized cancer treatment trials.

Keywords: next-generation sequencing; comprehensive cancer panel; personalized treatment

Share and Cite

MDPI and ACS Style

Ottestad, A.L.; Huang, M.; Emdal, E.F.; Mjelle, R.; Skarpeteig, V.; Dai, H.Y. Assessment of Two Commercial Comprehensive Gene Panels for Personalized Cancer Treatment. J. Pers. Med. 2023, 13, 42. https://doi.org/10.3390/jpm13010042

AMA Style

Ottestad AL, Huang M, Emdal EF, Mjelle R, Skarpeteig V, Dai HY. Assessment of Two Commercial Comprehensive Gene Panels for Personalized Cancer Treatment. Journal of Personalized Medicine. 2023; 13(1):42. https://doi.org/10.3390/jpm13010042

Chicago/Turabian Style

Ottestad, Anine Larsen, Mo Huang, Elisabeth Fritzke Emdal, Robin Mjelle, Veronica Skarpeteig, and Hong Yan Dai. 2023. "Assessment of Two Commercial Comprehensive Gene Panels for Personalized Cancer Treatment" Journal of Personalized Medicine 13, no. 1: 42. https://doi.org/10.3390/jpm13010042

APA Style

Ottestad, A. L., Huang, M., Emdal, E. F., Mjelle, R., Skarpeteig, V., & Dai, H. Y. (2023). Assessment of Two Commercial Comprehensive Gene Panels for Personalized Cancer Treatment. Journal of Personalized Medicine, 13(1), 42. https://doi.org/10.3390/jpm13010042

Note that from the first issue of 2016, this journal uses article numbers instead of page numbers. See further details here.

Article Menu

Assessment of Two Commercial Comprehensive Gene Panels for Personalized Cancer Treatment

Abstract

Share and Cite

Article Metrics

Article Access Statistics

Further Information

Guidelines

MDPI Initiatives

Follow MDPI