Assessment of Two Commercial Comprehensive Gene Panels for Personalized Cancer Treatment
(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...
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| Format: | Article |
| Language: | English |
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MDPI AG
2022-12-01
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| Series: | Journal of Personalized Medicine |
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| Online Access: | https://www.mdpi.com/2075-4426/13/1/42 |
| _version_ | 1797440154964590592 |
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| author | Anine Larsen Ottestad Mo Huang Elisabeth Fritzke Emdal Robin Mjelle Veronica Skarpeteig Hong Yan Dai |
| author_facet | Anine Larsen Ottestad Mo Huang Elisabeth Fritzke Emdal Robin Mjelle Veronica Skarpeteig Hong Yan Dai |
| author_sort | Anine Larsen Ottestad |
| collection | DOAJ |
| description | (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<sup>™</sup> 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. |
| first_indexed | 2024-03-09T12:03:02Z |
| format | Article |
| id | doaj.art-babe25d5026d44e3bc4f9f877b18cf57 |
| institution | Directory Open Access Journal |
| issn | 2075-4426 |
| language | English |
| last_indexed | 2024-03-09T12:03:02Z |
| publishDate | 2022-12-01 |
| publisher | MDPI AG |
| record_format | Article |
| series | Journal of Personalized Medicine |
| spelling | doaj.art-babe25d5026d44e3bc4f9f877b18cf572023-11-30T23:01:20ZengMDPI AGJournal of Personalized Medicine2075-44262022-12-011314210.3390/jpm13010042Assessment of Two Commercial Comprehensive Gene Panels for Personalized Cancer TreatmentAnine Larsen Ottestad0Mo Huang1Elisabeth Fritzke Emdal2Robin Mjelle3Veronica Skarpeteig4Hong Yan Dai5Department of Clinical and Molecular Medicine, Faculty of Medicine and Health Sciences, Norwegian University of Science and Technology (NTNU), 7030 Trondheim, NorwayDepartment of Clinical and Molecular Medicine, Faculty of Medicine and Health Sciences, Norwegian University of Science and Technology (NTNU), 7030 Trondheim, NorwayDepartment of Pathology, Clinic of Laboratory Medicine, St. Olavs Hospital, Trondheim University Hospital, 7030 Trondheim, NorwayDepartment of Clinical and Molecular Medicine, Faculty of Medicine and Health Sciences, Norwegian University of Science and Technology (NTNU), 7030 Trondheim, NorwayDepartment of Pathology, Clinic of Laboratory Medicine, St. Olavs Hospital, Trondheim University Hospital, 7030 Trondheim, NorwayDepartment of Clinical and Molecular Medicine, Faculty of Medicine and Health Sciences, Norwegian University of Science and Technology (NTNU), 7030 Trondheim, Norway(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<sup>™</sup> 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.https://www.mdpi.com/2075-4426/13/1/42next-generation sequencingcomprehensive cancer panelpersonalized treatment |
| spellingShingle | Anine Larsen Ottestad Mo Huang Elisabeth Fritzke Emdal Robin Mjelle Veronica Skarpeteig Hong Yan Dai Assessment of Two Commercial Comprehensive Gene Panels for Personalized Cancer Treatment Journal of Personalized Medicine next-generation sequencing comprehensive cancer panel personalized treatment |
| title | Assessment of Two Commercial Comprehensive Gene Panels for Personalized Cancer Treatment |
| title_full | Assessment of Two Commercial Comprehensive Gene Panels for Personalized Cancer Treatment |
| title_fullStr | Assessment of Two Commercial Comprehensive Gene Panels for Personalized Cancer Treatment |
| title_full_unstemmed | Assessment of Two Commercial Comprehensive Gene Panels for Personalized Cancer Treatment |
| title_short | Assessment of Two Commercial Comprehensive Gene Panels for Personalized Cancer Treatment |
| title_sort | assessment of two commercial comprehensive gene panels for personalized cancer treatment |
| topic | next-generation sequencing comprehensive cancer panel personalized treatment |
| url | https://www.mdpi.com/2075-4426/13/1/42 |
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