Diagnostic Validation of a Comprehensive Targeted Panel for Broad Mutational and Biomarker Analysis in Solid Tumors
The use of targeted Next Generation Sequencing (NGS) for the diagnostic screening of somatic variants in solid tumor samples has proven its high clinical value. Because of the large number of ongoing clinical trials for a multitude of variants in a growing number of genes, as well as the detection o...
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| Format: | Article |
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MDPI AG
2022-05-01
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| Series: | Cancers |
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| Online Access: | https://www.mdpi.com/2072-6694/14/10/2457 |
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| author | Guy Froyen Ellen Geerdens Severine Berden Bert Cruys Brigitte Maes |
| author_facet | Guy Froyen Ellen Geerdens Severine Berden Bert Cruys Brigitte Maes |
| author_sort | Guy Froyen |
| collection | DOAJ |
| description | The use of targeted Next Generation Sequencing (NGS) for the diagnostic screening of somatic variants in solid tumor samples has proven its high clinical value. Because of the large number of ongoing clinical trials for a multitude of variants in a growing number of genes, as well as the detection of proven and emerging pan-cancer biomarkers including microsatellite instability (MSI) and tumor mutation burden (TMB), the currently employed diagnostic gene panels will become vastly insufficient in the near future. Here, we describe the validation and implementation of the hybrid capture-based comprehensive TruSight Oncology (TSO500) assay that is able to detect single-nucleotide variants (SNVs) and subtle deletions and insertions (indels) in 523 tumor-associated genes, copy-number variants (CNVs) of 69 genes, fusions with 55 cancer driver genes, and MSI and TMB. Extensive validation of the TSO500 assay was performed on DNA or RNA from 170 clinical samples with neoplastic content down to 10%, using multiple tissue and specimen types. Starting with 80 ng DNA and 40 ng RNA extracted from formalin-fixed and paraffine-embedded (FFPE) samples revealed a precision and accuracy >99% for all variant types. The analytical sensitivity and specificity were at least 99% for SNVs, indels, CNVs, MSI, and gene rearrangements. For TMB, only values around the threshold could yield a deviating outcome. The limit-of-detection for SNVs and indels was well below the set threshold of 5% variant allele frequency (VAF). This validated comprehensive genomic profiling assay was then used to screen 624 diagnostic samples, and its success rate for adoption in a clinical diagnostic setting of broad solid tumor screening was assessed on this cohort. |
| first_indexed | 2024-03-10T03:13:01Z |
| format | Article |
| id | doaj.art-d2fe7e1f9dc44fa79c3bfb1afa9d978f |
| institution | Directory Open Access Journal |
| issn | 2072-6694 |
| language | English |
| last_indexed | 2024-03-10T03:13:01Z |
| publishDate | 2022-05-01 |
| publisher | MDPI AG |
| record_format | Article |
| series | Cancers |
| spelling | doaj.art-d2fe7e1f9dc44fa79c3bfb1afa9d978f2023-11-23T10:23:26ZengMDPI AGCancers2072-66942022-05-011410245710.3390/cancers14102457Diagnostic Validation of a Comprehensive Targeted Panel for Broad Mutational and Biomarker Analysis in Solid TumorsGuy Froyen0Ellen Geerdens1Severine Berden2Bert Cruys3Brigitte Maes4Laboratory of Molecular Diagnostics, Department of Clinical Biology, Jessa Hospital, B-3500 Hasselt, BelgiumLaboratory of Molecular Diagnostics, Department of Clinical Biology, Jessa Hospital, B-3500 Hasselt, BelgiumLaboratory of Molecular Diagnostics, Department of Clinical Biology, Jessa Hospital, B-3500 Hasselt, BelgiumLaboratory of Molecular Diagnostics, Department of Clinical Biology, Jessa Hospital, B-3500 Hasselt, BelgiumLaboratory of Molecular Diagnostics, Department of Clinical Biology, Jessa Hospital, B-3500 Hasselt, BelgiumThe use of targeted Next Generation Sequencing (NGS) for the diagnostic screening of somatic variants in solid tumor samples has proven its high clinical value. Because of the large number of ongoing clinical trials for a multitude of variants in a growing number of genes, as well as the detection of proven and emerging pan-cancer biomarkers including microsatellite instability (MSI) and tumor mutation burden (TMB), the currently employed diagnostic gene panels will become vastly insufficient in the near future. Here, we describe the validation and implementation of the hybrid capture-based comprehensive TruSight Oncology (TSO500) assay that is able to detect single-nucleotide variants (SNVs) and subtle deletions and insertions (indels) in 523 tumor-associated genes, copy-number variants (CNVs) of 69 genes, fusions with 55 cancer driver genes, and MSI and TMB. Extensive validation of the TSO500 assay was performed on DNA or RNA from 170 clinical samples with neoplastic content down to 10%, using multiple tissue and specimen types. Starting with 80 ng DNA and 40 ng RNA extracted from formalin-fixed and paraffine-embedded (FFPE) samples revealed a precision and accuracy >99% for all variant types. The analytical sensitivity and specificity were at least 99% for SNVs, indels, CNVs, MSI, and gene rearrangements. For TMB, only values around the threshold could yield a deviating outcome. The limit-of-detection for SNVs and indels was well below the set threshold of 5% variant allele frequency (VAF). This validated comprehensive genomic profiling assay was then used to screen 624 diagnostic samples, and its success rate for adoption in a clinical diagnostic setting of broad solid tumor screening was assessed on this cohort.https://www.mdpi.com/2072-6694/14/10/2457Next Generation Sequencing (NGS)precision medicinetargeted screeningTSO500validation |
| spellingShingle | Guy Froyen Ellen Geerdens Severine Berden Bert Cruys Brigitte Maes Diagnostic Validation of a Comprehensive Targeted Panel for Broad Mutational and Biomarker Analysis in Solid Tumors Cancers Next Generation Sequencing (NGS) precision medicine targeted screening TSO500 validation |
| title | Diagnostic Validation of a Comprehensive Targeted Panel for Broad Mutational and Biomarker Analysis in Solid Tumors |
| title_full | Diagnostic Validation of a Comprehensive Targeted Panel for Broad Mutational and Biomarker Analysis in Solid Tumors |
| title_fullStr | Diagnostic Validation of a Comprehensive Targeted Panel for Broad Mutational and Biomarker Analysis in Solid Tumors |
| title_full_unstemmed | Diagnostic Validation of a Comprehensive Targeted Panel for Broad Mutational and Biomarker Analysis in Solid Tumors |
| title_short | Diagnostic Validation of a Comprehensive Targeted Panel for Broad Mutational and Biomarker Analysis in Solid Tumors |
| title_sort | diagnostic validation of a comprehensive targeted panel for broad mutational and biomarker analysis in solid tumors |
| topic | Next Generation Sequencing (NGS) precision medicine targeted screening TSO500 validation |
| url | https://www.mdpi.com/2072-6694/14/10/2457 |
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