Analytical Validation and Clinical Utilization of the Oncomine Comprehensive Assay Plus Panel for Comprehensive Genomic Profiling in Solid Tumors

The detection of driver oncogenic variants and the recent identification of tumor-agnostic genomic biomarkers has driven the use of comprehensive genomic profiling (CGP) for disease diagnosis, prognosis, and treatment selection. The Oncomine™ Comprehensive Assay Plus (OCA+) panel uses DNA and RNA to...

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Bibliographic Details
Published in:Journal of Molecular Pathology 2023-06, Vol.4 (2), p.109-127
Main Authors: Dumur, Catherine I., Krishnan, Ramakrishnan, Almenara, Jorge A., Brown, Kathleen E., Dugan, Kailyn R., Farni, Christiana, Ibrahim, Fatima Z., Sanchez, Naomi A., Rathore, Sumra, Pradhan, Dinesh, Hughes, Jonathan H.
Format: Article
Language:English
Subjects:
Biomarkers
Cellular biology
comprehensive genomic profiling
Cytology
Endometrium
Genes
Genomes
Genomics
Homologous recombination
homologous recombination deficiency
Invoices
Laboratories
Medical prognosis
Microsatellite instability
Mutation
Oncomine Comprehensive Assay Plus
Ovarian cancer
Patients
Prostate cancer
Solid tumors
targeted NGS
tumor mutational burden
Tumors
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Summary:The detection of driver oncogenic variants and the recent identification of tumor-agnostic genomic biomarkers has driven the use of comprehensive genomic profiling (CGP) for disease diagnosis, prognosis, and treatment selection. The Oncomine™ Comprehensive Assay Plus (OCA+) panel uses DNA and RNA to detect single nucleotide variants (SNVs), small insertions/deletions (Indels), and structural variants (SVs) across 501 genes. Moreover, microsatellite instability (MSI), tumor mutational burden (TMB), and homologous recombination deficiency (HRD) status are assessed in a single workflow. Herein, we present the analytical validation and clinical utilization of OCA+. By using commercial reference materials, we found good analytical sensitivity, specificity, and precision for all biomarkers analyzed. The limit of detection (LoD) was validated for SNVs and Indels at 4%, except for Indels located in homopolymeric regions, where the LoD was 10%. An additional set of 81 tumor samples, including cytology smears, were sequenced to assess the clinical utility of the OCA+ across different tumor types. Among the clinical cohort, OCA+ demonstrated 100% accuracy, sensitivity, and specificity for all biomarkers analyzed, except for MSI assessment of endometrial cancer cases, where 83% accuracy and 67% sensitivity were achieved, compared to PCR and IHC. The validation of accuracy and robustness of this assay supports the OCA+’s utility for solid tumor CGP.
ISSN:2673-5261
2673-5261
DOI:10.3390/jmp4020012