Oncomine™ Comprehensive Assay v3 vs. Oncomine™ Comprehensive Assay Plus.

Abstract

Simple SummaryThe detection of genetic alterations in cancer is important to obtain knowledge of the underlying mutational tumor composition. Knowing the mutational profile can assist oncologists on tailoring optimal personalized treatments. Moreover, obtaining additional information from a broader cancer-related gene panel, without compromising performance, can benefit both current and future patients. In this study, we assessed the performance of gene mutations identified from sequencing using the newly Oncomine™ Comprehensive Assay Plus (OCA-Plus). The assessment was performed in comparison to gene mutations identified from sequencing using the Oncomine™ Comprehensive Assay v3 (OCAv3), currently used in our routine clinical setting. Therefore, an investigation of their performance was conducted on intersecting nucleotide positions within overlapping genes covered by both the OCA-Plus and the OCAv3. We show here that there is a 91% concordance between identified pathogenic and likely pathogenic classified variants. The usage of next generation sequencing in combination with targeted gene panels has enforced a better understanding of tumor compositions. The identification of key genomic biomarkers underlying a disease are crucial for diagnosis, prognosis, treatment and therapeutic responses. The Oncomine™ Comprehensive Assay v3 (OCAv3) covers 161 cancer-associated genes and is routinely employed to support clinical decision making for a therapeutic course. An improved version, Oncomine™ Comprehensive Assay Plus (OCA-Plus), has been recently developed, covering 501 genes (144 overlapping with OCAv3) in addition to microsatellite instability (MSI) and tumor mutational burden (TMB) assays in one workflow. The validation of MSI and TMB was not addressed in the present study. However, the implementation of new assays must be validated and confirmed across multiple samples before it can be introduced into a clinical setting. Here, we report the comparison of DNA sequencing results from 50 ovarian cancer formalin-fixed, paraffin-embedded samples subjected to OCAv3 and OCA-Plus. A validation assessment of gene mutations identified using OCA-Plus was performed on the 144 overlapping genes and 313,769 intersecting nucleotide positions of the OCAv3 and the OCA-Plus. Our results showed a 91% concordance within variants classified as likely-pathogenic or pathogenic. Moreover, results showed that a region of PTEN is poorly covered by the OCA-Plus assay, hence, we implemented rescue filters for those variants. In conclusion, the OCA-Plus can reflect the mutational profile of genomic variants compared with OCAv3 of 144 overlapping genes, without compromising performance.