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. 2021 Oct 18;13(20):5230.
doi: 10.3390/cancers13205230.

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

Lau K Vestergaard  1 , Douglas N P Oliveira  1 , Tim S Poulsen  1 , Claus K Høgdall  2 , Estrid V Høgdall  1
Affiliations

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

Lau K Vestergaard et al. Cancers (Basel). .

Abstract

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.

Keywords: Oncomine Comprehensive Assay Plus; Oncomine Comprehensive Assay v3; biomarker discovery; clinical research; genomic profiling; targeted NGS.

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Conflict of interest statement

The authors declare no conflict of interest.

Figures

Figure 1
Figure 1
Identification of overlapping genes and overlapping locus positions. Genes and amplicon coverage of nucleotide positions were extracted from Oncomine™ Comprehensive Assay v3 and Oncomine™ Comprehensive Assay Plus browser extensible data files, respectively. From left to right: Venn diagram showing that 144 genes are intersecting between OCAv3 and OCA-Plus. Out of the 144 genes, 313,769 nucleotide positions are covered in both OCAv3 and OCA-Plus.
Figure 2
Figure 2
Potential sequence artifactual mutations are harbored in variants below the first quartile of mean sample allele ratios. (A) Cluster map of proportional base substitutions in variants above the first quartile. (B) Cluster map of proportional base substitutions in variants below first quartile of allele ratio. OCA-Plus harbored statistical lower levels of C > T and G > A but also significantly higher levels of A > G and T > C substitutions.
Figure 3
Figure 3
Allele frequency-based distribution of base substitutions of variants below first quartile. Dotted lines represent our determined cut-off value by an allele frequency of 11%.
Figure 4
Figure 4
Counts and overlap of identified variants in OCAv3 and OCA-Plus. (A) Bar-chart showing locus variants count per samples. (B) Stacked bar-chart of percentual overlapping locus variants of OCAv3 and OCA-Plus per samples; 37/50 samples overlapped completely and 13/50 showed difference in locus variants, hence only identified in one of the assays.
Figure 5
Figure 5
Overlap of identified variants in OCAv3 and OCA-Plus of clinical relevance. Stacked bar-chart of percentual overlapping locus variants of OCAv3 and OCA-Plus per samples; 42/46 samples overlapped completely, 4/46 showed difference in locus variants, hence only identified in OCAv3.
See this image and copyright information in PMC

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