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Oncomine Comprehensive Assay Plus
Truly comprehensive genomic profiling without compromises
Comprehensive genomic profiling (CGP) is advancing precision oncology research through the analysis of multiple relevant biomarkers in a single next-generation sequencing (NGS) test. Current CGP solutions are hindered by technology limitations such as large sample input volumes, high quantity-not-sufficient (QNS) rates, and complex workflows with bioinformatics challenges. The Ion Torrent Oncomine Comprehensive Assay Plus delivers CGP without these sacrifices.
Key highlights of the Oncomine Comprehensive Assay Plus:
- Profile 500+ unique genes for single gene and multi-gene biomarker insights
- Enables analysis of various single-gene variants, such as SNVs, indels, fusions, splice variants, and CNV, including both copy number gains and losses across 500+ genes
- Detection of complex biomarkers associated with immunotherapies such as TMB, MSI
- Support Homologous Recombination Deficiency (HRD) research by detecting mutations in 46 HRR genes, including BRCA LGRs, and assessment genomic scarring with the genomic instability metric (GIM)
- Enables more samples are successfully tested due to low QNS readings and high sequencing success rates of >95%
- Highly automated workflow and streamlined bioinformatics analysis pipeline optimized for Oncomine Comprehensive Assay Plus delivers insights
- Content driven by the Oncomine Knowledgebase and experienced curation scientists helps assure coverage of key targets aligned to published evidence
Analyze multiple biomarkers simultaneously
Detect and analyze all single and multiple gene biomarkers simultaneously from just 20 ng of DNA and RNA from FFPE samples with the Oncomine Comprehensive Assay Plus.
Single gene biomarkers
Detect all types of single-gene variants for targeted-therapy research, such as single-nucleotide variants (SNVs), indels, fusions, splice variants, MET exon skipping at DNA and RNA level and copy number variants (CNVs), including both CNV gain and CNV loss.
Multi-gene biomarkers
Detect emerging biomarkers such as TMB for study of potential response to immunotherapies and MSI for study of predisposition to genetic hypermutability. Analyze mutational signatures, including homologous recombination deficiency (HRD) status through detection of the consequences of genomic instability using GIM.
Robust gene content and complex biomarker detection
The Oncomine Comprehensive Assay Plus covers over 500 unique genes, including key cancer driver genes such as EGFR, BRAF, KRAS, ERBB2, and MET, fusions involving ALK, ROS1, RET, and NTRK1/2/3, and more. Each and every gene is carefully selected by the oncology informatics team based on proprietary databases, peer-reviewed literature, and competitive/industry data, and confirmed with industry-leading pharmaceutical partners.
Single gene biomarkers | Multiple gene biomarkers |
|---|---|
| 166 genes with recurrent hotspot mutations | Genomic Instability Metric (GIM) for genomic instability |
| 333 genes with focal CNV gains or loss | Analysis and visualization of mutational signatures |
| >200 genes with full-coding DNA sequence (CDS) | >1 mb Exonic footprint for TMB |
| 49 fusion driver genes | MSI-H/MSS microsatellite markers for MSI detection |
| MET exon skipping detection at DNA and RNA level | Cellularity (Tumor Fraction) calculation |
| Large genomic alterations in BRCA1 and BRCA2 |
From FFPE sample to biomarker insights with only 60 min of hands-on time
Even with a broad, 500+ gene assay, the Oncomine workflow takes you from 20 ng FFPE sample to biomarker insights in as little as three days. After sample preparation (library and/or templating on Ion Chef System), four samples and one negative control can be multiplexed on the Ion 550 Chip and sequenced on the Ion GeneStudio S5 systems. The raw sequencing data is then analyzed with Oncomine informatics, a streamlined bioinformatics solution that turns sequencing data into annotated biomarker report.
End-to-end CGP research workflow solution with minimum hands-on time
Assay performance
Performance of the Oncomine Comprehensive Assay Plus was evaluated with commercially sourced reference controls and FFPE samples. Highly accurate and sensitive detection for all gene variants are shown, with CNV gain and CNV loss demonstrating exceptional 100% specificity.
| Variant type | Sensitivity | Specificity |
|---|---|---|
| SNVs | 99.6% | 97.6% |
| Indels | 99.5% | 98.1% |
| CNV gain | 100% | 100% |
| CNV loss | 93% | 100% |
| Fusions | 100% | 100% |
Figure 1. The performance of the Oncomine Comprehensive Assay Plus verified using both commercially sourced reference controls and FFPE samples.
Robust fusion detection
With FusionSync technology, the Oncomine Comprehensive Assay Plus covers >1300 isoforms with 49 fusion drivers, and enables:
- Fusion detection from low input samples
- Detection of low level of fusion transcripts
- Ability to detect novel fusions for driver genes
Homologous recombination deficiency
Homologous recombination deficiency (HRD) is becoming a hot biomarker in precision oncology clinical research. Under normal conditions, errors during homologous recombination are repaired in the HRR pathway. Errors in the HRR pathway, such as loss-of-function or deleterious mutations in the associated genes, lead to higher levels of genomic instability. The Oncomine Comprehensive Assay Plus covers 46 key genes in the HRR pathway and measures genomic instability using GIM.
TMB assessment
in-silico OCA Plus target regions with whole exome sequencing (WES)
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Comparison of OCA Plus with Assay F
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TMB harmonization studies
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Figure 3. TMB performance of Oncomine Comprehensive Assay Plus. Fig 3A. Whole exome sequencing (WES) has traditionally been the method of choice for TMB quantitation. In-silico analysis against WES was performed to characterize TMB performance of Oncomine Comprehensive Assay Plus. High correlation was demonstrated via scatter plots between the targeted assay (y-axis) and WES (x-axis) mutation counts which was downloaded from TCGA MC33. Fig 3B. In FFPE samples, TMB values measured using Oncomine Comprehensive Assay Plus are highly correlated with reference TMB (assay F). Fig 3C. OCA Plus has been independently evaluated against WES as part of Friends of Cancer Research’s TMB Harmonization Studies. OCA Plus 5.20 refers to data generated using the 5.20 Ion Reporter analysis workflow.
Learn more at https://www.oncomine.com/cgp