Comprehensive and simultaneous genomic profiling across 500+ genes, TMB, and MSI from 10ng FFPE sample

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 the sacrifices.


Key highlights of the Oncomine Comprehensive Assay Plus:

  • Profile 500+ unique genes for single gene and multiple gene biomarker insights
  • Detect single gene biomarkers from all variant types including SNVs, indels, CNVs, known and novel fusions, and splice variants
  • Analyze complex multi-gene biomarkers for mutational signatures, including tumor mutational burden (TMB) microsatellite instability (MSI) for immunotherapy research
  • Detect deficiencies in homology recombination repair (HRR) by assessing variants in 42 HRR pathway genes and genomic instability with sample level loss of heterozygousity (LOH)
  • Detect complex loss of function variants (including gene-level LOH) in key HRR genes, including BRCA1 and BRCA2
  • 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 in as little as 3 days


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

Single gene biomarkers

Detect all types of single-gene variants for targeted-therapy research, such as single-nucleotide variants (SNVs), indels, novel and known fusions, splice variants, MET exon skipping at DNA and RNA level and copy number variants (CNVs), including both CNV gain and CNV loss.

TMB

Multiple 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 and assess genomic instabilities, including homologous recombination deficiency (HRD) status through detection of gene-level and sample-level LOH

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

165 genes with recurrent hotspot mutations LOH detection—gene level and sample level
333 genes with focal CNV gains or loss Analysis and visualization of mutational signatures
227 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  


There is no CGP without CNV detection

CNV is a structural variant detected in oncogenes and tumor suppressor genes that results in duplication, deletion, or inversion of genetic sequences.  Currently, 116 unique CNV genes are studied in over 1,000 active clinical trials. These variants are critical to understanding of tumorigenesis and this importance is underscored with this statistic.  The exclusion of CNVs in genomic profiling means you are missing valuable insights and does not translate into truly comprehensive genomic profiling.


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

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 98.9% 99.7%
Indels 100% 96.6%
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.


Novel and known 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 repair pathway research

Homologous recombination repair 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 42 key genes in the HRR pathway and measures genomic instability using sample-level LOH with high concordance.


TMB assessment

in-silico OCA Plus target regions with whole exome sequencing (WES)

Comparison of OCA Plus with Assay F

TMB harmonization studies

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. Orthogonal TMB vs observed TMB from Oncomine Comprehensive Assay Plus.  A second comparison was conducted using a commercially available with FFPE samples, and demonstrated high correlation in TMB values. Fig 3C. Lastly, OCA Plus independently evaluated against WES and the Oncomine Tumor Mutation Load Assay as part of Friends of Cancer Research’s TMB Harmonization Studies.


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