A comprehensive next-generation sequencing (NGS) assay for translational and early clinical research

A comprehensive next-generation sequencing (NGS) assay for translational and early clinical research

The Oncomine Comprehensive Assay v3 is a multi-biomarker NGS assay that covers 161 of the most relevant cancer genes, based on the Oncomine Knowledgebase and from collaborations with leading cancer research institutions and pharmaceutical companies. The low sample input requirement enables the analysis of even small and challenging formalin-fixed paraffin-embedded (FFPE) samples.

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Highlights of the Oncomine Comprehensive Assay v3 include:

  • Only 10 ng of DNA or RNA sample input, making the Oncomine Comprehensive Assay v3 an ideal solution for the analysis of challenging FFPE samples
  • Detects relevant SNVs, CNVs, gene fusions, and indels from 161 unique cancer-associated genes in one streamlined workflow
  • High specificity, sensitivity, and reproducibility across different research laboratories, as demonstrated in translational and clinical research projects including the NCI Match Trial
  • Efficient workflow on Ion Chef System plus Ion GeneStudio S5 or Ion Torrent Genexus system with high multiplexing flexibility and fast time to results

"The requirement of a lower DNA input for the Oncomine assay is a significant advantage when primary samples are becoming increasingly limited."

—John Bartlett, PhD

Director of Transformative Pathology Platform
Ontario Institute for Cancer Research

Oncomine Comprehensive Assay v3 gene content

The Oncomine Comprehensive Assay v3 includes:

  • Hotspot SNVs and indels, CNVs, and gene fusions
  • Kinase domain coverage to span the entire kinase domain in several critical receptor tyrosine kinases. This increases the likelihood of detecting functionally relevant mutations in addition to known actionable and prevalent variants (ALK, BRAF, DDR2, EGFR, ERBB2, KIT, MET, PDGFRA, RET, ROS1.)
  • Representation of genes involved in DNA repair (31 genes in DNA repair pathway)
  • Coverage of MAPK, PI3K, and cell cycle pathway genes

Hotspot SNV CNV Gene Fusion

To see the full gene content of the Oncomine Comprehensive Assay v3, download the flyer.


Oncomine Comprehensive Assay v3 performance

 

True positive

False positive

False negative

Sensitivity

Positive predictive value

Hotspots

504

9

4

99.21%

98.25%

Indels

31

0

1

96.88%

100%

DeNovo SNV

602

11

18

97.10%

98.21%

De novo InDel

24

2

4

85.71%

92.31%

Fusions

82

4

4

95.35%

95.35%

Table 1. The performance of the Oncomine Comprehensive Assay v3 has been verified using 20 FFPE cancer tissue samples and commercially available standard material from HorizonDx and SeraCare.


Assay analytical validation—results of the NCI Match Trial

Assay analytical validation--results of the NCI Match Trial
Data adapted from: Lih CJ, et al. Analytical validation of the NGS assay for a nationwide signal-finding clinical trial molecular analysis for therapy choice clinical trial. J Mol Diagn. 2017 Mar;19(2):313-327.


Flexible configurations to fit your needs

The Oncomine Comprehensive Assay v3 has been optimized for throughput of eight samples on the Ion GeneStudio S5 Systems or six samples on the Ion Torrent Genexus System, with automated library preparation using the Ion Chef System. The assay is available in two configurations: manual and automated (using Ion Chef System for library preparation) and includes the DNA and RNA primer panel and library preparation reagents.