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Biomarker discovery for drug development and drug discovery

The Oncomine™ Comprehensive Assay is a targeted, next-generation sequencing (NGS) assay that enables the detection of relevant SNPs, CNVs, gene fusions, and indels from 143 unique genes to help inform clinical trial research programs.

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Designed for genetic analysis from limited amounts of sample tissue, the Oncomine Comprehensive Assay leverages Ion AmpliSeq™ technology to enable robust results from as little as 10 ng of nucleic acid extracted from an FFPE sample, per primer pool.*

To go from hundreds down to a few relevant cancer drivers, this assay is part of a comprehensive solution—including Ion Torrent™ sequencing and the Oncomine™ Knowledgebase—that enables NGS data analysis and includes a report with interpretations of the findings.

Content

  • Analysis of 143 genes in one sequencing run, including >2,500 amplicons, 170 biomarkers, and 5 positive control genes
  • Hotpots, SNVs, indels, CNVs, and gene fusions from DNA and RNA in a single workflow
  • Content driven by the Oncomine Knowledgebase and industry experts helps assure coverage of key targets aligned to approved therapies and indications
Summaryo-of-variants-740

Figure 1. Summary of variants targeted with the Oncomine Comprehensive Assay and associated relevant information included in the Oncomine Knowledgebase Reporter.

Performance

  • Characterized with molecular standards and >300 FFPE samples
  • NGS results match those of verified single-gene tests (Table 1)
  • Additional relevant variants detected
  • Results validate the multiplexed PCR-based RNA-Seq approach for detecting targeted gene fusions
  • Reproducible and sensitive detection of variants across multiple cancer types
  • Robust performance from as little as 10 ng isolated from FFPE samples including fine needle biopsies

Relative performance of Oncomine Comprehensive Assay

Gene test

Molecular pathology results

Sensitivity

Specificity

BRAF
V600

BRAF: 63 samples

  • 29 positive (26 V600E, 2 T599dup, 1 V600K)
  • 34 negative
  • Melanoma, colorectal adenocarcinoma, lung adenocarcinoma, endometrial adenocarcinoma

100%
(29/29)

100%
(34/34)

EGFR
L858R & Exon 19 del

EGFR: 22 samples

  • 3 positive (2 Exon 19 del, 1 L858R)
  • 19 negative
  • Lung adenocarcinoma, sarcomatoid carcinoma

100%
(3/3)

100%
(19/19)

KRAS
G12, G13, Q61

KRAS: 21 samples

  • 11 positive (1 G12A, 2 G12 D, 5 G12V, 2 G13D, 1 Q61K)
  • 10 negative
  • Colorectal adenocarcinoma, small bowel adenocarcinoma

100%
(11/11)

100%
(10/10)

Table 1. Comparison to verified single-gene test results. The Oncomine Comprehensive Assay demonstrates 100% sensitivity and 100% specificity across 103 verified single-gene tests. Source: Hovelson et al. (2015) Development and validation of a scalable next-generation sequencing system for assessing relevant somatic variants in solid tumors. Neoplasia 17:385-399.

Report

Oncomine Informatics—powerful tools for cancer research, based on a curated, verified knowledgebase and part of a comprehensive solution for NGS data analysis.

  • Filtering from hundreds to just a few key cancer driver variants
  • Annotation of the findings in context
    • Guidelines: US FDA, US NCCN, ESMO, EMA
    • On-market labels
    • Global clinical trials
  • Easy-to-use interface enabling user-generated reports in three steps: upload, filter, report
  • Pre-rendered supplementary information tables

Oncomine Comprehensive Assay Workflow

The Oncomine™ NGS oncology workflow enables you to go from hundreds of variants down to a few relevant cancer drivers, with a report including interpretation of the findings. A comprehensive workflow including the Ion PGM™ System is enabled.

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* The Oncomine Comprehensive Assay includes two DNA and one RNA primer pools. For each sample analyzed, a total of 30 ng input nucleic acid material is required.