A new paradigm in testing for targeted therapies in NSCLC and CC
In the era of personalized medicine, molecular profiling has become essential for the treatment of cancer patients. With an increasing number of genomic alterations becoming clinically relevant, sequential testing of individual mutations becomes a significant challenge for clinical laboratories. Next-generation sequencing (NGS), which can detect multiple alterations at once from a small amount of tissue, offers a solution.
The Oncomine Dx Target Test is currently available in the following commercial labs:
One test that can expedite treatment selection decisions
The Ion Torrent Oncomine Dx Target Test is the first targeted NGS-based in vitro diagnostic test for non-small cell lung cancer (NSCLC), simultaneously delivering multiple biomarker results for multiple targeted therapies from one sample within four days.
|Cancer type||Gene||Targeted therapies|
|NSCLC||BRAF||TAFINLAR® (dabrafenib) in combination with MEKINIST® (trametinib)|
|EGFR, L858R and exon 19 deletions||IRESSA® (gefitinib)|
Figure 1. List of genes for therapeutic use.
- Identify patients for multiple therapies—one test indicated as a companion diagnostic (CDx) device to aid in selecting NSCLC and CC patients for treatment with targeted therapies
- Multiple biomarkers from one limited sample—one test for detection of 23 genes, minimizing the risk of depleting tissues and requiring additional biopsies. Based on Ion AmpliSeq™ technology, the required input is as low as 10 ng DNA and RNA.
- One workflow, helps save time—laboratory results can be generated within 4 days
- Established performance—Concordance with FDA approved or validated reference methods based on FISH, PCR, Sanger sequencing, or NGS was established for all CDx biomarkers:
- 100% overall percent agreement (OPA), positive percent agreement (PPA) and negative percent agreement (NPA) for BRAF, EGFR exon 20 insertions, and ROS1 fusions
- 99% OPA, PPA, and NPA for EGFR exon 19 deletions and L858R
- 92% OPA, 91% PPA, and 92% NPA for RET fusions
- 98% OPA, 99% PPA, and 97% NPA for IDH1
Oncomine Dx Target Test content
Gene targets included for NSCLC
|Gene targets for therapeutic use|
|BRAF: mutation||EGFR: L858R, exon 19 deletions, and exon 20 insertions||ROS1: fusions||RET: fusions|
|Analytically validated targets|
Figure 2. Complete gene list. *The test reports fusion/translocation variants for ROS1 and RET only. The test only reports ALK and MET mutations. **Performance for the additional gene target variants has been validated based on a representative method. Only IDH1 is reported for CC.
The power of next generation sequencing
Next-generation sequencing (NGS) can sequence hundreds to thousands of genes and detect multiple biomarkers at the same time. The sequencing takes place in a chip that contains millions of wells (flow cells) with separate sequencing reactions taking place in each well, allowing many genes to be sequenced at once and multiple variations to be detected simultaneously, unlike traditional companion diagnostic technologies such as FISH, IHC, or PCR, which only analyze one target gene at the time.
Figure 3. The NGS process starts with extraction of the DNA and/or RNA, which is processed in the chip in the Ion PGM Dx instrument, and results are analyzed and reported by a dedicated bioinformatics solution.
Oncomine Dx Target Test report
The Oncomine Dx Target Test Clinical Test Report is automatically generated as a PDF and incorporates relevant patient, sample, and test information required to help ensure high-performance standards, regulatory compliance, and quality control. The test results are presented in two-parts: companion diagnostic marker results with associated therapy indications and cancer driver analytical-only biomarker results in a separate section. The report is customizable and LIMS system-compatible.
NSCLC results for sequence variations for therapeutic use (for illustrative purposes only: EGFR, BRAF, ROS1, and RET are mutually exclusive)
DNA Sequence Variants
Amino acid change
EGFR exon 20 insertions
|p.Ala767_Ser768insSerValAsp||c.2133_2312ins GCGTGGACA||POSITIVE||COSM13428||EXKIVITY™ (mobocertinib)|
TAFINLAR® + MEKINIST® (dabrafenib in combination with trametinib)
Gene Fusions (RNA)
|RET||RET Fusions||POSITIVE||GAVRETO™ (pralsetinib)|
CC results for sequence variations for therapeutic use (for illustrative purposes only)
Amino acid change
Figure 4. An example of the Oncomine Dx Target Test report format. The report includes a section with results of the validated biomarkers and information about relevant treatment indication, as well as a section with the other biomarkers not validated for treatment selection (not shown).
Abbreviated Intended Use: The Oncomine Dx Target Test is a qualitative in vitro diagnostic test that uses targeted high-throughput, parallel-sequencing technology to detect single-nucleotide variants (SNVs) and deletions in 23 genes from DNA and fusions in ROS1 and RET from RNA isolated from formalin-fixed, paraffin-embedded (FFPE) tumor samples from patients with non-small cell lung cancer (NSCLC) and IDH1 R132 mutations from FFPE tumor tissue samples from patients with cholangiocarcinoma (CC) using the Ion PGM Dx System.
Test limitations and warnings
- Use of this product must be limited to personnel trained in the techniques of PCR, NGS, and the use of the Oncomine Dx Target Test and the Ion PGM Dx System.
- The Oncomine Dx Target Test has only been validated for use with NSCLC and CC FFPE tumor slide specimens.
- The Oncomine Dx Target Test has been validated to detect the following somatic mutations: RNA fusions, single-nucleotide variations (SNVs), multi-nucleotide variations (MNVs), and deletions of 3, 6, 9, 12, 15, and 18 base pairs (bps) and insertions of 3, 6, 9, and 12 base pairs (bps) from DNA.
- The Oncomine Dx Target Test is only validated for use with the Ion PGM Dx System and the Veriti Dx 96-Well Thermal Cycler.
- The Oncomine Dx Target Test is only validated for use with 10 ng each of DNA and RNA per sample. Input amounts lower or higher than 10 ng are not recommended.
- Both the DNA and RNA from a single sample extraction must meet the concentration requirements specified in the procedure. Do not use DNA from one extraction with RNA from a different extraction.
- The effects of potential variations in FFPE specimen fixation have not been evaluated.
- Extraction from FFPE sample curls has not been evaluated.
- A potential source of contamination in the procedure is nucleic acid from previous sample processing steps. Follow good laboratory practices and all precautions and guidelines in these user guides to avoid cross-contamination between samples.
- The Oncomine Dx Target Test is a qualitative test. The test is not for quantitative measurements of percent mutation.
- The Ion OneTouch Rack Kit has only been designed to work with GeneMate SnapStrip 8-Strip 0.2 mL PCR Tubes. Tubes from other manufacturers may not fit properly in the rack, resulting in a higher risk of user error.
For NSCLC, the Oncomine Dx Target Test assay definition file includes prevalent but not all rare or newly identified RET isoforms, ROS1 isoforms, and EGFR exon 20 insertions. The Oncomine Dx Target Test may miss rare or newly identified:
- RET isoforms carried by a subset of patients who may derive benefit from GAVRETO™ (pralsetinib)
- ROS1 isoforms carried by a subset of patients who may derive benefit from XALKORI® (crizotinib)
- EGFR exon 20 insertions carried by a subset of patients who may derive benefit from EXKIVITY™(mobocertinib)
For In Vitro Diagnostic Use.