A new paradigm in testing for NSCLC targeted therapies

In the era of personalized medicine, molecular profiling has become essential for the treatment of patients with metastatic non-small cell lung carcinoma (NSCLC).  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.

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The Oncomine Dx Target Test will be available in July 2017. LabCorp, NeoGenomics, and Cancer Genetics Inc. will be among the first customers to implement testing.

One test that can expedite NSCLC treatment selection decisions

The Ion Torrent Oncomine Dx Target Test is the first targeted NGS-based in vitro diagnostic test for NSCLC, simultaneously delivering multiple biomarker results from one sample within four days and helping inform treatment decisions.

  • Multiple therapies—one test indicated as a companion diagnostic device to aid in selecting NSCLC patients for treatment with targeted therapies, including IRESSA® (gefitinib) for EGFR L858R and exon 19 deletion, TAFINLAR + MEKINIST® (dabrafenib in combination with trametinib) for BRAF V600E, or XALKORI® (crizotinib) for ROS1 fusion.
  • Multiple biomarkers—one test for detection of 369variants in 23 cancer-associated genes that are clinically associated with NSCLC
  • One sample—one sample used to deliver multiple biomarker results, minimizing the risk of depleting tissues and requiring additional biopsies
  • Fast results— From sample extraction to clinical test report, the total workflow turn-around time is 4 days.
  • Automated clinical report—The Oncomine Dx Target Test results are presented in a single, two-part Clinical Test Report that incorporates NSCLC biomarker results, associated therapy indication(s), and other biomarker results.
  • Established performance—Concordance with comparator methods based on FISH or PCR was established for EGFR, BRAF and ROS1.

Technical and validation data for the Oncomine Dx Target Test ›

Oncomine Dx Target Test content

Currently, five NSCLC-associated biomarkers are targeted by first line treatment (left side of Figure 2). Additional biomarkers have been recommended by scientific guidelines for adding potential value in the patient stratification process. The Oncomine Dx Target Test is the only available diagnostic test that delivers multiple biomarker identification at once (right side of Figure 2). The test includes three biomarkers, validated for selection of relevant targeted therapies (EGFR, ROS1, or BRAF), and twenty additional genes, relevant for NSCLC pathogenesis analytically validated for variant detection from NSCLC tissue.

Figure 2. NSCLC biomarkers for selection of first line therapies and currently used techniques.
*The test reports fusions/translocations variants for ROS1 only. The test only reports ALK, MET, and RET mutations and does not report ALK,MET and RET fusions/translocations.


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.

Download an example of an Oncomine Dx Target Test report ›

DNA  Sequence Variants

Gene

Display name

Amino acid change

Nucleotide change

Test result

Hotspot ID

Associated therapy

EGFR

EGFR L858R

p.Leu858Arg

c.2573T>G

POSITIVE

COSM6224

IRESSA® (gefitinib)

BRAF

BRAF V600E

p.Val600Glu

c.1799T>A

POSITIVE

COSM476

TAFINLAR + MEKINIST® (dabrafenib in combination with trametinib)

Gene Fusions (RNA)

Gene

Display name

Test result

Associated therapy

ROS1

ROS1 Fusion

POSITIVE

XALKORI® (crizotinib)

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. (For illustrative purposes only. EGFR, BRAF and ROS1 are mutually exclusive.)

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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 from RNA isolated from formalin-fixed, paraffin-embedded (FFPE) tumor tissue samples from patients with non-small cell lung cancer (NSCLC) 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 FFPE tumor slide specimens.
  • The Oncomine Dx Target Test has been validated to detect the following somatic mutations: single-nucleotide variations (SNVs), multi-nucleotide variations (MNVs), and deletions of 3, 6, 9, 12, 15, and 18 base pairs (bps).
  • 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.