Oncomine Dx Target Test—US

The Ion Torrent Oncomine Dx Target Test is the first distributable NGS-based in vitro diagnostic test for non-small cell lung cancer (NSCLC), cholangiocarcinoma (CC), astrocytoma (AC), oligodendroglioma (OG), anaplastic thyroid cancer (ATC), medullary thyroid cancer (MTC), and thyroid cancer (TC), simultaneously delivering multiple biomarker results for multiple targeted therapies from one sample within four days.

Figure 1. List of genes for therapeutic use.

Figure 2. Complete gene list. *The test reports fusion/translocation variants for ROS1 and RET only. This test only reports mutations for ALK and MET. **Performance for the additional gene target variants has been validated based on a representative method. Only IDH1 is reported for CC. Only RET mutations are reported for MTC and only RET fusions are reported for TC.

Table 1: Variants with established analytical performance only.

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 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 ›

NSCLC results for sequence variations for therapeutic use (for illustrative purposes only: EGFR, BRAF, ERBB2/HER2, ROS1, and RET are mutually exclusive)

DNA  Sequence Variants

Gene Fusions (RNA)

CC results for sequence variations for therapeutic use (for illustrative purposes only)

AG or OG results for sequence variations for therapeutic use (for illustrative purposes only)

ATC results for sequence variations for therapeutic use (for illustrative purposes only)

MTC results for sequence variations for therapeutic use (for illustrative purposes only)

TC results for sequence variations for therapeutic use (for illustrative purposes only)

Figure 4. Examples of the Oncomine Dx Target Test report formats. The report includes a section with results of validated bimarkers and information about relevant treatment indication, as well as a section with the other biomarkers not validated for treatment selection (not shown).

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Abbreviated Intended Use: The Oncomine Dx Target Test is a qualitative in vitro diagnostic test that uses targeted highthroughput, parallel-sequencing technology to detect single nucleotide variants (SNVs), deletions, and insertions in 23 genes from DNA and fusions in ROS1 and RET from RNA isolated from formalin-fixed paraffin-embedded (FFPE) tumor tissue samples from patients with non-small cell lung cancer (NSCLC), IDH1 SNVs from FFPE tumor tissue samples from patients with cholangiocarcinoma (CC), BRAF V600E mutations from FFPE tumor tissue samples from patients with anaplastic thyroid cancer (ATC), IDH1 and IDH2 SNVs from FFPE tumor tissue samples from patients with astrocytoma (AC) or oligodendroglioma (OG), RET SNVs, multi-nucleotide variants (MNVs), and deletions from DNA isolated from FFPE tumor samples from patients with medullary thyroid cancer (MTC), and RET fusions from RNA isolated from FFPE tumor tissue samples from patients with thyroid cancer (TC) 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 FFPE tumor slide specimens. The use of fine needle aspirates for thyroid cancer (TC) specimens has not been validated.
• The Oncomine Dx Target Test has been validated to detect the following somatic mutations: single-nucleotide variations (SNVs), multi nucleotide variations (MNVs), deletions of 3, 6, 9, 12, 15, and 18 base pairs, and insertions of 3, 6, 9, and 12 base pairs in DNA, and fusions in RNA.
• The Oncomine Dx Target Test is only validated for use with the Ion PGM Dx System and the Veriti Dx 96‑well Thermal Cycler, 0.2 mL.
• The Oncomine Dx Target Test is only validated for use with 10 ng each of DNA and RNA per sample. Input amounts less than or greater 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.
• Interference in variant calling can be observed at higher concentrations of chenodeoxycholic acid (≥30 nmol/mL bile acid) in cholangiocarcinoma (CC) clinical FFPE samples with IDH1 variants present at an allelic frequency near the limit of detection (LoD).
• The Oncomine Dx Target Test has not been validated for the detection of RET insertions.
• Users are cautioned that DNA variant-positive calls in the RET genomic region have been observed to produce multiple variant calls, even when only one variant is present. These RET variants are all activating and do not change the patient’s clinical appropriateness for selpercatinib.
• High variation in fusion reads can be observed with fusion-positive samples. A decrease in fusion reads over time has been observed when testing slides from TC tissue under storage.
• For non-small cell lung cancer (NSCLC), the Oncomine Dx Target Test assay definition file includes prevalent but not all rare or newly identified RET isoforms, ROS1 isoforms, EGFR exon 20insertions, EGFR exon 19 deletions, and ERBB2/HER2 activating mutations. The Oncomine Dx Target Test may miss rare, complex, or newly identified:
  • RET isoforms carried by a subset of patients who may derive benefit from pralsetinib or selpercatinib
  • ROS1 isoforms carried by a subset of patients who may derive benefit from crizotinib
  • EGFR exon 20 insertions carried by a subset of patients who may derive benefit from amivantamab-vmjw
  • EGFR exon 19 deletions carried by a subset of patients who may derive benefit from gefitinib
  • ERBB2/HER2 activating mutations carried by a subset of patients who may derive benefit from fam-trastuzumab deruxtecan-nxki
• For TC, the Oncomine Dx Target Test assay definition file includes the most prevalent but not all rare or newly identified RET isoforms. The Oncomine Dx Target Test may miss a subset of patients carrying these rare or newly identified RET isoforms who may derive benefit from selpercatinib.
• For medullary thyroid cancer (MTC), the Oncomine Dx Target Test assay definition file includes the most prevalent but not all rare or newly identified RET SNVs, MNVs and deletions. The Oncomine Dx Target Test may miss a subset of patients carrying these rare or newly identified RET SNVs, MNVs and deletions who may derive benefit from selpercatinib.
• For astrocytoma (AC) and oligodendroglioma (OG), the Oncomine Dx Target Test included prevalent but not all rare IDH2 variant clinical specimens in the assay reproducibility study. The Oncomine Dx Target Test may miss rare IDH2 variants carried by patients who may derive benefit from vorasidenib.
• The Oncomine Dx Target Test has only been validated for use with FFPE tumor slide specimens. The validation of the use of derivative core needle biopsy (CNB) samples and stereotactic biopsy (STB) samples for astrocytoma (AC) and oligodendroglioma (OG), with the Oncomine Dx Target Test to support inclusion of these type of samples has not been performed.
• The safe and effective use of the variants reported in Table 1 has not been established for selecting therapy using this device. The variants for KRAS (COSM512/p.Gly12Phe/c.34_35delGGinsTT and COSM516/p.Gly12Cys/ c.34G>T), MET (COSM707/p.Thr1010Ile/c.3029C>T) and PIK3CA (COSM754/p.Asn345Lys/c.1035T>A) have been analytically validated. Performance of all other variants identified by the test, other than the clinically validated therapeutic variants and analytically validated variants, has not been directly demonstrated.

For In Vitro diagnostic use.