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Solid tumour panel (FIND IT)

Test category:

Oncology - Solid tumour

Use of test

Purpose:

The Contextual Genomics FIND IT® Cancer Hotspot Panel is a multiplex next generation sequencing assay, designed to identify common, clinically actionable genomic alterations in most solid tumour samples. The FIND IT panel provides a personalised understanding of a patient’s tumour.

Utility:

This is an assay of mutations in solid tumours to inform decisions regarding the choice of chemotherapy. The mutations targeted by this assay are not selected on the basis of providing diagnostic or prognostic information.

​The assay simultaneously evaluates the mutation status of tumour DNA at more than 140 well-characterised positions (hotspots) and 20 exons in 30 cancer-associated genes. Mutations are reported with information linking them to details on treatment sensitivity and resistance, as well as clinical trial information. 

Ethical considerations:

This is an assay for non-heritable mutations. It does not raise issues of ethics or consent that are different from most other investigations ordered in the routine care of a patient. However, it is possible that a mutation identified in cancer tissue is familial rather than having occurred during the development of the cancer. A familial mutation could have significant implications for the patient tested and relatives. The probability that a mutation identified by the assay is familial varies from gene to gene.

Methodology:

This test involves targeted sequence analysis of hotspot mutations/coding exons of the requested genes and transcripts (listed below, see Hotspot Panel table). DNA is extracted and targets of interest amplified using a highly multiplexed in-house designed PCR assay, sequenced using Illumina technology and analysed using a validated, custom-built bioinformatics pipeline. Hotspot variants are categorised into clinical significance tiers as per Li et al. 2017 (PMID 27993330). Variants of strong or potential clinical significance (tier I or II) will be reported. VUS and likely benign variants (tier III and IV) will not be reported. Please contact the laboratory if tier III or IV variants are required.

Single nucleotide changes, insertions (1-18 bp) and deletions (1-24 bp) are detected by this assay. Limit of detection is approximately 5% variant allele ratio; the ability to detect a particular mutation may depend upon the tumour content of the tested sample and the proportion of the mutant tumour clone. Rare genetic variation can interfere with this assay.

CNVs (e.g. gene amplification or large deletions) and gene rearrangement events (e.g. gene fusions) will not be detected by this assay. Approximately 20% of MET exon 14 skipping mutations are large deletions, and will not be detected. BRCA gene mutations, MSI and tumour mutational burden are not assessed in this assay. This assay does not differentiate between germline (hereditary)and somatic mutations. The therapeutic implications of these results should be considered in conjunction with other clinical information available to the treating oncologist.

Requesting the test

Ordering:

This test is usually requested by a surgeon or oncologist.

Request form:

Download the solid tumour somatic mutation request form.

Sample required:

Formalin-fixed, paraffin embedded tissue (FFPE) - 15 sections of 4 uM thickness, dried overnight at 37°C onto charged/coated slides.

Special instructions:

Please stain the first section with H&E, and label each slide with patient and block identifiers. Label the unstained sections sequentially (slides 2-15). The request should be accompanied by the somatic mutation request form (above) and a copy of the original histopathology report.

Turnaround time:

7 business days from receipt of sections by the testing laboratory.

Price:

$350 - $595.

If the patient is eligible for rebated testing of a focused panel for lung cancer, colorectal cancer, or melanoma, the price of expanding the test to the full FIND IT panel is $350.

If the patient is not eligible for any of these rebates, the price for the full FIND IT panel is $595.

Rebate:

This test is not rebated by Medicare in full. Patients who fulfill the Medicare requirements for one of the FIND IT focused gene panels would be eligible for a partial rebate. The laboratory assumes that the patient or client has provided informed financial consent for the test.

Click here for our billing policy.