The NEY GLH offers molecular testing of all appropriate appropriate melanoma referrals (primary melanomas at high risk of recurrence i.e. stage 2C / 3 / 4, metastatic) in a single assay through the use of the Illumina Trusight TSO500 523 gene panel.

This panel can test all of the essential DNA and RNA targets (see table below) listed in the NHSE National Genomic Test Directory for Cancer v7.2, published on 8th June 2023 – NHS England » National genomic test directory. Use of the TSO500 panel will mean that the majority of melanomas will no longer be tested by the methods employed in recent years.

CI Code Clinical Indication Name Test Code Test Name Target Gene(s) Test Scope Technology Eligibility criteria
M7 Adult melanomas

 

M7.1 Multi-target NGS panel – small variant (BRAF, KIT, NRAS) BRAF, KIT, NRAS Small variant detection Panel Primary melanomas at high risk of recurrence i.e. stage 2C / 3 / 4 (metastatic)
M7.2 BRAF hotspot BRAF Small variant detection Simple targeted mutation testing Primary melanomas at high risk of recurrence i.e. stage 2C / 3 / 4 (metastatic),  in rare cases where this cannot be delivered by panel testing. NB will be subject to close audit
M7.3 Multi-target NGS panel – structural variant (NTRK1, NTRK2, NTRK3) NTRK1, NTRK2, NTRK3 Structural variant detection Panel Patient’s clinical status means they are eligible for an NTRK inhibitor in the event an NTRK rearrangement is detected

We will test for small variants in BRAF, NRAS and KIT from extracted DNA in all appropriate referrals (primary melanomas at high risk of recurrence i.e. stage 2C / 3 / 4, metastatic).

Testing for NTRK1, NRK2 and NTRK3 from extracted RNA will only be undertaken after specific clinical request is indicated. This would expect to be where the patient’s clinical status means they are eligible for an NTRK inhibitor in the event an NTRK rearrangement is detected.

Please note that the default pathway is to extract only DNA for BRAF, NRAS and KIT testing. A new sample for RNA extraction will be required if at a subsequent stage NTRK testing is needed. The NTRK status cannot be ascertained from the DNA assay.

TERT promoter status testing will only be made available on specific clinical request.

Reports will include a summary of any variants identified in those genes tested.

Please note that the above changes do not apply to uveal or conjunctival melanomas – please contact the laboratory for more information on the testing pathway for these tumours.

Samples with >20% neoplastic cells across the whole section:

Where only BRAF, NRAS and KIT testing is required, please send one tube (Eppendorf or Universal) containing 5-10 x 10μm FFPE curls.

Where only NTRK testing is required, please send one tube (Eppendorf or Universal) containing 5-10 x 10μm FFPE curls.

Where BRAF, NRAS, KIT and NTRK status are required, please send two tubes (Eppendorf or Universal): each containing 5-10 x 10μm FFPE curls.

Samples with <20% tumour across the whole section where a tumour rich region can be macrodissected out: please send either:

DNA only – macro dissected tumour-rich regions split into one tube as above (preferred); if RNA only, macro dissected tumour-rich regions split into one tube as above (preferred); if DNA and RNA, macro dissected tumour-rich regions split into two tubes as above (preferred); or

DNA only – 10 x 5μm slide mounted sections along with marked H&E with tumour rich area(s) marked; If RNA only, 10 x 5μm slide mounted sections along with marked H&E with tumour rich area(s) marked; if DNA and RNA, 20 x 5μm slide mounted sections along with marked H&E with tumour rich area(s) marked

Samples with <20% tumour across the whole section with diffusely spread tumour cells: send curls as for >20% tumour, though there is an increased risk of false negative results for these samples.

Note exception:

Targeted BRAF hotspot testing will only be undertaken where there is a specific clinical requirement to achieve a rapid result or where samples are of poor quality. This will be tested by an alternative technology, with a target turnaround time of 2-3 days. Please send one tube (Eppendorf or Universal) containing 5-10 x 10μm FFPE curls.

Section preparation is done in the local Cellular Pathology lab under standardised molecular laboratory protocols which includes a clean molecular microtome and histopathologist training/quality assurance in marking up and assessing specimens for molecular testing

However, if your local Cellular Pathology lab is unable to undertake this type of preparation, it would need to make contractual arrangements with another Cellular Pathology lab in order to provide appropriate material to the NEY GLH for genomic testing.

As testing and reporting may be carried out at any one of the three genomic laboratories within the GLH, please send samples to your local NEY GLH Genetics Laboratory. They will direct the testing and reporting as appropriate so that they can act as your single point of call for any queries within the GLH. Costs from that point, including transport and test costs, are commissioned and paid for by NHSE directly to the GLH, so do not need to be paid for by the referring cellular pathology lab.

Please use the NEY GLH Solid Cancer Genomics Referral form. Please ensure that the form:

  • Includes email addresses for your Cellular Pathology secretaries and pathologist;
  • Clearly specifies which tests are needed;
  • Clearly specifies tumour cell nuclei as a percent of nucleated cells (in macrodissected area if macrodissection used).

Reports will be emailed to the referring cellular pathology email address for integration into the full histopathology report and should not be acted upon out of context of those findings. Reports will include a summary of any variants identified in the essential target genes tested.

The TSO500 panel will be run on a weekly basis, with plans to increase the regularity of this as sample numbers increase. Efforts will be made to achieve a 14 day turnaround time. In the first instance though, this is likely to be closer to 21 days. Any urgent targeted BRAF testing will be reported within 2-3 days.