Gastrointestinal stromal tumours (GISTs)
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The NEY GLH offers molecular testing of all appropriate Gastrointestinal stromal tumours (GIST) referrals 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 National Genomic Test Directory for Cancer v7.2 (published 8th June 2023). Use of the TSO500 panel will mean that GISTs will no longer be tested by Sanger sequencing.

CI Code Clinical Indication Name Test Code Test Name Target Gene(s) Test Scope Technology
M8 GISTS

 

 M8.1 Multi-target NGS panel – small variant (KIT, PDGFRA) KIT, PDGRFA Small variant detection Panel
M8.2 Multi-target NGS panel – structural variant (NTRK1, NTRK2, NTRK3) NTRK1, NTRK2, NTRK3 Structrual variant detection Panel

 

We will test KIT and PDGFRA from extracted DNA in all appropriate referrals. Testing for NTRK1, NRK2 and NTRK3 from extracted RNA will only be undertaken after specific clinical request is indicated.

Please note that the default pathway is to extract only DNA for KIT and PDGFRA 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.

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

1. For samples with >20% neoplastic cells across the whole section:

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

2. For samples with <20% tumour across the whole section where a tumour rich region can be macrodissected out, please send either:

  • DNA only – macrodissected tumour-rich regions split into one tube as above (preferred); if RNA only, macrodissected tumour-rich regions split into one tube as above (preferred); if DNA and RNA, macrodissected 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

3. 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.

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 genetics 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 percentage of all 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.