Molecular Oncology Diagnostics
The Molecular Oncology Diagnostic team is built on a collaboration of clinicians, scientists and researchers, and contributes to an integrated Solid Tumour Diagnostic Service.
Requests for any molecular testing (including IHC, FISH, sequencing) should be addressed to:
Solid Tumour Specialist Diagnostic Services Team
Yorkshire and North East Genomic Laboratory Hub (Y&NE GLH), Central Lab
Genomic Specimen Reception (Histopathology Department)
Bexley Wing (Level 5)
St James's University Hospital
Beckett Street
Leeds
LS9 7TF
Email: leedsth-tr.leedsmolecularhistology@nhs.net
To contact the Genetics laboratory regarding any molecular oncology testing please email: mod.lth@nhs.net
Recent advances in our understanding of the molecular basis of cancer have led to the introduction of a number of targeted cancer therapies which are effective only in certain sub-populations of patients with a particular tumour type. Treatment tailored to an individual’s genetic tumour profile will be an important step towards personalised therapy with several potential benefits for the patient: improvement of quality of life; reduction of toxicity; shorter hospital stays; and improved overall survival. For the specific testing available please see the different tumour web pages.
Sample Requirements
Please use the new molecular genetic testing request form (download here), and estimate the % tumour nuclei within the circled area in the material provided for testing.
Please use clear patient identifiers on the sample containers, slides and referral form.
All patient samples must be labelled with at least three patient identifiers.
FISH Testing - Two labelled H&E stained slides are required as above, plus 4 sections of 4µm thickness for 1p/19q FISH studies. Slides for FISH studies should be coated and positively charged
Mutation and/or Methylation Testing - Two labelled H&E stained slides are required as above, plus 10 sections (these don't need to be coated or positively charged) of 4µm thickness.
BRAF Fusion Testing - Two labelled H&E stained slides are required as above, plus 20 sections of 4µm thickness (not coated or positively charged) for BRAF-KIAA1549 fusion testing by RNA analysis. Special precautions should be in place to reduce the risk of contamination of RNases. Gloves should be worn at all times when handling FFPE blocks/sections for RNA work
Circulating Tumour DNA Testing – Testing is performed on cfDNA samples extracted from plasma, after plasma separation from whole blood by centrifugation. Whole blood samples for cfDNA extraction must be either transported in blood stabilization tubes, which must have been transported and stored according to the requirements of the particular tubes used, or must be transported in EDTA, in which case plasma separation must occur within four hours of the blood being taken. Please contact the laboratory on 0113 2064570. The request card can be downloaded here.
Turnaround times
The table below is the turnaround times given by NHS England.
|
Clinical Urgency |
Category (mapping to test directory) |
Sub-categories |
Calendar Days |
Examples |
|
URGENT |
Ultra Rapid |
N/A |
3 days |
QF-PCR for rapid trisomy detection |
|
|
|
|
|
Urgent haemato-oncology FISH/RT-PCR |
|
|
|
|
|
PCR-based tests where the result is needed urgently for prenatal diagnosis |
|
URGENT |
Ultra rapid |
NA |
7 days |
NIPT |
|
URGENT |
Rapid |
Rapid |
14 days |
Microarray for prenatal / urgent postnatal (e.g. neonatal referrals) |
|
|
|
|
Urgent Haemato-oncology karyotyping |
|
|
|
|
|
Mutation specific molecular pathology tests |
|
|
|
|
|
Southern blot tests where the result is needed urgently for prenatal diagnosis |
|
|
|
|
|
PCR-based tests for predictive testing and confirmation of neonatal results |
|
|
|
|
Complex rapid |
21 days |
Urgent panels and exomes for relevant indications NIPD |
|
|
|
|||
|
NON-URGENT |
Standard |
Somatic Cancer |
21 days |
Standard HO karyotyping (e.g. MDS) |
|
|
|
|
|
NGS panels for HO referrals |
|
|
|
|
|
NGS panels for molecular pathology referrals |
|
|
|
Rare Disease |
42 days (6 weeks) |
Standard paediatric microarray Standard single gene and small gene panel (<10 gene) sequencing Known familial mutation testing Standard STR based analysis Postnatal karyotyping (e.g. fertility or familial microarray follow-up) |
|
NON-URGENT |
Complex Standard |
Rare Disease |
84 days (12 weeks) |
Large gene-panels (>10 genes) or WES for standard referral indications |
|
|
|
|
Part a) 42 days (6 weeks) |
Expectation for delivery of centralised WGS (from DNA sample receipt to return of vcf and/or filtered variants to GLH) |
|
|
|
|
Part b) 42 days (6 weeks) |
Validation/reporting of centralised WGS results after receipt at GLH |
Local Turnaround Times (Working Days)
- FISH = 2-5 days
- NGS Mutation Testing = 5-10 days
- Methylation Testing = 5-10 days
- BRAF fusion = 5 working days
- Priority can be adjusted in line with clinical urgency and the need to present at MDT meetings
- Most urgent FISH results can be reported within 2-3 days of sample receipt
In Development
We are currently looking at expanding the range of genes tested by NGS to ensure the lab can offer all the tests described in the NHSE national cancer test directory published in 2018 - https://www.england.nhs.uk/publication/national-genomic-test-directories/.
The following test is unaccredited:
Testing for MLH1 methylation by pyrosequencing
Whilst the majority of our tests are accredited to ISO15189 by UKAS, the test above has recently been introduced into service and is not yet accredited.
