Requesting genomic tests in England
Overview
This section explains:
This does not cover whole genome sequencing (WGS). Learn more about whole genome sequencing →
The Test Directory
The National Genomic Test Directory for Cancer lays out the genomic tests which NHS England funds. It also states:
The tumour types for which they may be requested;
The technologies by which they may be performed;
The situations under which testing may be requested.
Each tumour type is given a clinical indication code, and each test is given a test code.
In general, the thrust of the Test Directory is that genomic testing in cancer should be undertaken by next-generation sequencing (NGS) panel testing wherever possible. It does, however, allow for targeted testing in select situations.
Genomic Laboratory Hubs (GLHs)
Each GLH is responsible for making the Test Directory available to its population. England is divided between seven GLHs.
Each GLH is led by a trust which usually hosts the GLH’s main genomics lab. The idea is that the bulk of NGS panel testing should be centralised within the GLH.
A GLH may choose to subcontract other centres within its geography to undertake some testing on its behalf. This may include niche tests which cannot be easily implemented at the centralised laboratory or targeted testing for cases not suitable for NGS panel testing. These are Local Genomic Laboratories (LGLs).
How do I request a genomic test?
They key steps are:
Check the Test Directory to make sure that the test is available →
Send the completed request form, histopathology report, marked H&E and sections to the GLH →
Particular details may differ slightly between GLHs, especially:
Sample requirements (e.g. neoplastic cell percentage, total cellularity and percentage area necrosis);
Requirements for numbers of sections, section thickness and preparation methods;
The request form to be used.
This information is available from the respective GLH’s website.
Note that the GLHs - in general - are not able to cut sections themselves. Sending a paraffin block will likely result in it being returned.
Check the Test Directory
The National Genomic Test Directory for Cancer lays out the tests which are funded by NHS England and which the GLHs need to provide.
See the National Genomic Test Directory →
Not every GLH will be able to provide every test on the Test Directory. However, it is usually still possible to send requests to your local GLH which will then forward the material to a site which can provide testing.
If a test is not listed on the Test Directory, it is not funded by NHS England and the GLHs are not obliged to provide it. If you request anything which is not on the Test Directory, it may well not be performed and - if it is - you will likely be invoiced for it.
There are some potential areas of confusion:
Some molecular targets are included under multiple tests for a single tumour type. For example, for KRAS small variants in colon cancer, the options are a multi-gene NGS panel (M1.1) or KRAS hotspot testing (M1.2). The default approach should be to request NGS panels to cover all the required targets. This testing is generally more comprehensive and allows additional targets to be assessed simultaneously. However, an NGS panel may not be the most appropriate option is very rapid results are needed or if the sample is very small; here, more targeted testing may be appropriate. Seek advice from your GLH if in doubt.
DPYD hotspot testing on tumour tissue is usually not needed. Testing is generally organised by clinicians and is done on a blood sample. It is extremely unlikely that this testing will be requested by pathologists.
ALK small variant (or point mutation or simply mutation) is different to ALK structural variant (or rearrangement or translocation or fusion) in non-small cell lung cancer. ALK structural variant determines eligibility for targeted therapy and is usually required for all patients with advanced non-small cell lung cancer. ALK small variant is a mechanism of resistance to targeted therapies and is seldom required.
MET exon 14 skipping variant is different to MET copy number variant (or amplification) in non-small cell lung caner. MET exon 14 skipping variant determines eligibility for targeted therapy. MET amplification is a mechanism of resistance to targeted therapies and is seldom required.
RET structural variant (or rearrangement or translocation or fusion) is different to RET small variant (or point mutation or simply mutation). RET structural variant determines eligibility for targeted therapy in non-small cell lung cancer and thyroid cancers. RET small variant determines eligibility for targeted therapy and may indicate an underlying germline mechanism specifically for medullary thyroid carcinoma.
MLH1, PMS2, MSH2 and MSH6 testing by NGS panel is not the same as MMR immunohistochemistry or MSI testing. Panel testing for these genes is usually only undertaken in cases where there is a serious concern for Lynch syndrome and is invariably initiated by clinical genetics, not by pathologists.
Check whether explicit consent is required
As a general rule, where testing is being undertaken with the primary aim of guiding a patient’s personal management, explicit testing is not required; it is assumed that implicit consent was given when the patient consented to the procedure used to acquire tissue. This is true even though any variant detected in tumour tissue could (in theory) be a germline variant.
There are a few exceptions to this rule, however. Here, the requesting clinician must communicate to the pathologist that explicit consent has been obtained before the test can be requested:
Explicit consent is required prior to BRCA1 and BRCA2 small variant testing In ovarian carcinoma. HRD testing encompasses BRCA1 and BRCA2 testing, and so the same rule applies.
See BGCS/BAGP guidance on BRCA1/2 variant testing in ovarian cancer →
Explicit consent is generally required prior to MLH1, PMS2, MSH2 and MSH6 small variant testing. This is invariably initiated by clinical genetics to work up cases of suspected Lynch syndrome and should not normally be initiated by pathologists anyway.
Identify the most appropriate block for testing
The success of genomic testing is entirely dependent on the quality of the quality of the tissue used for testing. Pathology departments have an essential role in selecting the most appropriate block from the most appropriate specimen.
Assess and mark up an H&E-stained section
The histopathologist’s assessment of the tissue is essential to interpretation of the results of genomic testing. Usually, some combination of neoplastic cell percentage, total cellularity and percentage area necrosis will be required.
Prepare sections
In general, GLHs are not set up to cut sections themselves. Histopathology departments must prepare sections and send these to GLHs for testing.
Sections should be cut to the specifications laid out by the respective GLH. They should be freshly cut under sterile conditions. Individual GLHs will stipulate on their websites the number of sections, their thickness, and whether they should be prepared as scrolls/curls or whether they should be slide-mounted. GLHs generally prefer to receive scrolls/curls. However, if the tissue has a low neoplastic cell content which could be improved with macrodissection, the tissue should generally be sent mounted on slides.
The use of pre-cut spare sections for genomic testing should be very much avoided:
Nucleic acids degrade rapidly in cut sections, increasing the likelihood of failed tests.
Sections cut for routine histology are generally thinner than those used for genomic testing (around 3 microns compared to around 5 microns); use of thinner sections is generally not validated for genomic testing.
Sections cut for routine histology are not prepared in a sterile fashion, and so there is a risk of nucleic acid contamination from other samples.
Clearly, if pre-cut spare sections are the only material available they may be used, but this should be done with caution.
It is important that sections are prepared under sterile conditions to minimise the risk of contamination by nucleic acids from other samples. This includes:
Using a clean pair of gloves for each new case.
Using a fresh microtome blade to cut sections for each case.
Cleaning any instruments with alcohol or bleach solutions prior to use.
Thoroughly decontaminating the microtome and preparation area with alcohol or bleach solutions prior to cutting.
Sterilising slides, slide holders or universal containers prior to use.
The use of water baths should be avoided wherever possible (by preparing scrolls/curls rather than slide-mounted sections). If required, the water should be replaced between cases.
Complete the GLH’s request form
Each GLH has its own request forms which can be obtained from the GLH website. Regardless of the GLH, the forms will require similar information:
Details of the test(s) to be undertaken, usually including Test Directory code(s), target genes and - in some cases - whether a DNA or RNA panel is required. DNA panels are usually used to detect small variants and copy number variants, whereas RNA panels are usually used to detect structural variants. To avoid ambiguity, it is generally best to provide Test Directory codes.
Details of the sample. These will usually include some combination of neoplastic cell percentage, cellularity and percentage area necrosis.
Send material to the GLH
The request should be sent to the GLH, including:
The completed request form;
A copy of the pathology report;
The marked H&E-stained section;
The unstained sections for testing.