Presentation: Patient with localised colorectal cancer

A 72-year-old male is diagnosed with 3cm colorectal tumour at the right hepatic flexure. He undergoes a right hemicolectomy and is found to have a poorly differentiated adenocarcinoma, pT3N0M0, with clear margins and no lymphovascular invasion. There is no significant family history of cancer. You wish to undertake genomic testing and are considering what constitutional (germline) and somatic (tumour) genomic testing is available and appropriate for him.

Constitutional (germline) testing

• If microsatellite instability (MSI) testing demonstrates instability, if the MSH2, MSH6 or PMS2 IHC results are abnormal, or if the MLH1 +/- PMS2 results are abnormal and the MLH1 promoter hypermethylation test is negative, the patient should be tested for Lynch syndrome by genomic testing of constitutional (germline) DNA.
• Broader panel-based testing of genes associated with polyposis and other rare hereditary causes of colorectal cancer is available for patients with colorectal cancer if they fulfil one of the following criteria:
  • diagnosis of colorectal cancer:
    • >40 years; and
    • ≥5 adenomatous polyps
  • ≥5 adenomatous polyps <40 years, ≥10 adenomatous polyps <60 years, or ≥20 adenomatous polyps at any age;
  • ≥5 adenomatous polyps <60 years and first-degree relative with ≥5 adenomatous polyps or colorectal cancer (<60 years)
  • Serrated polyposis:
    • ≥5 serrated lesions/polyps proximal to the rectum all ≥5mm in size, with ≥2 that are ≥10mm in size; or
    • ≥20 serrated lesions/polyps of any size distributed through the large bowel with ≥5 being proximal to the rectum.
  • hamartomatous polyposis syndromes:
    • ≥5 hamartomatous polyps of the colorectum;
    • ≥2 hamartomatous polyps throughout the GI tract; or
    • ≥1 hamartomatous polyp and a first- or second-degree relative has hamartomatous polyp.
• If this patient is mismatch repair (MMR) proficient or negative, then this patient would be eligible for fluoropyrimidine chemotherapy and would therefore require testing for constitutional dihydropyrimidine dehydrogenase (DPD) deficiency.

Somatic (tumour) testing:

• All patients with colorectal cancer are eligible for testing of MMR or MSI of the tumour.
  • In the context of an intermediate risk stage II colorectal cancer, MMR/MSI status provides important prognostic information and predicts likely benefit from adjuvant chemotherapy.
  • MMR/MSI status may be assessed by an immunohistochemistry (IHC) 4‑panel test for MLH1, MSH2, MSH6 and PMS2 proteins (not a genomic test), or PCR for MSI (a genomic test).
  • If tumour IHC results demonstrate loss of MLH1/PMS2, BRAF analysis should be undertaken. Pathogenic BRAF variants (most commonly BRAF V600E) are common in sporadic MMR-deficient colorectal cancers, but rare in tumours associated with Lynch syndrome.
    • If BRAF testing does not identify a pathogenic variant in an MLH1/PMS2-deficient colorectal cancer, MLH1 promoter hypermethylation testing should be performed.
  • If IHC/ MSI/ MLH1 methylation analysis has indicated that Lynch syndrome is indicated and a germline sample is not available or a germline MMR variant has not been detected, then genomic analysis of somatic MMR genes can be requested.

• Consult the National Genomic Test Directory to ensure your patient is eligible for testing. You can also access a spreadsheet containing details of all available tests.
  • For information about how to arrange testing in Wales, Scotland or Northern Ireland, see our dedicated Knowledge Hub resource.
• For information on the genes that are included on different gene panels for constitutional (germline) testing, see the NHS Genomic Medicine Service signed-off panels resource.
• Decide which tests best suit the needs of your patient. For patients affected with colorectal cancer, options include the following.

Constitutional (germline) testing:

• R210 Inherited MMR deficiency (Lynch syndrome) after working through the tumour-based MSI/MMR IHC pathway; and
• R211 Inherited polyposis and early onset colorectal cancer, for patients with polyps fulfilling eligibility.

Somatic testing:

• M1.1 Multi-target NGS panel for patients with colorectal cancer (CRC) eligible for anti-EGFR therapy and/or BRAF required, or where BRAF or MMR genes required for Lynch testing (KRAS, NRAS, BRAF);
• M1.2 KRAS hotspot testing in CRC patients eligible for anti-EGFR therapy where NGS panel has failed;
• M1.3 NRAS hotspot testing in CRC patients eligible for anti-EGFR therapy where NGS panel has failed;
• M1.4 MSI testing testing in CRC patients where MMR testing has failed;
• M1.5 MLH1 promoter hypermethylation in CRC patients where this is indicated by the Lynch testing algorithm. This is best done alongside constitutional (germline) DNA to facilitate detection of constitutional hypermethylation of the MLH1 promoter; and
• M1.6 NTRK rearrangement panel for CRC patients who may be clinically eligible for NTRK inhibitor (advanced disease only).
• M1.9 Multi-target NGS panel for the analysis of MMR genes (MLH1, MSH2, MSH6, PMS2, POLE, POLD1).
• For constitutional (germline) testing for Lynch syndrome, a record of discussion (RoD) form is required. If you have not completed an RoD form before and/or do not have access to one, please review this Knowledge Hub article on how to complete an RoD form.
• All of the above somatic tests can be performed on formalin-fixed tumour tissue. Testing of tumour tissue for MMR or MSI, as well as subsequent somatic testing, may be done reflexively by your histopathology department, but you may need to follow this up within the multidisciplinary team meeting and clarify patient eligibility.
• Depending on the details you provide and the test that is chosen, a range of different genomic investigation techniques will be applied to your patient’s/their family’s (if appropriate) DNA. These include (but are not restricted to):
  • Single gene sequencing
  • Gene panel sequencing
  • MLPA
  • Methylation testing
• Information about patient eligibility and test indications was correct at the time of writing. When requesting a test, please refer to the National Genomic Test Directory to confirm the right test for your patient.

For clinicians

• ESMO: Clinical practice guidelines – localised colon cancer
• NHS England: National Genomic Test Directory and eligibility criteria (note that somatic (tumour) tests are listed in the directory for cancer, while constitutional (germline) tests are listed in the directory for rare and inherited disease)
• NICE: Molecular testing strategies for Lynch syndrome in people with colorectal cancer

For patients

• Macmillan: Lynch syndrome
• Royal Marsden NHS Foundation Trust: Beginner’s guide to Lynch syndrome (PDF, 64 pages)