Presentation: Patient with metastatic colorectal cancer

A 42-year-old woman with a history of weight loss and jaundice comes to clinic following a CT scan, which reveals an 18cm liver lesion and circumferential sigmoid thickening. Sigmoid biopsy reveals a moderately differentiated adenocarcinoma. 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 her.

Constitutional (germline) testing

Constitutional (germline) testing

• If the tumour demonstrates microsatellite instability (MSI), or if MSH2, MSH6 or PMS2 IHC results are abnormal, or the MLH1 +/- PMS2 IHC is abnormal and MLH1 promoter hypermethylation test is negative, the patient should be tested for Lynch syndrome by genomic testing of constitutional (germline) DNA.
• Consideration should be given to broader panel testing in patients with bowel polyps. Patients with bowel cancer are eligible for testing of the following genes: APC, BMPR1A, GREM1, EPCAM (3’ CNV analysis only), MLH1, MSH2, MSH6, MUTYH, NTHL1, PMS2, POLD1*, POLE*, (*exonuclease domains only) PTEN, RNF43, SMAD4 and STK11 if they meet one of the following criteria:
  • Any colorectal cancer diagnosis <40 years.
  • ≥5 adenomatous polyps and colorectal cancer.
  • ≥5 adenomatous polyps <40 years, ≥10 adenomatous polyps <60 years, or ≥20 adenomatous polyps at any age; or
  • ≥5 adenomatous polyps (<60 years) and first-degree relative ≥5 adenomatous polyps or colorectal cancer (<60 years).
  • A clinical diagnosis of serrated polyposis syndrome; if
    • diagnosed <50 years; or
    • if the patient has a family history of ≥1 affected first-degree relative with serrated polyposis syndrome; or
    • if there is evidence of dysplasia within any polyp.
  • hamartomatous polyposis syndromes:
    • ≥5 hamartomatous polyps of the colorectum; or
      ≥2 hamartomatous polyps throughout the GI tract; or
      ≥1 hamartomatous polyp and a first-/second-degree relative has hamartomatous polyp.
• This patient would be eligible for fluoropyrimidine chemotherapy and would therefore require testing for constitutional (germline) dihydropyrimidine dehydrogenase (DPD) deficiency.
• Testing for select recurrent DPYD variants is performed on constitutional (germline) DNA (indication M1.7).

Somatic (tumour) testing

• All patients with metastatic colorectal cancer are eligible for a multi-target next-generation sequencing (NGS) panel to check for variants in KRAS, NRAS and BRAF
  • Patients who are KRAS or NRAS wild-type are eligible for anti-epidermal growth factor receptor (EGFR) monoclonal antibodies (cetuximab and panitumumab) in combination with 5-fluoropyrimidine doublet chemotherapy in the metastatic setting.
  • Patients with tumours demonstrating KRAS or NRAS mutations do not usually benefit from anti-EGFR monoclonal antibodies.
  • Patients with tumours demonstrating BRAF V600E mutations may also be eligible for treatment with the BRAF inhibitor encorafenib, in combination with cetuximab, via the Cancer Drugs Fund.
  • Somatic testing for NTRK1, NTRK2 and NTRK3 fusion genes is available for metastatic colorectal cancer patients as an biomarker for treatment with an NTRK inhibitor when all other approved lines of treatment have been exhausted.
• All patients with colorectal cancer are eligible for testing of MMR or MSI.
  • In the context of a metastatic colorectal cancer, MMR/MSI status provides important prognostic information and guides potential benefit from immunotherapy.
  • This may be done by immunohistochemistry (IHC) four‑panel test for MLH1, MSH2, MSH6 and PMS2 protein expression or by PCR for MSI (a genomic test)
  • If the MLH1 IHC result is abnormal, BRAF gene analysis shoul0d be undertaken to determine if further (constitutional) germline genomic testing for Lynch syndrome is indicated.
    • Pathogenic somatic variants in BRAF are a surrogate marker of MLH1 promoter hypermethylation – being present in around two-thirds of MLH1 hypermethylated tumours, but being rare in tumours associated with Lynch syndrome. If the BRAF V600E test is negative, an MLH1 promoter hypermethylation test should be performed.
  • If IHC/ MSI/ MLH1 methylation analysis has indicated that Lynch syndrome testing is indicated and a constitutional (germline) sample is not available (e.g. in the case of deceased index case) or a constitutional MMR variant has not been detected, then genomic analysis of somatic MMR genes can be requested. This should be co-ordinated by the clinical genetics team.
• All patients with solid tumours who have exhausted all standards of care testing and treatment are eligible for whole genome sequencing (WGS) in order to explore clinical trial options.

• 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, constitutional (germline) genomic testing options include:
  • R210 Inherited MMR deficiency (Lynch syndrome); and
  • R211 Inherited polyposis and early-onset colorectal cancer.
• Testing of tumour tissue for MMR or MSI, as well as other somatic testing, are performed on formalin-fixed tumour tissue. These tests 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. Tests available are:
  • M1.1 Multi-target NGS panel – small variant (KRAS, NRAS, BRAF)
  • M1.2 KRAS hotspot;
  • M1.3 NRAS hotpot;
  • M1.4 MSI testing; and
  • M1.5 MLH1 promoter hypermethylation testing – for tumours demonstrating loss of MLH1/PMS2 deficiency on IHC, without evidence of a pathogenic somatic BRAF variant.
• NTRK1, NTRK2 and NTRK3 fusion gene analysis can be requested as test M1.6. This consists of NGS structural variant analysis.
• DPYD testing is undertaken on constitutional (germline) DNA (M1.7).
• For constitutional (germline) testing, 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. No RoD form is required for DPYD mutation testing.
• For DNA-based tests (constitutional (germline) DPYD, Lynch syndrome or polyposis tests), and EDTA blood sample is required. Please refer to your local Genomics Laboratory Hub (GLH) for details of test request forms and where to send samples.
• 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; and
  • methylation testing
• WGS of solid tumours where the patient has exhausted all standards of care testing and treatment is requested as code M232. WGS requires access to a fresh tumour sample and a matched EDTA blood sample for constitutional (germline) testing. An RoD form must be completed for this investigation. Please discuss with your local GLH before submitting samples for WGS to confirm the local test pathway details.
• 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 for metastatic 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. See this article for more information)
• NICE: Molecular testing strategies for Lynch syndrome in people with colorectal cancer

For patients

• Cancer Research UK: DPD deficiency
• Macmillan: Lynch syndrome
• Macmillan: Targeted therapies and immunotherapies for bowel cancer
• Royal Marsden NHS Foundation Trust: Beginner’s guide to Lynch syndrome (PDF, 64 pages)