MLH1 promoter methylation (sporadic versus Lynch mismatch repair loss)

What is measured: whether the MLH1 gene has been silenced by promoter methylation rather than by an inherited mutation. How: after mismatch repair immunohistochemistry shows loss of MLH1 (with PMS2), the tumour is tested by methylation-specific PCR or pyrosequencing of the MLH1 promoter; in colorectal cancer BRAF V600E sequencing serves the same purpose because it is present in about 70 percent of sporadic methylated tumours and virtually never in Lynch syndrome (it is not useful in endometrial cancer). About three-quarters of MLH1-deficient colorectal cancers and 70 to 90 percent of MLH1-deficient endometrial cancers are methylated and sporadic; the rest go to germline testing of MLH1, MSH2, MSH6, PMS2 and EPCAM, with the rare constitutional MLH1 epimutation in mind. What a result changes: a methylated result closes the germline question, though the tumour remains mismatch repair-deficient and eligible for pembrolizumab, nivolumab or dostarlimab, and a BRAF-mutant microsatellite-unstable colorectal cancer carries a worse prognosis; an unmethylated result triggers genetic counselling, cascade testing, colonoscopy surveillance for relatives, aspirin chemoprevention (CAPP2) and consideration of risk-reducing hysterectomy in Lynch syndrome. Where it matters: MSI-high colorectal cancer, mismatch repair-deficient endometrial cancer and MSI-high gastric cancer.