Aims: Lynch syndrome is an autosomal dominant, hereditary cancer condition that predisposes mutation carriers to early-onset colorectal and endometrial cancer. Diagnostic genetic testing examines the exons (coding regions) of the four DNA mismatch repair genes (MLH1, MSH2, MSH6, PMS2) for pathogenic mutations, yet up to 30% of people with a clinical suspicion of Lynch syndrome have no identifiable genetic alterations. We aimed to determine if a constitutional epimutation (soma-wide hypermethylation of one allele) in MLH1 (family 1) and an inversion in MSH2 (family 2) accounted for two cases of Lynch syndrome with no coding mutations.

Method: In family 1 we used a combination of pyrosequencing, methylation specific PCR, allelic bisulphite sequencing and genotyping to determine the origin and inheritance pattern of a constitutional MLH1 epimutation. In family 2 we used a PCR strategy to identify a novel inversion within MSH2.

Results: In family 1 we show that a 29-year-old man had a constitutional MLH1 epimutation and allele-specific loss of expression that was stable over a 16-year period. We established the epimutation was inherited without a genetic alteration from his asymptomatic mother, who showed methylation on the same allele but in less than 5% of her cells. In family 2 we identified and characterised the breakpoints of a previously undescribed paracentric inversion of exons 2-6 in MSH2 and developed a diagnostic PCR test for this rearrangement.

Conclusions: Our findings indicate that (i) low-level somatic mosaicism for an epimutation in an asymptomatic parent can produce a non-mosaic constitutional epimutation in a child, meaning that low-level methylation in some individuals may be associated with significant cancer risk to their offspring, and (ii) inversions may account for unexplained cases of Lynch syndrome that lack coding mutations. These findings have implications for assessing cancer risk in these and other families with suspected Lynch syndrome.