Large Cancer Pedigree Involving Multiple Cancer Genes including Likely Digenic MSH2 and MSH6 Lynch Syndrome (LS) and an Instance of Recombinational Rescue from LS

SIMPLE SUMMARY: Lynch syndrome is a hereditary cancer condition caused by a pathogenic variant (mutation) within one of the mismatch repair (MMR) genes. Risks for cancer vary by which MMR gene is mutated and sex, although colorectal and uterine cancers are most common. A major challenge in genetic testing is that this frequently reveals a variant of uncertain significance (VUS), which hinders clinical decision-making. We describe a large, four-generation, 13-branched, cancer-affected family with a mutation in MSH2 (c.2006G>T) in which one branch also carries a VUS in MSH6 (c.3936_4001+8dup). Functional studies in samples from family members show this MSH6 VUS is likely to be pathogenic. In addition, other cancer-relevant mutations were identified in branches without either MMR gene mutation so genetic counseling was highly individualized. Our study suggests multi-cancer gene panel testing should be offered to all members of cancer-effected families rather than targeted testing for specific mutations for accurate genetic diagnosis. ABSTRACT: Lynch syndrome (LS), caused by heterozygous pathogenic variants affecting one of the mismatch repair (MMR) genes (MSH2, MLH1, MSH6, PMS2), confers moderate to high risks for colorectal, endometrial, and other cancers. We describe a four-generation, 13-branched pedigree in which multiple LS branches carry the MSH2 pathogenic variant c.2006G>T (p.Gly669Val), one branch has this and an additional novel MSH6 variant c.3936_4001+8dup (intronic), and other non-LS branches carry variants within other cancer-relevant genes (NBN, MC1R, PTPRJ). Both MSH2 c.2006G>T and MSH6 c.3936_4001+8dup caused aberrant RNA splicing in carriers, including out-of-frame exon-skipping, providing functional evidence of their pathogenicity. MSH2 and MSH6 are co-located on Chr2p21, but the two variants segregated independently (mapped in trans) within the digenic branch, with carriers of either or both variants. Thus, MSH2 c.2006G>T and MSH6 c.3936_4001+8dup independently confer LS with differing cancer risks among family members in the same branch. Carriers of both variants have near 100% risk of transmitting either one to offspring. Nevertheless, a female carrier of both variants did not transmit either to one son, due to a germline recombination within the intervening region. Genetic diagnosis, risk stratification, and counseling for cancer and inheritance were highly individualized in this family. The finding of multiple cancer-associated variants in this pedigree illustrates a need to consider offering multicancer gene panel testing, as opposed to targeted cascade testing, as additional cancer variants may be uncovered in relatives.