Rare germline variants in known melanoma susceptibility genes in familial melanoma

Abstract

Known high-risk cutaneous malignant melanoma (CMM) genes account for melanoma risk in <40% of melanoma-prone families, suggesting the existence of additional high-risk genes or perhaps a polygenic mechanism involving multiple genetic modifiers. The goal of this study was to systematically characterize rare germline variants in 42 established melanoma genes among 144 CMM patients in 76 American CMM families without known mutations using data from whole-exome sequencing. We identified 68 rare (<0.1% in public and in-house control datasets) nonsynonymous variants in 25 genes. We technically validated all loss-of-function, inframe insertion/deletion, and missense variants predicted as deleterious, and followed them up in 1, 559 population-based CMM cases and 1, 633 controls. Several of these variants showed disease co-segregation within families. Of particular interest, a stopgain variant in TYR was present in five of six CMM cases/obligate gene carriers in one family and a single population-based CMM case. A start gain variant in the 5'UTR region of PLA2G6 and a missense variant in ATM were each seen in all three affected people in a single family, respectively. Results from rare variant burden tests showed that familial and population-based CMM patients tended to have higher frequencies of rare germline variants in albinism genes such as TYR, TYRP1, and OCA2 (P < 0.05). Our results suggest that rare nonsynonymous variants in low- or intermediate-risk CMM genes may influence familial CMM predisposition, warranting further investigation of both common and rare variants in genes affecting functionally important pathways (such as melanogenesis) in melanoma risk assessment.

Figure 1.

The family (A2) with the TYR R402X variant. Black square or circle: melanoma cases; Square with diagonal stripes: obligate gene carriers. ‘+’: subjects with the TYR R402X variant; ‘−’: the non-carrier subject for R402X. Age under each subject denotes the age at diagnosis of first melanoma (for cases) or the age at exam/last status/death (for unaffected subjects).

Figure 2.

The ATM missense variant (N3003S). (A) The family (FE1) with the ATM variant. Black square or circle: melanoma cases. ‘+’: Carriers for the ATM N3003S variant; ‘−’: non-carriers. Age under each subject denotes the age at diagnosis of first melanoma (for cases) or the age at exam/last status/death (for unaffected subjects). (B) Amino acid conservation among ATM homologs.