The pathogenic mutations in melanoma have largely been catalogued, but the order of their occurrence is not known. We identified 82 cases of melanocytic neoplasia with two or more histopathologically distinct precursor and descendent portions. These portions spanned several histopathologic stages including benign nevi, intermediate neoplasms such as dysplastic nevi, melanoma in situ, invasive melanoma, and metastatic melanoma. In total, 277 histopathogically distinct areas were microdissected and sequenced using a panel of several hundred cancer-genes at an average of 275-fold coverage. In all cases precursor lesions harbored mutations known to activate the MAPK pathway, most commonly affecting BRAF or NRAS, and thus these were considered initiating mutations. TERT promoter mutations were the earliest secondary mutations to occur, emerging in intermediate neoplasms and in situ melanomas. Bi-allelic CDKN2A mutations and/or deletions arose predominantly at the transition to invasive melanoma. TP53 and PTEN mutations occurred comparatively later in thicker primary melanomas. In the 12 cases in which matched primaries and metastases were sequenced, no pathogenic mutations were specifically associated with the transition to metastatic melanoma, suggesting that metastatic capability was already present in the primary tumors. Unequivocally benign neoplasms, which mostly consisted of conventional nevi, disproportionately harbored BRAFV600E mutations as the only apparent pathogenic alteration. Lesions that were histopathologically intermediate, such as dysplastic nevi, had two or more pathogenic mutations and were enriched for NRAS mutations. These findings provide genetic support for the existence of an intermediate stage of melanocytic neoplasia, resolving a long-standing controversy. We also found that melanomas with different initiating mutations evolve through distinct evolutionary trajectories linked to specific histopathologic precursors. A mutational signature of UV-radiation-induced DNA damage predominated in lesions from all histopathologic stages, implicating UV-radiation in both the initiation and progression of melanoma. The point mutation burden increased steadily from one progression stage to the next, stabilizing once melanomas became invasive. By contrast, copy number alterations only became prevalent at the transition to invasive melanoma. Melanomas evolve from benign lesions linearly, whereas, they show patterns of branched evolution when they evolve from intermediate lesions; this indicates that evolution may accelerate once a melanocytic neoplasm reaches an intermediate stage. In summary, our study outlines a framework of the genetic evolution of melanocytic neoplasms from precursor lesions and unveils the rate-limiting homeostatic factors that become disrupted as neoplasms progress from one stage to the next, as well as the pathogenic factors driving this evolution.

Citation Format: Alan H. Shain, Richard Yu, Iwei Yeh, Jamal Benhamida, Ivanka Kovalyshyn, Aravindhan Sriharan, Eric Talevich, Reinhard Dummer, Jeffrey North, Laura Pincus, Beth Ruben, William Rickaby, Corrado D’Arrigo, Alistair Robson, Robert Judson, Nancy Joseph, Boris Bastian. The genetic evolution of melanoma. [abstract]. In: Proceedings of the 107th Annual Meeting of the American Association for Cancer Research; 2016 Apr 16-20; New Orleans, LA. Philadelphia (PA): AACR; Cancer Res 2016;76(14 Suppl):Abstract nr 2372.