To reveal the clonal architecture of
melanoma and associated driver mutations, whole genome sequencing (WGS) and targeted extension sequencing were used to characterize 124
melanoma cases. Significantly mutated gene analysis using 13 WGS cases and 15 additional paired extension cases identified known
melanoma genes such as BRAF, NRAS, and CDKN2A, as well as a novel gene EPHA3, previously implicated in other
cancer types. Extension studies using
tumors from another 96 patients discovered a large number of truncation mutations in
tumor suppressors (TP53 and RB1),
protein phosphatases (e.g., PTEN, PTPRB, PTPRD, and PTPRT), as well as chromatin remodeling genes (e.g., ASXL3, MLL2, and ARID2). Deep sequencing of mutations revealed subclones in the majority of metastatic
tumors from 13 WGS cases. Validated mutations from 12 out of 13 WGS patients exhibited a predominant UV signature characterized by a high frequency of C->T transitions occurring at the 3' base of dipyrimidine sequences while one patient (MEL9) with a hypermutator phenotype lacked this signature. Strikingly, a subclonal mutation signature analysis revealed that the founding clone in MEL9 exhibited UV signature but the secondary clone did not, suggesting different mutational mechanisms for two clonal populations from the same
tumor. Further analysis of four
metastases from different geographic locations in 2
melanoma cases revealed phylogenetic relationships and highlighted the genetic alterations responsible for differential drug resistance among metastatic
tumors. Our study suggests that clonal evaluation is crucial for understanding
tumor etiology and drug resistance in
melanoma.