The Prognostic Significance of Low-Frequency Somatic Mutations in Metastatic Cutaneous Melanoma

<b>Background:</b> Little is known about the prognostic significance of somatically mutated genes in metastatic melanoma (MM). We have employed a combined clinical and bioinformatics approach on tumor samples from cutaneous melanoma (SKCM) as part of The Cancer Genome Atlas project (TCGA) to identify mutated genes with potential clinical relevance. <b>Methods:</b> After limiting our DNA sequencing analysis to MM samples (<i>n</i> = 356) and to the CANCER CENSUS gene list, we filtered out mutations with low functional significance (snpEFF). We performed Cox analysis on 53 genes that were mutated in ≥3% of samples, and had ≥50% difference in incidence of mutations in deceased subjects versus alive subjects. <b>Results:</b> Four genes were potentially prognostic [<i>RAC1, FGFR1, CARD11, CIITA</i>; false discovery rate (FDR) < 0.2]. We identified 18 additional genes (e.g., <i>SPEN, PDGFRB, GNAS, MAP2K1, EGFR, TSC2</i>) that were less likely to have prognostic value (FDR < 0.4). Most somatic mutations in these 22 genes were infrequent (< 10%), associated with high somatic mutation burden, and were evenly distributed across all exons, except for <i>RAC1</i> and <i>MAP2K1</i>. Mutations in only 9 of these 22 genes were also identified by RNA sequencing in >75% of the samples that exhibited corresponding DNA mutations. The low frequency, UV signature type and RNA expression of the 22 genes in MM samples were confirmed in a separate multi-institution validation cohort (<i>n</i> = 413). An underpowered analysis within a subset of this validation cohort with available patient follow-up (<i>n</i> = 224) showed that somatic mutations in <i>SPEN</i> and <i>RAC1</i> reached borderline prognostic significance [log-rank favorable (<i>p</i> = 0.09) and adverse (<i>p</i> = 0.07), respectively]. Somatic mutations in <i>SPEN</i>, and to a lesser extent <i>RAC1</i>, were not associated with definite gene copy number or RNA expression alterations. High (>2+) nuclear plus cytoplasmic expression intensity for SPEN was associated with longer melanoma-specific overall survival (OS) compared to lower (≤ 2+) nuclear intensity (<i>p</i> = 0.048). We conclude that expressed somatic mutations in infrequently mutated genes beyond the well-characterized ones (e.g., <i>BRAF, RAS, CDKN2A, PTEN, TP53</i>), such as <i>RAC1</i> and <i>SPEN</i>, may have prognostic significance in MM.