Gene expression signature as an ancillary method in the diagnosis of desmoplastic melanoma

Desmoplastic melanoma (DM) is a rare fibrosing variant of melanoma that can be difficult to diagnose. One of the diagnostic challenges is its distinction from a melanocytic nevus with desmoplasia. Here we investigate the use of a 23-gene signature, which has previously been shown to distinguish benign from malignant melanocytic neoplasms. We assessed 50 cases with a differential diagnostic consideration of DM that underwent gene expression testing. Hematoxylin and eosin-stained sections were reviewed, and the final cohort included 20 DMs, 5 nondesmoplastic melanomas, and 27 desmoplastic melanocytic nevi. Of the 20 DMs, the gene expression score was positive ("likely malignant") in 15 tumors, indeterminate in 1, and negative ("likely benign") in 4. None of the desmoplastic melanocytic nevi were positive. The gene expression score was negative in 24 of the melanocytic nevi and indeterminate in the remaining 3. Nine DMs were also analyzed cytogenetically by single-nucleotide polymorphism (SNP) array. The SNP array revealed chromosomal copy number aberrations consistent with melanoma in 7 DMs and failed to show any aberrations in 2. The results of SNP array analysis and gene expression testing were discordant in 4 cases. Our results document limitations in the sensitivity of both the gene expression signature and SNP array for the detection of DM. Nonetheless, our findings suggest a potential role of the gene expression signature as ancillary supportive evidence for the distinction of DM from desmoplastic nevus because positive scores were only seen in melanomas.