Abstract

There is well-established diagnostic discordance in the interpretation of melanocytic proliferations, up to 24%, with even experienced dermatopathologists unable to confidently render a definitive diagnosis. In cases with diagnostic uncertainty, guidelines support using molecular testing to differentiate benign from malignant melanocytic neoplasms. One means to differentiate benign from malignant lesions is analyzing DNA methylation patterns, which are often aberrant in malignant neoplasms. A novel set of 4 differentially methylated regions (DMRs) was identified that could differentiate melanoma from nevi in microarray DNA methylation data. In addition, 3 DMRs were identified that are specifically hypermethylated in all melanocytes. Shave biopsy of formalin-fixed, paraffin-embedded specimens from 62 patients (24 females and 38 males, aged 42 to 89 years), previously diagnosed as either melanoma in situ or compound nevus, were evaluated. The DNA methylation status of 10 loci by methylation specific qPCR of bisulfite converted DNA from 34 nevi and 28 melanomas in situ was analyzed. Our panel was designed to quantify four melanoma-specific DMRs, 3 melanocyte-specific DMRs, and 3 constitutively methylated DNA load control regions. The relative methylation of each melanoma marker was estimated by normalizing to the melanocyte controls and to a melanoma cell line known to be hypermethylated at all regions of interest. The overall performance of the 4-marker set demonstrated a sensitivity of 93% (26/28), a specificity of 97% (32/34), and an AUC of 95%. These results support further exploration of a new molecular approach for the diagnosis of melanocytic lesions.