Droplet digital PCR for detection of mutation in formalin-fixed, paraffin-embedded melanoma tissues: a comparison with Cobas 4800, Sanger sequencing, and allele-specific PCR.

Cutaneous melanoma has the worst prognosis of all skin cancers. Although emerging targeted therapies, such as B-Raf kinase inhibitor vemurafenib, improve prognosis they require an accurate and sensitive means of detecting the pathogenic mutation. We compared the sensitivity of four detection methods in formalin-fixed, paraffin-embedded melanoma biopsies from 87 consecutive melanoma patients with Breslow stage I-V disease (staging based on the depth of tumor of invasion). The methods assessed were the widely used Cobas 4800 system based on real-time PCR amplification, Sanger sequencing, allele-specific PCR (AS-PCR), and droplet digital PCR (ddPCR). The mutation was found in 8 (9.2%), 23 (26.4%), 23 (26.4%) and 31 (35.6%) biopsies, respectively. The (LoD) was determined by three different methods: Poisson confidence limits, calibration regression and Tzonev's method. Pair-wise agreement between the methods was as follows: Cobas vs. Sanger, P = 0.33; Cobas 4800 vs. AS-PCR, P = 0.33; Cobas 4800 vs. ddPCR, P = 0.65; Sanger vs. AS-PCR, P = 1; Sanger vs. ddPCR, P = 0.08; AS-PCR vs. ddPCR, P = 0.06. Multinomial logistic regression was used for predictive modeling of the Breslow-Clark score; ddPCR emerged as the best predictor, the other predictors were mitotic activity, type of malignant melanoma and patient's age. Our results demonstrate that ddPCR is the most sensitive method of detecting the mutation.