Sensitive droplet digital PCR method for detection of promoter mutations in cell free DNA from patients with metastatic melanoma.

Background: Currently mainly mutant circulating tumor DNA (ctDNA) is utilized to monitor patients with melanoma. promoter mutations are common in various cancers and found in up to 70% of melanomas, including half of wild-type cases. Therefore, a sensitive method for detection of promoter mutations would increase the number of patients that could be monitored through ctDNA analysis.

Methods: A droplet digital PCR (ddPCR) assay was designed for the concurrent detection of chr5:1,295,228 C>T and chr5:1,295,250 C>T promoter mutations. The assay was validated using 39 melanoma cell lines and 22 matched plasma and tumor samples. In addition, plasma samples from 56 metastatic melanoma patients and 56 healthy controls were tested for promoter mutations.

Results: The established ddPCR assay detected promoter mutations with a lower limit of detection (LOD) of 0.17%. Total concordance was demonstrated between ddPCR and Sanger sequencing in all cell lines except one, which carried a second mutation within the probe binding-site. Concordance between matched plasma and tumor tissue was 68% (15/22), with a sensitivity of 53% (95% CI, 27%-79%) and a specificity of 100% (95% CI, 59%-100%). A significantly longer PFS (p=0.028) was evident in ctDNA negative patients. Importantly, our promoter mutations ddPCR assay allowed detection of ctDNA in 11 wild-type cases.

Conclusions: The promoter mutation ddPCR assay offers a sensitive test for molecular analysis of melanoma tumors and ctDNA, with the potential to be applied to other cancers.