The predictive and prognostic significance of cell‐free DNA concentration in melanoma

Abstract

Background Melanoma is the leading cause of skin cancer‐related deaths worldwide. While there have been significant improvements in the treatment of advanced melanoma in the past decade, biomarker development lagged behind. Objectives The majority of liquid biopsy biomarkers rely on the analyses of oncogenic mutations; however, about 20% of melanoma patients are wild type. Therefore, validation of universal predictive and prognostic biomarkers is urgently needed. Methods We analysed plasma samples in a discovery cohort (n = 20) and expansion cohort (n = 166) of metastatic melanoma patients and healthy donors (n = 116). Total plasma circulating cell‐free DNA (cfDNA) concentrations were measured on the Qubit® platform using assays for single‐(ss) and double (ds)‐stranded DNA, DNA spectrophotometry and RNase P qPCR. We explored the diagnostic, predictive and prognostic potential of cfDNA concentration by bio‐statistical methods and established a cfDNA threshold for risk stratification. Results Our selected best method was Qubit® dsDNA assay which quantified higher plasma cfDNA concentrations in melanoma patients than in healthy controls (AUC 72%). Measurement of baseline cfDNA concentration revealed that high cfDNA was associated with presence of metastases and higher AJCC stage (P < 0.05). Furthermore, high baseline cfDNA was an indicator of shorter overall survival in patients with oncogenic mutations (HR 2.12, P = 0.0008), and in wild‐type patients (HR 5.55, P < 0.0001). Conclusions We provide evidence that total cfDNA can be used as a biomarker for melanoma irrespective of the tumour genotype and can provide information on tumour load, risk of progression and risk of death.

Validation of a Circulating Tumor DNA-Based Next-Generation Sequencing Assay in a Cohort of Patients with Solid tumors: A Proposed Solution for Decentralized Plasma Testing

“…In agreement with the literature, 14,15 cfDNA yield varied widely between cancer patients, tumor types, and tumor burden. The range of plasma volumes was 2.4mL to 6mL with a median of 5mL.…”

Updates on liquid biopsy: current trends and future perspectives for clinical application in solid tumors

“…Currently, 22 clinical trials are registered in the ClinicalTrials.gov database aiming to study either the prognostic value of BRAF-or NRAF-mutated ctDNAs, their modulation during treatments and the standardization of methods for ctDNA quantification and mutation detection. Interestingly, although total cfDNA cannot be considered a melanomaspecific biomarker, Varaljai et al in 2020, demonstrated that high levels of cfDNA can provide information on tumor load, risk of progression and risk of death irrespective of the tumor genotype [235].…”

Liquid Biopsy in Melanoma: Significance in Diagnostics, Prediction and Treatment Monitoring

“…Finally, ctDNA can be applied for non-typical melanoma mutation detection (wild-type patients, constituting ca. 20% of all melanoma cases) [ 136 ] and tumor-specific gene methylation detection and be used for early diagnosis of melanoma [ 137 ]. Several study results showed that the presence of hypermethylation in the promoter region of PTEN , TFPI2 , RARB2 , MGMT , and RASSF1A genes in ctDNA enabled differentiation of melanoma patients from healthy individuals [ 138 , 139 , 140 ], with elevated levels of methylated RASSF1A ctDNA more attributed to metastatic cases compared to early-stage melanoma [ 140 ].…”