Ngs analysis of liquid biopsy (Lb) and formalin‐fixed paraffin‐embedded (ffpe) melanoma samples using oncomine™ pan‐cancer cell‐free assay

Abstract

Next‐generation sequencing (NGS) in liquid biopsies may contribute to the diagnosis, monitoring, and personalized therapy of cancer through the real‐time detection of a tumor’s genetic profile. There are a few NGS platforms offering high‐sensitivity sequencing of cell‐free DNA (cfDNA) samples. The aim of this study was to evaluate the Ion AmpliSeq HD Technology for targeted sequencing of tumor and liquid biopsy samples from patients with fourth‐stage melanoma. Sequencing of 30 samples (FFPE tumor and liquid biopsy) derived from 14 patients using the Oncomine™ Pan‐Cancer Cell‐Free Assay was performed. The analysis revealed high concordance between the qPCR and NGS results of the BRAF mutation in FFPE samples (91%), as well as between the FFPE and liquid biopsy samples (91%). The plasma‐tumor concordance of the non‐BRAF mutations was 28%. A total of 17 pathogenic variants in 14 genes (from 52‐gene panel), including TP53, CTNNB1, CCND1, MET, MAP2K1, and GNAS, were identified, with the CTNNB1S45F variant being the most frequent. A positive correlation between the LDH level and cfDNA concentration as well as negative correlation between the LDH level and time to progression was confirmed in a 22‐patient cohort. The analysis showed both the potential and limitations of liquid biopsy genetic profiling using HD technology and the Ion Torrent platform.