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.
Highlights
The main aim of our study was to evaluate the applicability of this platform and technology for next-generation sequencing of tumor and liquid biopsy melanoma samples using OncomineTM Pan-Cancer
Twenty-two patients with fourth-stage melanoma according to the TNM Classification of Malignant Tumors, 8th edition, treated for the first time with either targeted therapy or immunotherapy in the Maria Sklodowska-Curie National Research Institute of Oncology (NRIO), Gliwice Branch, were included in this study
Patients with brain metastasis detected by computed tomography (CT) or magnetic resonance (MR) imaging were treated with surgery and/or radiotherapy, depending on the clinical indication, before the systemic treatment
Summary
Liquid biopsy provides representative tumor material and is accessible; it seems to be a convenient tool especially for monitoring disease progression, response to therapy, and tumor evolution [3]. NGS analysis enables the identification of many genetic variants in many samples in a short time, with the sensitivity reaching 0.1% of the variant allele frequency (VAF) for some NGS technologies [4]. The combination of these two tools (NGS of ctDNA) enables genetic profiling of the tumor, which may be used for monitoring tumor resistance and evolution as well as the selection of therapeutic targets [5]
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