Multiplatform Liquid Biopsy-based analysis to track Melanoma
Background: Melanoma heterogeneity is an obstacle in metastatic disease management. Although the advent of targeted therapy has significantly improved patient outcome, the occurrence of resistance makes monitoring of the tumor genetic landscape mandatory. Liquid biopsy could represent an important biomarker to track the evolution of the disease in real time. Thus, we aimed to correlate liquid biopsy dynamics with treatment response/progression by devising a multiplatform approach applied to longitudinal monitoring. We exploited Next Generation Sequencing and droplet digital PCR to analyze circulating tumor DNA genetic profile. The approach was applied to 17 stage IV melanoma patients treated with BRAF/MEK inhibitors, longitudinally tracked for up to 28 months. Description: Data of hybridization capture-based target enrichment sequencing (SureSelect XT HS Target Enrichment System, Agilent Technologies) for 17 patients longitudinally followed for up to 28 months (median follow-up of 480 days, range: 77-853) for a total of 48 samples. Patients had a median age of 64 and there was equal representation of males and females (47% females). The following genes were sequenced on a NextSeq 550 instrument (Illumina) with a 300-cycle NextSeq 500/550 Mid Output v2 kit: ABL1, ADAMTS18, ARID2, ATM, BAP1, BRAF, CDK4, CDKN2A, CTNNB1, CYSLTR2, EGFR, EIF1AX, ERBB2, ERBB4, FBXW7, FGFR1, FGFR2, FGFR3, GNA11, GNAQ, GRIN2A, HOXD8, HRAS, IDH1, KDR, KIT, KRAS, MAP2K1, MAP2K2, MC1R, MET, MITF, MLH1, NF1, NRAS, PDGFRA, PIK3CA, PLCB4, PPP6C, PREX2, PTEN, PTPN11, RAC1, RB1, SF3B1, SRC, SRSF2, STK11, STK19, TERT, TP53, U2AF1 for SNP/INDEL analysis, and BRAF, CDC42, CDK4, ERBB2, FGFR1, FGFR3, NEDD9, NFAT5, PIK3CA, PPARG, PTK2, TUSC3 for CNV assessment.