Abstract
Aim:Single biomarker diagnostic test of BRAFV600 locus in metastatic melanoma is mandatory for treatment decision; however, multiple-gene based techniques, such as targeted next-generation sequencing (NGS) are being used to maximize the number of patients that can benefit from a targeted therapy. The main objective of this study is to investigate whether an NGS panel could be adopted in routine clinical care for advanced melanoma.Methods:Patients diagnosed with advanced melanoma at our center from 2017 to 2019 were included. Presence of genetic alterations was performed using two methods: real-time polymerase chain reaction-based Idylla test (Biocartis) and NGS with the oncomine solid tumor DNA kit (Thermo Fisher Scientific). Total genomic DNA was extracted from formalin-fixed and paraffin embedded samples for sequencing.Results:A total of 155 samples were evaluated for molecular analysis but 40 samples (25.8%) were inadequate for sequencing. The clinical utility of BRAFV600 real-time polymerase chain reaction and targeted-NGS was compared in 29 samples and a very good concordance was observed (Kappa = 0.89, 95% confidence interval 0.68 ± 1.05). An oncogenic mutation by NGS was found in 75 samples (65%)–53% of whom were candidates for personalized therapies. The most prevalent mutated genes were BRAF (39%), TP53 (23%), and NRAS (14%). Other genes identified at lower incidence (< 5%) were: PIK3CA, ERBB4, CTNNB1, STK11, FGFR1, SMAD4, KRAS, FGFR3, PTEN and AKT. Co-occurrence of oncogenic mutations was detected in 40% of the samples. Among the mutations identified, TP53 was significantly more prevalent in men (men 31.8% versus women 12.2%, P = 0.03) and NRAS in women (men 9.1% versus women 24.4%, P = 0.03).Conclusions:Targeted-NGS testing is a feasible technique to implement in the routine clinical practice. Based on our results, NGS has provided more information on target-genes than RT-PCR technique, maximizing the benefit for patients with advanced melanoma.
Highlights
In the last decade, the treatment of oncology patients has made a major shift from a one-size-fits-all approach towards personalized medicine
The clinical utility of BRAFV600 real-time polymerase chain reaction and targeted-next-generation sequencing (NGS) was compared in 29 samples and a very good concordance was observed (Kappa = 0.89, 95% confidence interval 0.68 ± 1.05)
TP53 was significantly more prevalent in men and NRAS in women
Summary
The treatment of oncology patients has made a major shift from a one-size-fits-all approach towards personalized medicine. The identification of oncogenic mutations as drivers in advanced disease provide targeted therapies that have led to improvements in response rates and survival in a subgroup of patients [3,4,5]. BRAF testing is considered mandatory in patients with advanced (unresectable or metastatic) melanomas stage III or stage IV, and is highly recommended in high-risk resected disease stage IIC [13]. These analyzes have been based on the isolated BRAFV600E identification using real-time quantitative polymerase chain reaction (RT-PCR), but clinically validated next-generation sequencing (NGS) panels covering key oncogenic drivers are increasingly being performed routinely. As therapies for locally advanced and metastatic melanoma become more complex, and more targetable drivers’ alterations modulating the clinical decisions are found, there is an urgent need to validate and establish diagnostic algorithms for molecular testing at every institution according to established guidelines [14,15,16]
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