Year: 2025
Type: article
Abstract: Background BRAF p.V600 mutation is the most frequent molecular driver alteration in melanoma. Detection of BRAF mutations in circulating-free DNA (cfDNA) reflects the shedding of tumor DNA and offers a potential non-invasive biomarker for disease monitoring and prognosis. However, the lack of standardized methodologies and inter-assay variability hinders its clinical implementation. Methods The sensitivity, agreement and concordance of seven BRAF mutation detection assays were assessed across four laboratories. BRAF p.V600 mutation in pretreatment plasma samples was analyzed in 51 patients diagnosed with advanced stage melanoma using two digital PCR-based assays (droplet digital PCR -ddPCR- Bio-Rad and microfluidic digital PCR -Absolute Q, ThermoFisher Scientific-), three RT-PCR based assays (Idylla®, Cobas®, PNA-Q-PCR) and two NGS based assays (Oncomine™ Pan-Cancer Cell-Free Assay and Illumina Platforms). Results digital PCR-based assays and Cobas® exhibited the highest sensitivity (51.0%), followed by NGS Illumina® (45.1%), Oncomine NGS / PNA-Q-PCR (43.1%) and Idylla® (37.2%). Results of different techniques showed a moderate to strong agreement, except for the comparison of Cobas with Idylla that was poor (Kappa=0.57). There was near-perfect agreement on detection of BRAF mutation between both NGS platforms and the NGS Illumina® with PNA-Q-PCR (Kappa = 0.92). Concordance of the quantitative results in terms of mutant allele frequency was near-perfect between NGS Illumina and ddPCR Bio-Rad assays (ICC = 0.99). Conclusions Our study demonstrates substantial agreement among multiple cfDNA BRAF mutation detection assays, particularly between NGS and digital PCR assays. These findings support the potential utility of different techniques for BRAF testing in cfDNA.
Source: EJC Skin Cancer
Authors: Clara Mayo de las Casas, Eloisa Jantus-Lewintre, Sebastian Ortiz Reina, Ana Drozdowskyj, Pablo Cerezuela-Fuentes, Jose Luis Manzano, Pablo Ayala de Miguel, Ana Arance Fernandez, Miguel Angel Berciano-Guerrero, Almudena Garcia-Castaño, Teresa Puertolas, Guillermo Crespo, Maria Quindos-Varela, Juan Francisco Rodriguez-Moreno, Alfonso Berrocal, Eva Muñoz-Couselo, Enrique Espinosa, Joselyn Valarezo, Susana Muñoz, Silvia Calabuig-Fariñas, Miguel Angel Molina, Rafael Rosell, Joan Anton Puig-Butille, Maria Gonzalez-Cao
Institutions: Instituto Oncológico Dr. Rosell, Hospital Universitario Dexeus, Hospital General Universitario De Valencia, Centro de Investigacion Principe Felipe, Universitat Politècnica de València, Hospital Universitario Virgen de la Arrixaca, Institut Català d'Oncologia, Hospital San Pedro de Alcántara, Hospital Clínic de Barcelona, Hospital Regional Universitario de Málaga, Hospital Universitario de Burgos, Complexo Hospitalario Universitario A Coruña, Universidad San Pablo CEU, HM Hospitales, Vall d'Hebron Hospital Universitari, Hospital Universitario La Paz, Universitat de València, Centro de Investigación Biomédica en Red de Cáncer, Fundacio Investigacio Hospital General Universitari De Valencia, Fundació Clínic per a la Recerca Biomèdica, Consorci Institut D'Investigacions Biomediques August Pi I Sunyer, Universitat de Barcelona
Language: English
Subfield: Cancer Research
Domain: Life Sciences
Open Access status: gold
Estimated APC paid: $2,340
Funders: Novartis, Novartis Farmacéutica
OpenAlex ID: W4412711094