Detection of clinically relevant variants in the <i>TP53</i> gene below 10% allelic frequency: A multicenter study by ERIC, the European Research Initiative on CLL
Authors: Sarka Pavlova, Jitka Malcikova, Lenka Radova, Silvia Bonfiglio, Jack B. Cowland, Christian Brieghel, Mette K. Andersen, Maria Karypidou, Bella Biderman, Michael Doubek, Gregory Lazarian, Inmaculada Rapado, Matthijs Vynck, Naomi A. Porret, Martin Andres, Dina Rosenberg, Dvora Sahar, Carolina Martínez‐Laperche, Ismael Buño, Andrew Hindley, David Donaldson, Julio B. Sánchez, José A. García‐Marco, Alicia Serrano‐Alcalá, Blanca Ferrer‐Lores, Concepción Fernández‐Rodriguez, Beatriz Bellosillo, Stephan Stilgenbauer, Eugen Tausch, Hero Nikdin, Fiona Quinn, Emer Atkinson, Lisette van de Corput, Cafer Yildiz, Cristina Bilbao‐Sieyro, Yanira Florido, Christian Thiede, Caroline Schuster, Anastazja Stoj, Sylwia Czekalska, Anastasia Chatzidimitriou, Stamatia Laidou, Audrey Bidet, Charles Dussiau, Friedel Nollet, Giovanna Piras, Maria Monne, Svetlana Smirnova, Eugene Nikitin, Ivan Sloma, Alexis Claudel, Laetitia Largeaud, Loïc Ysebaert, Peter J. M. Valk, Amy Christian, Renata Walewska, David Oscier, Marta Sebastião, Maria Gomes da Silva, Piero Galieni, Mario Angelini, Davide Rossi, Valeria Spina, Sónia Matos, Vânia Martins, Tomasz Stokłosa, Monika Pepek, Panagiotis Baliakas, Rafa Andreu, Irene Luna, Tiina Kahre, Ülle Murumets, Tereza Pikousova, Terezia Kurucova, Sophie Laird, Daniel Ward, Miguel Alcoceba, Ana Balanzategui, Lydia Scarfo, Francesca Gandini, Ettore Zapparoli, Adoración Blanco, Pau Abrisqueta, Ana E. Rodríguez‐Vicente, Rocío Benito, Clotilde Bravetti, Frédéric Davi, Paula Gameiro, Joaquin Martinez‐Lopez, Bárbara Tazón‐Vega, Fanny Baran‐Marszak, Zadie Davis, Mark Catherwood, Andrey Sudarikov, Richard Rosenquist, Carsten U. Niemann, Kostas Stamatopoulos, Paolo Ghia, Sarka Pospisilova
Journal: HemaSphere (2025)

Abstract In chronic lymphocytic leukemia, the reliability of next‐generation sequencing (NGS) to detect TP53 variants ≤10% allelic frequency (low‐VAF) is debated. We tested the ability to detect 23 such variants in 41 different laboratories using their NGS method of choice. The sensitivity was 85.6%, 94.5%, and 94.8% at 1%, 2%, and 3% VAF cut‐off, respectively. While only one false positive (FP) result was reported at &gt;2% VAF, it was more challenging to distinguish true variants &lt;2% VAF from background noise (37 FPs reported by 9 laboratories). The impact of low‐VAF variants on time‐to‐second‐treatment (TTST) and overall survival (OS) was investigated in a series of 1092 patients. Among patients not treated with targeted agents, patients with low‐VAF TP53 variants had shorter TTST and OS versus wt‐ TP53 patients, and the relative risk of second‐line treatment or death increased continuously with increasing VAF. Targeted therapy in ≥2 line diminished the difference in OS between patients with low‐VAF TP53 variants and wt‐ TP53 patients, while patients with high‐VAF TP53 variants had inferior OS compared to wild type‐ TP53 cases. Altogether, NGS‐based approaches are technically capable of detecting low‐VAF variants. No strict threshold can be suggested from a technical standpoint, laboratories reporting TP53 mutations should participate in a standardized validation set‐up. Finally, whereas low‐VAF variants affected outcomes in patients receiving chemoimmunotherapy, their impact on those treated with novel therapies remains undetermined. Our results pave the way for the harmonized and accurate TP53 assessment, which is indispensable for elucidating the role of TP53 mutations in targeted treatment.