AUTHOR=Peixoto Ana , Cirnes Luís , Carvalho Ana Luísa , Andrade Maria João , Brito Maria José , Borralho Paula , Coimbra Nuno , Borralho Pedro M. , Carneiro Ana Sofia , Castro Lisandra , Correia Lurdes , Dionísio Maria Rita , Faria Carlos , Figueiredo Paulo , Gomes Ana , Paixão Joana , Pinheiro Manuela , Prazeres Hugo , Ribeiro Joana , Salgueiro Natália , Schmitt Fernando C. , Silva Fátima , Silvestre Ana Rita , Sousa Ana Carla , Almeida-Tavares Joana , Teixeira Manuel R. , André Saudade , Machado José Carlos 

TITLE=Evaluation of PIK3CA mutations in advanced ER+/HER2-breast cancer in Portugal – U-PIK Project

JOURNAL=Frontiers in Molecular Biosciences

VOLUME=10

YEAR=2023

URL=https://www.frontiersin.org/journals/molecular-biosciences/articles/10.3389/fmolb.2023.1082915

DOI=10.3389/fmolb.2023.1082915

ISSN=2296-889X

ABSTRACT=<p><bold>Background:</bold> Around 40% of ER+/HER2-breast carcinomas (BC) present mutations in the <italic>PIK3CA</italic> gene. Assessment of <italic>PIK3CA</italic> mutational status is required to identify patients eligible for treatment with PI3Kα inhibitors, with alpelisib currently the only approved tyrosine kinase inhibitor in this setting. U-PIK project aimed to conduct a ring trial to validate and implement the <italic>PIK3CA</italic> mutation testing in several Portuguese centers, decentralizing it and optimizing its quality at national level.</p><p><bold>Methods:</bold> Eight Tester centers selected two samples of patients with advanced ER+/HER2- BC and generated eight replicates of each (n = 16). <italic>PIK3CA</italic> mutational status was assessed in two rounds. Six centers used the cobas<sup>®</sup><italic>PIK3CA</italic> mutation test, and two used PCR and Sanger sequencing. In parallel, two reference centers (IPATIMUP and the Portuguese Institute of Oncology [IPO]-Porto) performed <italic>PIK3CA</italic> mutation testing by NGS in the two rounds. The quality of molecular reports describing the results was also assessed. Testing results and molecular reports were received and analyzed by U-PIK coordinators: IPATIMUP, IPO-Porto, and IPO-Lisboa.</p><p><bold>Results:</bold> Overall, five centers achieved a concordance rate with NGS results (allele frequency [AF] ≥5%) of 100%, one of 94%, one of 93%, and one of 87.5%, considering the overall performance in the two testing rounds. NGS reassessment of discrepancies in the results of the methods used by the Tester centers and the reference centers identified one probable false positive and two mutations with low AF (1–3%, at the analytical sensitivity threshold), interpreted as subclonal variants with heterogeneous representation in the tissue sections processed by the respective centers. The analysis of molecular reports revealed the need to implement the use of appropriate sequence variant nomenclature with the identification of reference sequences (HGVS-nomenclature) and to state the tumor cell content in each sample.</p><p><bold>Conclusion:</bold> The concordance rates between the method used by each tester center and NGS validate the use of the <italic>PIK3CA</italic> mutational status test performed at these centers in clinical practice in patients with advanced ER+/HER2- BC.</p>