Concordance analysis of non-invasive techniques for PIK3CA and ESR1 mutations in advanced HR+/HER2- breast cancer: the CANIPE study

Hormone receptor-positive (HR+) and HER2-negative (HER2−) breast cancer represents ~70% of breast tumors. Accurate detection of PIK3CA and ESR1 mutations is crucial for guiding targeted therapies, particularly in advanced disease. Liquid biopsy testing is increasingly recommended, especially for ESR1 mutation, but standardized genotyping methods remain limited. The CANIPE study, a prospective, multicenter Spanish trial, evaluated mutation prevalence in 106 baseline blood samples. PIK3CA mutations were identified in 41.9% by ddPCR droplet digital PCR (ddPCR) and 42.8% by targeted next-generation sequencing (NGS), while ESR1 mutations were detected in 7.8 and 9.5%, respectively. A concordance analysis between ddPCR and NGS was performed in 62 paired samples, demonstrating excellent agreement (Kappa >0.85) and strong correlation in variant allele frequency for PIK3CA , confirming the reliability of the methods. Baseline circulating free DNA levels were prognostic for survival. These results, derived from real-world patient samples, support ddPCR and NGS as robust, complementary tools for mutation detection and therapeutic decision-making.