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PIK 3 CA   mutations are common activating mutations associated with breast cancer (occurring in 20–30% of all cases) and are potent predictive markers for responses to  PI 3K inhibitors. Thus, it is important to develop sensitive methods to detect these mutations. We established a novel detection method using a quenching probe ( QP ) system to identify   PIK 3 CA   mutations, using  DNA  from 309 breast cancer tissues. In a developmental cohort, we determined the optimal detection threshold of the  QP  system with human tumor  DNA  from 119 freshly frozen tumor samples. We found a 96% concordance rate with the  QP  system between  DNA  from 26 matching fresh‐frozen specimens and formalin‐fixed paraffin‐embedded ( FFPE ) specimens from the same patients, and known   PIK 3 CA   mutation status in the developmental cohort. In a validation cohort, we evaluated whether the threshold for judging mutations using the  QP  system with frozen specimen‐derived  DNA  was applicable with  FFPE ‐derived  DNA . In the validation cohort, 30  DNA  samples from 190  FFPE ‐derived  DNA  samples with known   PIK 3 CA   mutation status were analyzed by direct sequencing ( DS ) and droplet digital PCR, in a blinded manner. The sensitivity and specificity of the droplet digital  PCR  results were 100% and 100% ( QP  system), and 60% and 100% ( DS ), respectively. We also analyzed the relationship between clinical outcomes and the   PIK 3 CA   mutational status of 309 breast cancer samples, including the developmental cohort and validation cohort samples. Multivariate analysis suggested that   PIK 3 CA   mutations, especially H1047R, were prognostic factors of relapse‐free survival. Our novel detection system could be more useful than  DS  for detecting clinical   PIK 3 CA   mutations.

PIK 3 CA mutation profiling in patients with breast cancer, using a highly sensitive detection system