Analytical and clinical validation of a novel CE-IVD kit for PIK3CA hotspot mutations in liquid biopsy samples

Abstract

PIK3CA mutations have been implicated in the prognosis and therapeutic response in HER2-positive early breast cancer, with variants located in exon 9 and exon 20 shown to modulate sensitivity to neoadjuvant chemotherapy. Several molecular diagnostic platforms based on PCR or NGS have been developed for the detection of PIK3CA mutations in both tumor tissues and plasma-derived cfDNA, and some commercially available assays have already received FDA approval. The aim of this study was to evaluate the analytical and clinical performance of a novel CE-IVD molecular assay (Oncolipsy, PIK3CA kit, Pharmassist, Greece) for hotspot PIK3CA mutations (p.E542K, p.E545K, p.E545Q, p.H1047R) in liquid biopsy (LB) specimens. Analytical validation included assessment of sensitivity, specificity and reproducibility using certified liquid biopsy reference standards. Subsequently, the clinical utility of the assay was evaluated by analyzing plasma-cfDNA, CTC-derived gDNA and primary tumor samples for PIK3CA hotspot mutations. A total of 55 peripheral blood samples from breast cancer (BrCa) patients and 30 primary tumors (FFPEs) were examined. The same samples were also tested with two commercially available assays, the cobas® PIK3CA Mutation Test (Roche Diagnostics) and the ddPCR PIK3CA mutation test (BioRad), and the results were directly compared. Our findings demonstrate that the Oncolipsy PIK3CA kit exhibits high analytical detectability and excellent specificity for detecting PIK3CA hotspot mutations, at low variant allele frequencies. Clinical evaluation confirmed its robustness for liquid biopsy applications, with p.H1047R identified as the most frequent PIK3CA mutation. Concordance with both commercially available assays was high, with minor discrepancies attributable to differences in mutation coverage or detection thresholds. In conclusion, the CE-IVD Oncolipsy PIK3CA kit represents a highly detectability, specific and cost-effective real-time PCR-based solution for high throughput detection of four clinically relevant PIK3CA hotspot mutations in liquid biopsy samples.