Detection of hotspot PIK3CA mutations in primary tumors and plasma-cfDNA of breast cancer patients using a novel highly sensitive CE-IVD kit

Introduction: Oncolipsy PIK3CA CE-IVD kit is intended to be used for the detection of PIK3CA mutations based on the combination of allele-specific priming, asymmetric PCR, and melting curve analysis. The aim of the present study is to: a) evaluate the performance of the novel CE-IVD kit both in FFPEs and plasma-cfDNA samples from patients with metastatic breast cancer (MBC) and directly compared the derived results with two commercially available assays, the cobas® PIK3CA Mutation Test and a ddPCR PIK3CA mutation test (Bio-Rad).

Patients and methods: 30 primary tumors (FFPEs) and 25 plasma-cfDNA samples from patients with HR positive and HER2 negative MBC were analyzed. Genomic DNA was isolated from FFPEs using the QIAamp DNA FFPE Tissue Kit (Qiagen, Hilden, Germany), while cfDNA was extracted from 2.00 mL of plasma using the QIAamp DSP cNA Kit (Qiagen, Hilden, Germany).

Results: Direct comparison between the Oncolipsy PIK3CA CE-IVD kit and the cobas® PIK3CA Mutation Test using the same gDNA isolated from FFPEs revealed a concordance of 20/29 (69%) for PIK3CA p.E542K, 24/30 (80%) for PIK3CA p.H1047R and 28/30 (93.3%) for PIK3CA p.E545K mutation. The corresponding concordance between the Oncolipsy PIK3CA CE-IVD kit and ddPCR was 19/29 (86.2%) for PIK3CA p.E542K, 26/30 (86.7%) for PIK3CA p.H1047R and 18/30 (60%) for PIK3CA p.E545K mutation (Table 1). Direct comparison between the Oncolipsy PIK3CA CE-IVD kit and ddPCR assays using the same gDNA isolated from plasma samples revealed a concordance of 13/15 (86.7%) for PIK3CA p.E542K, 21/25 (84%) for PIK3CA p.H1047R and 26/26 (100%) for PIK3CA p.E545K mutation (Table 2).

Conclusions: The commercially available Oncolipsy PIK3CA CE-IVD kit is highly sensitive and specific for the detection of four PIK3CA hotspot mutations in primary tumors and plasma-cfDNA.