Working Paper Article Version 2 This version is not peer-reviewed

Chip-Based Digital Pcr Improves the Detection of Low-Rate pik3ca Mutations in Breast Cancer Patients

Version 1 : Received: 24 June 2021 / Approved: 28 June 2021 / Online: 28 June 2021 (09:50:48 CEST)
Version 2 : Received: 5 July 2021 / Approved: 5 July 2021 / Online: 5 July 2021 (14:00:22 CEST)

How to cite: Giannoni-Luza, S.; Acosta Conchucos, O.; Carrasco, A.G.M.; Danos, P.; Cotrina Concha, J.M.; Guerra Miller, H.; Pinto, J.A.; Cartagena, A.A.; Araujo, J.M.; Fujita, R.; Buleje Sono, J.L. Chip-Based Digital Pcr Improves the Detection of Low-Rate pik3ca Mutations in Breast Cancer Patients. Preprints 2021, 2021060631 Giannoni-Luza, S.; Acosta Conchucos, O.; Carrasco, A.G.M.; Danos, P.; Cotrina Concha, J.M.; Guerra Miller, H.; Pinto, J.A.; Cartagena, A.A.; Araujo, J.M.; Fujita, R.; Buleje Sono, J.L. Chip-Based Digital Pcr Improves the Detection of Low-Rate pik3ca Mutations in Breast Cancer Patients. Preprints 2021, 2021060631

Abstract

PIK3CA is a gene usually mutated in breast cancer and has an important role in tumor progression and treatment. Therefore, there is required a technique to detect low-rate PIK3CA mutations improving the clinical conduct. This study aimed to compare chip-based dPCR and Sanger sequencing to detect PIK3CA mutations in breast cancer patients. Fifty-seven tumor samples from breast cancer patients were collected and analyzed by Sanger sequencing and dPCR for PIK3CA mutations (E545K, H1047R, and H1047L). Digital PCR sensitivity, specificity, and overall performance were estimated by contingency tables, receptor operator characteristic (ROC), and area under the curve (AUC). Sanger sequencing identified PIK3CA mutations in six patients (10.5%), two with H1047R, and four with E545K. Digital PCR confirmed those mutations and identified 19 additional patients with at least one mutation. Comparison between dPCR and Sanger sequencing showed a sensitivity of 100% (95% CI 53-100%), and a specificity of 84.2% (95% CI 83 - 84.2%). Besides, H1047R mutation showed a significant association with breast cancer phenotype (p =0.019) and lymphatic node infiltration (p =0.046). Digital PCR showed a high sensitivity to detect mutations in tumor samples and it might be capable to detect low-rate mutations and tumor subpopulations not detected by Sanger sequencing.

Subject Areas

Breast cancer; PIK3CA; digital PCR; Sanger sequencing

Comments (1)

Comment 1
Received: 5 July 2021
Commenter: Alexis Murillo Carrasco
Commenter's Conflict of Interests: Author
Comment: Some editions in authors' names and addition of references to further discussion of results.
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