Initial validation of liquid biopsy mass sequencing assay for detection of the oncogenic marker PIK3CA in breast cancer patients

Abstract

In Chile, the techniques approved for mutation detection in liquid biopsies are variants of the polymerase chain reaction. However, massive sequencing has certain advantages, serving for the monitoring and treatment selection for pathologies such as breast cancer. According to international clinical laboratory standards, a comparison between the evaluated technique and the reference one was carried out, necessary for the validation and implementation of this technique in patients with breast cancer. Objective: To carry out the initial validation of a massive sequencing protocol capable of detecting PIK3CA mutations in the circulating tumor DNA of these patients. Methodology: 11 blood samples were obtained from patients with advanced breast cancer, where the extracted DNA was sequenced and the detection of 3 mutations in PIK3CA was evaluated by a real time polymerase chain reaction, and the results were compared using a table of contingency and the McNemar test. Result: McNemar's exact test gave a p value > 0,05 and the evaluated technique had a sensitivity and specificity of 100%, with an agreement of 1 according to Cohen's kappa coefficient. Discussion: The cost-effectiveness of massive sequencing is greater than single genetic assays, but the limitations of both techniques must be taken into account. Conclusion: A high level of agreement was found between the techniques, but the results were not statistically significant. Even so, the validation of this assay should continue in the future with a larger number of samples.