Abstract PR10: PIK3CA mutations in plasma cell-free DNA predict survival and treatment outcomes in patients with advanced cancers
Authors: Ileana Dumbrava Ecaterina E. , Huang Helen J. , Stuckett Ana , Madwani Kiran , Adat Abha , Hong David S. , Piha-Paul Sarina A. , Subbiah Vivek , Karp Daniel D. , Fu Siqing , Naing Aung , Tsimberidou Apostolia M. , Moulder Stacey , Koenig Kimberly , Barcenas Carlos H. , Kee Bryan , Fogelman David , Kopetz Scott , Meric-Bernstam Funda , Janku Filip 
Published: December 2020

Abstract
Background: Cell-free DNA (cfDNA) analysis from plasma offers a minimally invasive detection of genomic alterations in personalized cancer therapy. PIK3CA is an actionable gene, which can be targeted with PI3K, AKT and mTOR inhibitors. We hypothesized that common hot-spot PIK3CA mutations can be detected in small amount of plasma cfDNA from patients with progressing advanced cancers.
Methods: PIK3CA mutations (p.H1047R, p.H1047L, p.E542K and p.E545K) were detected by droplet digital PCR (QX 200, BioRad) using 16 ng of unamplified cfDNA from plasma of 68 patients with advanced cancer. Results were compared to the clinical molecular testing of archival tumor tissue performed by next-generation sequencing or PCR during the clinical care.
Results: Of 68 patients (breast cancer, n=41; colorectal cancer, n=13; other tumor types, n=14), 58 patients (85%) had a PIK3CA mutation in the tumor. Testing of plasma cfDNA was in agreement with tumor tissue in 72% of samples (kappa 0.38), sensitivity 67% and specificity 100%. Of 19 falsely negative plasma cfDNA samples, 6 were found to be collected from patients not having disease progression. Additional 9 samples with available cfDNA were retested with increased DNA input (22-247 ng) and 4 had a PIK3CA mutation resulting in agreement for patients with progressing cancers of 85% (kappa 0.61), sensitivity 83% and specificity 100%. Patients with plasma PIK3CA-mutant cfDNA variant-allele frequency (VAF) &lt; 8.5% (&lt;5% trimmed mean) had a longer median survival compared to patients with VAF ≥ 8.5% (68 vs. 40 weeks; P=0.01). Serial collections of plasma cfDNA during systemic therapies were available for 18 patients with a median of 5 time points (range 2-22). Patients with decrease in PIK3CA-mutant VAF in cfDNA compared to increase or no change had a longer time to treatment failure to PI3K pathway-targeted therapies (46 vs. 11 weeks; p=0.04).
Conclusion: Common PIK3CA mutations can be detected in plasma cfDNA with high sensitivity and specificity in patients with progressing cancer if the cfDNA input is sufficient. Low amount of PIK3CA-mutant cfDNA is associated with longer survival. Changes in PIK3CA VAF could be an early surrogate biomarker for time to treatment failure to PI3K-targeted therapies.
This abstract is also being presented as Poster B16.
Citation Format: Ecaterina E. Ileana Dumbrava, Helen J. Huang, Ana Stuckett, Kiran Madwani, Abha Adat, David S. Hong, Sarina A. Piha-Paul, Vivek Subbiah, Daniel D. Karp, Siqing Fu, Aung Naing, Apostolia M. Tsimberidou, Stacey Moulder, Kimberly Koenig, Carlos H. Barcenas, Bryan Kee, David Fogelman, Scott Kopetz, Funda Meric-Bernstam, Filip Janku. PIK3CA mutations in plasma cell-free DNA predict survival and treatment outcomes in patients with advanced cancers [abstract]. In: Proceedings of the AACR Special Conference on Targeting PI3K/mTOR Signaling; 2018 Nov 30-Dec 8; Boston, MA. Philadelphia (PA): AACR; Mol Cancer Res 2020;18(10_Suppl):Abstract nr PR10.