Abstract PS4-05-06: Comparative Analysis of PIK3CA, AKT1, and PTEN Reporting Across Commercial NGS Tests in Breast Cancer (BC)

Abstract Introduction: Genomic alterations in PIK3CA, AKT1 and PTEN are biomarkers for the AKT inhibitor Capivasertib (Capi), an approved treatment for metastatic BC (mBC) patients who progressed on ≥1 endocrine therapy or recurred during/within 12 months of adjuvant therapy. Several NGS assays include these genes in their panels; however, it is often unclear which types of alterations are evaluated, particularly PTENloss, and how the results compare across platforms. This study aimed to retrospectively compare two commercially available tissue NGS tests for the detection of short variant mutations (mut) in PIK3CA, AKT1, and PTEN, as well as homozygous PTEN copy loss (PTENloss) and PTEN rearrangements (re) in patients with BC: FoundationOne/FoundationOne®CDx (F1CDx®) and Caris NGS tests. Methods: This study included patients with BC who underwent F1CDx tissue comprehensive genomic profiling and had Caris tissue NGS testing. Data was obtained from the U.S.-wide de-identified Flatiron Health and Foundation Medicine real-world clinicogenomic breast database (CGDB), from ∼280 U.S. cancer clinics (∼800 sites of care) between 01/2011 and 12/2024. A comparison between F1CDx on-label Capi alterations and Caris NGS, abstracted from electronic health records (EHR)1, was conducted for patients with both tests performed on tumor tissue specimens collected on the same day. Caris NGS specific mutations are not available, so we could not assess if they were on-label for Capi. Positive percentage agreement (PPA) was calculated using F1CDx as a reference. Caris IHC PTEN protein loss results abstracted from EHR were also assessed when available. Results: A total of 74, 85 and 80 patients had PIK3CA, AKT1, and PTEN NGS results available from both assays, respectively, and 68 patients also had a Caris IHC PTEN result available. For PIK3CAmut, we observed an agreement of 98.6 % (73/74), with 53 (71.6%) negative and 20 (27%) positive for both tests, and 1 patient F1CDx-/Caris+ (100% PPA). For AKT1mut, the agreement was 100% with all cases negative for both tests. For PTEN, a 95% (76/80) agreement was observed, with 75 (93.7%) being negative for both tests, 1 (1.25%) with both positive, and 4 (5%) F1CDx+/Caris- (20% PPA). No PTENloss or PTENre was reported by Caris NGS, while 3 patients (3.7%) were positive for PTENloss and 1 patient (1.25%) for PTENre by FMI (0% PPA). Of 8 patients with a PTEN alteration not reported by Caris NGS test and detected on F1CDx, 6 had an IHC PTEN protein loss reported by Caris. Additionally, 4 patients were identified to have PTEN protein loss by Caris’s IHC PTEN results, but no PIK3CA/AKT1/PTEN alterations were identified by either NGS test and two functional copies of PTEN were detected on F1CDx. Conclusions: 29% (8/28) BC patients with on-label Capi alterations detected with F1CDx were not reported by Caris NGS tissue testing. 89% (8/9) of PTEN alterations were not reported by Caris NGS tissue testing, including all PTENloss and PTENre. 75% (6/8) Caris IHC PTEN results reported PTEN protein loss (not a current Capi indication). Further investigation on variations in reporting of different NGS assays in both tissue and plasma and their ability to identify on-label alternations are needed to understand true differences between testing results. Footnotes1 All data analyzed in this study related to the Caris tissue test is based on reported data only. Citation Format: H. Rugo, A. Schrock, J. Lee, R. Graf, M. Gearing, A. Heilmann, A. Gasco, N. Vasan, J. Quintanilha. Comparative Analysis of PIK3CA, AKT1, and PTEN Reporting Across Commercial NGS Tests in Breast Cancer (BC) [abstract]. In: Proceedings of the San Antonio Breast Cancer Symposium 2025; 2025 Dec 9-12; San Antonio, TX. Philadelphia (PA): AACR; Clin Cancer Res 2026;32(4 Suppl):Abstract nr PS4-05-06.