Characterization of PIK3CA mutation testing in metastatic breast adenocarcinomas: a multi-site, single institution study

Abstract

Abstract Introduction Detection of somatic mutations in advanced breast cancer may inform prognosis and therapy for patients. In ER+ breast cancer, nearly 40% of tumors have activating mutations in PI3 kinase (PIK3CA) for which targeted PI3 kinase inhibitors are available. At our institution, reflex ordered testing of PIK3CA in ER-positive, HER2-negative advanced breast cancers was implemented in 2017 to standardize the molecular biomarker testing in these tumors. Methods We analyzed 219 cases of advanced breast carcinoma diagnosed from 1/1/2017 to 12/31/2022 across the Houston Methodist system. With IRB approval, records were collated through full-text searching of interpretation, comment, and tumor synoptic fields in the anatomic pathology (AP) reports for “breast” and keywords for molecular oncologic testing, including “PIK3CA” and “MOLECULAR DIAGNOSTICS”, and then manually reviewed to exclude indeterminate/undifferentiated carcinomas and carcinomas of non-breast sites. Only molecular tests performed within this timeframe were considered. PIK3CA testing, both single-gene and targeted panels, was performed in 179 cases. Turnaround time (TAT) statistics, defined as days from AP report signout to molecular signout, were available for 102 cases. Cases with TATs greater than 60 days and referral laboratory testing were excluded. Data extraction, transformation, and loading was performed in Microsoft SQL Server (SSMS 18.0) and VS Code (Python 3.6). Analysis was performed using R-4.2.1 and Microsoft Excel. Results PIK3CA mutation testing was performed in 179 of 219 (82%) cases of all specimen types. The most common reasons for lack of reflex ordered molecular testing included insufficient tissue quantity and specimen decalcification. At least one PIK3CA genomic alteration was detected in 57 of 179 (32%) of cases. The most common alterations included p.H1047R (23/179, 13%), p.E545K (18/179, 10%), and p.E542K (8/179, 4%). One case had PIK3CA amplification, and one case had co-mutations of PIK3CA (p.G106V, p.H1047R). 217/219 (99%) of patients were female; no PIK3CA alterations were identified in the 2 male patients. PIK3CA frequency was not associated with age (mean age 65.4 for PIK3CA alteration detected and 63.8 for not detected, p=0.41). Mean TAT was 16.4 days (n=102), and 56% (57/102) of cases were resulted within 2 weeks of AP reporting. 22% (40/179) of cases had PIK3CA performed at a referral laboratory, largely occurring during the COVID-19 pandemic. Conclusion A reflex ordered strategy for PIK3CA mutations in advanced breast cancers led to the prompt availability of appropriate molecular results for most patients. PIK3CA alterations were present in 32% of cases, with the most common mutations being p.H1047R, p.E545K, and p.E542K. No significant differences in PIK3CA alterations by patient age was observed. Some cases had extended TATs for molecular results, which may be due to ordering practices, the specific PIK3CA testing procedure, and test send-out. Further studies will investigate the association of PIK3CA mutations and clinical staging.