Background: As the role of precision medicine in metastatic breast cancer (MBC) expands, there is an increasing emphasis on diagnostic tools to characterize both somatic and germline alterations that drive carcinogenesis. Circulating tumor DNA (ctDNA) has provided an important means for real-time, non-invasive detection and monitoring of tumor somatic alterations without standard paired white blood cell testing. However, its application for the detection of germline mutations remains relatively understudied. Here, we characterize the role of BRCA1&2 ctDNA mutant allele frequency (MAF) to identify underlying putative germline BRCA1&2 mutations.

Methods: Patient data were retrospectively obtained under an IRB-approved protocol to review ctDNA data at Northwestern University between 2015 and 2020. All ctDNA samples were analyzed using the Guardant360 next-generation sequencing (NGS) assay (Guardant Health). Patients with ctDNA alterations in the BRCA genes were identified at all mutant allele frequencies (MAF). Clinical data were collected including breast cancer subtype, prior lines of therapy, tissue-based NGS and germline testing information. Separate CLIA-approved testing performed per standard of care was used as the gold standard for germline testing. Statistical analysis was used to test the association of MAF cut-offs with the presence or absence of a germline alteration. Receiver operating characteristic (ROC) analysis was performed.

Results: We identified 127 patients with breast cancer who underwent ctDNA collection. There were 69 HR+ HER2-, 24 HER2+, and 34 triple negative breast cancer (TN) patients. Of these, 8 patients had known BRCA1 germline mutations, as confirmed with separate germline testing, and 9 patients had known BRCA2 germline mutations. BRCA1 germline mutations were significantly association with age < 40 (p=0.016) and triple negative subtype (p=0.042). Mean ctDNA BRCA1 MAF was 2.27% (Standard Deviation {SD} 10.19%) and mean BRCA2 MAF was 2.04% (SD 9.51%). BRCA1/2 MAF was analyzed with respect to germline mutations through ROC analysis. For BRCA1 ctDNA MAF cut-off 32.4% was associated with confirmed putative germline mutation. This cutoff demonstrated sensitivity of 1 and specificity of 0.99. Area under the curve (AUC) was 1.00 at this cut-off. For BRCA2, ctDNA MAF cutoff of 28.5% was associated with confirmed putative germline mutations. This cutoff demonstrated sensitivity of 0.86, specificity of 0.99 and AUC of 0.93.

Discussion: ctDNA alterations of BRCA1 with MAF>32.4% and BRCA2 with MAF>28.5% in clinical ctDNA testing were useful criterion to identify germline BRCA mutations. The data suggest the potential to utilize ctDNA as a diagnostic tool to predict germline mutations based on MAF thresholds. Future prospective studies are needed to determine how ctDNA testing may be incorporated into existing clinical algorithms to refer patients for germline testing.

Citation Format: Saya Jacob, Andrew Davis, Paolo D'Amico, Lorenzo Gerratana, Michael Burns, Ami Shah, Neelima Katam, Firas Wehbe, Qiang Zhang, Elena Vagia, Lisa Flaum, Kalliopi Siziopikou, Leonidas Platanias, Amir Behdad, William Gradishar, Massimo Cristofanilli. Circulating tumor DNA (ctDNA) as a diagnostic tool to identify putative germline BRCA mutations [abstract]. In: Proceedings of the 2020 San Antonio Breast Cancer Virtual Symposium; 2020 Dec 8-11; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2021;81(4 Suppl):Abstract nr PS2-10.