Cell-Free Tumor DNA Analysis in Advanced or Metastatic Breast Cancer Patients: Mutation Frequencies, Testing Intention, and Clinical Impact

Oncology Medicine
cell-free tumor DNA breast cancer mutation frequencies clinical impact genetic testing

Academic Background

Breast cancer is one of the most common cancers among women worldwide, particularly advanced or metastatic breast cancer, which is challenging to treat and has a poor prognosis. With the development of precision medicine, the role of molecular biomarkers in breast cancer treatment has become increasingly prominent. Circulating tumor DNA (ctDNA), as a non-invasive biomarker, can detect tumor gene mutations through blood samples, providing new possibilities for personalized treatment. However, the application of ctDNA in clinical practice still faces many challenges, such as the distribution of mutation frequencies, the motivation for testing, and its impact on clinical decision-making.

To explore the potential of ctDNA in breast cancer treatment, the German PraegNANT registry study (Prospective Academic Translational Research Network for the Optimization of Oncological Health Care Quality in the Adjuvant and Advanced/Metastatic Setting) conducted a study aimed at evaluating the mutation frequencies, testing motivations, and clinical impact of ctDNA testing in patients with advanced or metastatic breast cancer. By analyzing somatic mutations in ctDNA, the study explored its potential as a biomarker for targeted therapy and assessed the impact of ctDNA test results on clinical decision-making.

Source of the Paper

The study was conducted by Hanna Huebner, Pauline Wimberger, Elena Laakmann, and other co-authors, with the research team coming from several renowned medical institutions in Germany, including the University Hospital Erlangen, the University Hospital Dresden, and the University Medical Center Hamburg-Eppendorf, among others. The paper was published in 2025 in the journal Precision Clinical Medicine, with the DOI 10.1093/pcmedi/pbae034.

Research Process

1. Patient Recruitment and Sample Collection

The study enrolled 49 patients with advanced or metastatic breast cancer, all of whom were part of the PraegNANT registry study (NCT02338167). The study used the FDA-approved and CE-certified Guardant360 CDx assay to analyze ctDNA in patient blood samples. Blood samples were collected using Streck cell-free DNA (cfDNA) blood collection tubes and sent to the Guardant Health central laboratory in Redwood City, USA, for DNA extraction and analysis.

2. ctDNA Testing and Analysis

The Guardant360 CDx assay employs a 74-gene targeted sequencing panel, covering various mutation types such as single nucleotide variants (SNVs), insertions/deletions (indels), gene fusions (fusions), gene amplifications (amplifications), and microsatellite instability (MSI). Test results were generated through the Guardant Health secure portal and provided to the treating physicians. Additionally, physicians received a questionnaire regarding the motivation for testing and its clinical impact.

3. Data Analysis and Interpretation

The study used IBM SPSS Statistics 24 for data analysis, with GraphPad Prism 9.5.1 and Microsoft Excel 2018 for chart creation. The study defined a variant allele frequency (VAF) cutoff of <40% for somatic mutations and set the ctDNA positivity criterion at VAF ≥0.4%. The study analyzed the mutation frequencies of different genes and evaluated the impact of these mutations on treatment decisions.

Key Findings

1. ctDNA Mutation Frequencies

Among the 49 patients, 37 (76%) had at least one somatic mutation detected, with 14 (29%) patients carrying TP53 mutations, 12 (24%) carrying PIK3CA mutations, and 6 (12%) carrying ESR1 mutations. BRCA1 and BRCA2 mutations were detected in 3 (6%) and 4 (8%) patients, respectively. The frequency of these mutations was higher in patients with hormone receptor-positive (HR+), human epidermal growth factor receptor 2-negative (HER2-) breast cancer.

2. Targetable Mutations

The Guardant360 CDx report provided treatment suggestions for 8 (16%) patients with approved therapies for breast cancer and for 13 (27%) patients with therapies approved for other cancers. For example, patients with PIK3CA mutations could consider treatment with Alpelisib, while patients with BRCA1/2 mutations could consider PARP inhibitors (e.g., Olaparib). Additionally, 7 (14%) patients had mutations associated with resistance to certain treatments.

3. Testing Motivation and Clinical Impact

In the questionnaires completed for 48 (98%) patients, ctDNA testing influenced treatment decisions for 35% of patients. For example, 2 (12%) patients chose PARP inhibitor therapy based on the test results, 7 (41%) chose PI3K inhibitor therapy, and 9 (53%) chose other treatment options. Most physicians believed that ctDNA testing was beneficial for patients, but only 26% of the test results were validated in tumor tissue.

Research Conclusions

The study confirmed the importance of ctDNA testing in patients with advanced or metastatic breast cancer, revealing the frequencies of mutations in genes such as TP53, PIK3CA, ESR1, and BRCA1/2 and their potential as biomarkers for targeted therapy. The study also demonstrated that ctDNA test results significantly influenced clinical treatment decisions, particularly in the selection of targeted therapies such as PARP inhibitors and PI3K inhibitors. Furthermore, the study highlighted the feasibility of ctDNA testing in clinical practice and recommended its integration into routine treatment protocols.

Research Highlights

  1. High Mutation Frequencies: The study revealed the frequencies of mutations in genes such as TP53, PIK3CA, ESR1, and BRCA1/2 in ctDNA, providing critical insights for targeted therapy.
  2. Clinical Impact: ctDNA test results significantly influenced treatment decisions for 35% of patients, underscoring its value in personalized treatment.
  3. Innovative Testing Technology: The study employed the Guardant360 CDx assay, using a 74-gene targeted sequencing panel to comprehensively analyze somatic mutations in ctDNA.
  4. Multicenter Collaboration: The research team included members from several renowned medical institutions in Germany, ensuring the breadth and representativeness of the data.

Research Significance

The study provided strong evidence for the application of ctDNA testing in the treatment of advanced or metastatic breast cancer, advancing the field of precision medicine. The findings not only help optimize breast cancer treatment strategies but also offer important references for future clinical trials and drug development. With the approval of targeted drugs such as Elacestrant, the importance of ctDNA testing in clinical practice will further increase.

Through this study, we have gained a clearer understanding of the potential of ctDNA testing in breast cancer treatment, providing patients with more personalized treatment options and laying a solid foundation for future research and clinical practice.