Medizinische Universität Graz - Research portal
Selected Publication:
Potocnik, N.
Genomic profiling of circulating tumor DNA using targeted capture sequencing in advanced HR+/HER- breast cancer patients
[ Diplomarbeit/Master Thesis (UNI) ] TU Graz; 2025. pp.66.
- Authors Med Uni Graz:
- Advisor:
- Dandachi Nadia
- Altmetrics:
- Abstract:
- Background: HR-positive, HER2-negative breast cancer (HR+/HER2-) is the most common subtype of breast cancer, accounting for around 60-70%. PIK3CA mutations occur in up to 40% of patients and permanently activate the PI3K/AKT/mTOR signaling pathway. This can lead to resistance to therapy and worsen the prognosis. While these mutations are usually determined from tumor tissue, the analysis of cell-free tumor DNA (ctDNA) in plasma offers a minimally invasive alternative, especially for metastases that are difficult to biopsy. The aim of this study was to compare the detection of PIK3CA mutations using SiMSen-Seq, and the AVENIO ctDNA Expanded Kit and to test whether AVENIO can detect additional clinically relevant alterations.
Methods: 47 patients with HR+/HER2- metastatic breast cancer (mBC) were examined. Blood samples were taken before starting palliative therapy (32 before first-line and 15 before second-line therapy). Tumor fraction was estimated using mFAST-SeqS (z-score). Two methods were used for mutation analysis. On the one hand, SiMSen-Seq, a PCR-based NGS method for the highly sensitive detection of eleven PIK3CA hotspot mutations. On the other hand, AVENIO ctDNA Expanded Kit, an NGS panel for 77 cancer-relevant genes. Sequencing was performed on Illumina platforms and resulting data were analyzed bioinformatically.
Results: PIK3CA mutations were detected in 21 of 47 patients (44.7%). The most frequent variants were H1047R, E542K and C420R. 35 of 40 mutations (87.5%) were detected by both methods. Only few mutations (n = 4, corresponding to 8.5%) were detected exclusively by one method and these were mostly at low VAF (variant allele frequency) (<1%). AVENIO additionally identified mutations in TP53, ESR1, SMAD4, GATA3 and AKT1. Higher tumor proportions (z-scores) correlated with visceral metastasis.
Conclusion: The AVENIO ctDNA Expanded Kit showed comparable sensitivity to SiMSen-Seq in PIK3CA detection but additionally enabled a broader molecular analysis. The combination of AVENIO, SiMSen-Seq and mFAST-SeqS provides a powerful tool for non-invasive characterization and monitoring of HR+/HER2- mBC. This would allow therapies to be adapted more specifically and resistance developments to be detected at an early stage. Especially in situations where tissue samples are difficult to obtain.