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Molecular Diagnostics

Sensitive and robust liquid biopsy-based detection of PIK3CA mutations in hormone-receptor-positive metastatic breast cancer patients



The benefit of alpelisib in hormone-receptor-positive (HR+) metastatic breast cancer patients provided clinical evidence for the increasing importance of PIK3CA testing. We performed a comparison of liquid biopsy and tissue-based detection of PIK3CA mutations.

Materials and methods

PIK3CA hotspot mutation analysis using a high-resolution SiMSen-Seq assay was performed in plasma from 93/99 eligible patients with HR+/HER2− breast cancer. Additionally, mFAST-SeqS was used to estimate the tumour fractions in plasma samples. In 72/93 patients, matched tissue was available and analysed using a customised Ion Torrent panel.


PIK3CA mutations were detected in 48.6% of tissue samples and 47.3% of plasma samples, with identical PIK3CA mutation detected in 24/72 (33.3%) patients both in tissue and plasma. In 10 (13.9%) patients, mutations were only found in plasma, and in 6 (8.3%) patients, PIK3CA mutations found in tissue were not detectable in ctDNA. In 49/93 plasma samples without detectable PIK3CA mutations, 22 (44.9%) samples had elevated tumour fractions, implying true negative results.


SiMSen-Seq-based detection of PIK3CA mutations in plasma shows advantageous concordance with the tissue analyses. A combination with an untargeted approach for detecting ctDNA fractions may confirm a negative PIK3CA result and enhance the performance of the SiMSen-Seq test.

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Fig. 1: CONSORT diagram for the study.
Fig. 2: Concordance of PIK3CA mutation status between ctDNA and tissue samples in our study and in the SOLAR-1 study.

Data availability

Data are available at request from authors and were partially (SiMSen-Seq and mFAST-SeqS) deposited at the European Genome-phenome Archive (EGA; under study accession number EGAS00001004940 as following dataset: PIK3CA SiMSen-Seq data of plasma samples.


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We thank Klara Balic for English proofreading. In addition, we want to acknowledge that part of this manuscript was published as a doctoral thesis.


This work was supported by the Christian Doppler Research Fund for Liquid Biopsies for Early Detection of Cancer led by EH supported by the Federal Ministry of Digital and Economic Affairs and by Novartis and Pfizer.

Author information

Authors and Affiliations



CS, AT, ND and MB designed the study. RG and KK performed sequencing experiments, SJ and PR performed pathological evaluation, CS, EVK, AT, FP and MB contributed to patient care and data acquisition. ND and FP performed the statistical analysis, CS, AT, ND, MB, EH and PJJ performed interpretation of results. CS, ND, MB and FP drafted and revised the manuscript. ND, EH and MB supervised the study. All authors reviewed the manuscript and approved its final version.

Corresponding authors

Correspondence to Nadia Dandachi or Marija Balic.

Ethics declarations

Ethics approval and consent to participate

The study was approved by the ethics committee of the Medical University Graz (ethical approval number 21–227 ex 09/10), and written informed consent was obtained from all patients.

Competing interests

CS received travel expenses, consulting fees and honoraria from Amgen, Astra Zeneca, Eli Lilly, Novartis, Pfizer, Roche and Samsung, SJ received honoraria from Novartis and Roche, EVK has received travel expenses and honoraria from Astra Zeneca and Pierre- Fabre, RB had a consulting role, received honoraria, research funding and travel expenses from Astra Zeneca, Daiichi, Eisai, Eli Lilly, MSD, Novartis, Pfizer, Pierre-Fabre, Puma, Roche, AT received honoraria and research funding from Astra Zeneca, BMS, Merck and Roche. KK received honoraria and advisory from Astra Zeneca, Thermo Fischer, Novartis and BMS. PR received consulting fees, honoraria and travel expenses from Diaceutics, Novartis, and Roche, PJJ has had a consulting or advisory role, received honoraria, research funding and/or travel/accommodation expenses from Abbvie, Bayer, Boehringer, Novartis, Pfizer, Servier, Roche, BMS and Celgene, HG is a full time/part-time employee by Novartis, EH Servier, has received funding from Servier, Freenome, CA and PreAnalytiX and had an advisory role for Roche. MB has received honoraria, consulting fees research funds and/or travel expenses from Amgen, Astra Zeneca, Daichii, Eli Lilly, MSD, Novartis, Pierre- Fabre, Pfizer, Roche and Samsung.

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Suppan, C., Graf, R., Jahn, S. et al. Sensitive and robust liquid biopsy-based detection of PIK3CA mutations in hormone-receptor-positive metastatic breast cancer patients. Br J Cancer 126, 456–463 (2022).

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