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Priskin K, Pólya S, Pintér L, Jaksa G, Csányi B, Enyedi MZ, Sági-Zsigmond E, Sükösd F, Oláh-Németh O, Kelemen G, Nikolényi A, Uhercsák G, Sántha D, Dobi Á, Szilágyi É, Valicsek E, Tordai L, Tóth R, Kahán Z, Haracska L. BC-Monitor: Towards a Routinely Accessible Circulating Tumor DNA-Based Tool for Real-Time Monitoring Breast Cancer Progression and Treatment Effectiveness. Cancers (Basel) 2021; 13:3489. [PMID: 34298704 PMCID: PMC8305126 DOI: 10.3390/cancers13143489] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2021] [Revised: 07/05/2021] [Accepted: 07/07/2021] [Indexed: 12/12/2022] Open
Abstract
Circulating tumor DNA (ctDNA) is increasingly employed in the screening, follow-up, and monitoring of the continuously evolving tumor; however, most ctDNA assays validated for clinical use cannot maintain the right balance between sensitivity, coverage, sample requirements, time, and cost. Here, we report our BC-monitor, a simple, well-balanced ctDNA diagnostic approach using a gene panel significant in breast cancer and an optimized multiplex PCR-based NGS protocol capable of identifying allele variant frequencies below 1% in cell-free plasma DNA. We monitored a cohort of 45 breast cancer patients prospectively enrolled into our study receiving neoadjuvant chemotherapy or endocrine therapy or palliative therapy for metastatic diseases. Their tumor mutation status was examined in the archived tumor samples and plasma samples collected before and continuously during therapy. Traceable mutations of the used 38-plex NGS assay were found in approximately two-thirds of the patients. Importantly, we detected new pathogenic variants in follow-up plasma samples that were not detected in the primary tumor and baseline plasma samples. We proved that the BC-monitor can pre-indicate disease progression four-six months earlier than conventional methods. Our study highlights the need for well-designed ctDNA monitoring during treatment and follow-up, integrated into a real-time treatment assessment, which could provide information on the active tumor DNA released into the blood.
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Affiliation(s)
- Katalin Priskin
- Delta Bio 2000 Ltd., 6726 Szeged, Hungary; (K.P.); (L.P.); (G.J.); (M.Z.E.); (E.S.-Z.)
| | - Sára Pólya
- Visal Plus Ltd., 6726 Szeged, Hungary; (S.P.); (B.C.)
| | - Lajos Pintér
- Delta Bio 2000 Ltd., 6726 Szeged, Hungary; (K.P.); (L.P.); (G.J.); (M.Z.E.); (E.S.-Z.)
| | - Gábor Jaksa
- Delta Bio 2000 Ltd., 6726 Szeged, Hungary; (K.P.); (L.P.); (G.J.); (M.Z.E.); (E.S.-Z.)
| | | | - Márton Zsolt Enyedi
- Delta Bio 2000 Ltd., 6726 Szeged, Hungary; (K.P.); (L.P.); (G.J.); (M.Z.E.); (E.S.-Z.)
| | - Eszter Sági-Zsigmond
- Delta Bio 2000 Ltd., 6726 Szeged, Hungary; (K.P.); (L.P.); (G.J.); (M.Z.E.); (E.S.-Z.)
| | - Farkas Sükösd
- Department of Pathology, University of Szeged, 6701 Szeged, Hungary;
| | - Orsolya Oláh-Németh
- Department of Oncotherapy, University of Szeged, 6720 Szeged, Hungary; (O.O.-N.); (G.K.); (A.N.); (G.U.); (D.S.); (Á.D.); (É.S.); (E.V.); (L.T.); (R.T.); (Z.K.)
| | - Gyöngyi Kelemen
- Department of Oncotherapy, University of Szeged, 6720 Szeged, Hungary; (O.O.-N.); (G.K.); (A.N.); (G.U.); (D.S.); (Á.D.); (É.S.); (E.V.); (L.T.); (R.T.); (Z.K.)
| | - Alíz Nikolényi
- Department of Oncotherapy, University of Szeged, 6720 Szeged, Hungary; (O.O.-N.); (G.K.); (A.N.); (G.U.); (D.S.); (Á.D.); (É.S.); (E.V.); (L.T.); (R.T.); (Z.K.)
| | - Gabriella Uhercsák
- Department of Oncotherapy, University of Szeged, 6720 Szeged, Hungary; (O.O.-N.); (G.K.); (A.N.); (G.U.); (D.S.); (Á.D.); (É.S.); (E.V.); (L.T.); (R.T.); (Z.K.)
| | - Dóra Sántha
- Department of Oncotherapy, University of Szeged, 6720 Szeged, Hungary; (O.O.-N.); (G.K.); (A.N.); (G.U.); (D.S.); (Á.D.); (É.S.); (E.V.); (L.T.); (R.T.); (Z.K.)
| | - Ágnes Dobi
- Department of Oncotherapy, University of Szeged, 6720 Szeged, Hungary; (O.O.-N.); (G.K.); (A.N.); (G.U.); (D.S.); (Á.D.); (É.S.); (E.V.); (L.T.); (R.T.); (Z.K.)
| | - Éva Szilágyi
- Department of Oncotherapy, University of Szeged, 6720 Szeged, Hungary; (O.O.-N.); (G.K.); (A.N.); (G.U.); (D.S.); (Á.D.); (É.S.); (E.V.); (L.T.); (R.T.); (Z.K.)
| | - Erzsébet Valicsek
- Department of Oncotherapy, University of Szeged, 6720 Szeged, Hungary; (O.O.-N.); (G.K.); (A.N.); (G.U.); (D.S.); (Á.D.); (É.S.); (E.V.); (L.T.); (R.T.); (Z.K.)
| | - László Tordai
- Department of Oncotherapy, University of Szeged, 6720 Szeged, Hungary; (O.O.-N.); (G.K.); (A.N.); (G.U.); (D.S.); (Á.D.); (É.S.); (E.V.); (L.T.); (R.T.); (Z.K.)
| | - Rozália Tóth
- Department of Oncotherapy, University of Szeged, 6720 Szeged, Hungary; (O.O.-N.); (G.K.); (A.N.); (G.U.); (D.S.); (Á.D.); (É.S.); (E.V.); (L.T.); (R.T.); (Z.K.)
| | - Zsuzsanna Kahán
- Department of Oncotherapy, University of Szeged, 6720 Szeged, Hungary; (O.O.-N.); (G.K.); (A.N.); (G.U.); (D.S.); (Á.D.); (É.S.); (E.V.); (L.T.); (R.T.); (Z.K.)
| | - Lajos Haracska
- HCEMM-BRC Mutagenesis and Carcinogenesis Research Group, Biological Research Centre, Institute of Genetics, 6726 Szeged, Hungary
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Enyedi MZ, Jaksa G, Pintér L, Sükösd F, Gyuris Z, Hajdu A, Határvölgyi E, Priskin K, Haracska L. Simultaneous detection of BRCA mutations and large genomic rearrangements in germline DNA and FFPE tumor samples. Oncotarget 2018; 7:61845-61859. [PMID: 27533253 PMCID: PMC5308695 DOI: 10.18632/oncotarget.11259] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2016] [Accepted: 07/19/2016] [Indexed: 11/25/2022] Open
Abstract
The development of breast and ovarian cancer is strongly connected to the inactivation of the BRCA1 and BRCA2 genes by different germline and somatic alterations, and their diagnosis has great significance in targeted tumor therapy, since recently approved PARP inhibitors show high efficiency in the treatment of BRCA-deficient tumors. This raises the need for new diagnostic methods that are capable of performing an integrative mutation analysis of the BRCA genes not only from germline DNA but also from formalin-fixed and paraffin-embedded (FFPE) tumor samples. Here we describe the development of such a methodology based on next-generation sequencing and a new bioinformatics software for data analysis. The diagnostic method was initially developed on an Illumina MiSeq NGS platform using germline-mutated stem cell lines and then adapted for the Ion Torrent PGM NGS platform as well. We also investigated the usability of NGS coverage data for the detection of copy number variations and exon deletions as a replacement of the conventional MLPA technique. Finally, we tested the developed workflow on FFPE samples from breast and ovarian cancer patients. Our method meets the sensitivity and specificity requirements for the genetic diagnosis of breast and ovarian cancers both from germline and FFPE samples.
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Affiliation(s)
- Márton Zsolt Enyedi
- Institute of Genetics, Biological Research Centre of the Hungarian Academy of Sciences, Szeged 6726, Hungary
| | | | | | - Farkas Sükösd
- Department of Pathology, Faculty of Medicine, University of Szeged, Szeged 6720, Hungary
| | | | - Adrienn Hajdu
- Delta Bio 2000 Ltd., Szeged 6726, Hungary.,Department of Pathology, Faculty of Medicine, University of Szeged, Szeged 6720, Hungary
| | | | | | - Lajos Haracska
- Institute of Genetics, Biological Research Centre of the Hungarian Academy of Sciences, Szeged 6726, Hungary
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