Publikácie

@article{Rendek2024b,

title = {Current Challenges of Methylation-Based Liquid Biopsies in Cancer Diagnostics},

author = {T. Rendek and O. Pos and T. Duranova and R. Saade and J. Budis and V. Repiska and T. Szemes},

url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-85195678349&doi=10.3390%2fcancers16112001&partnerID=40&md5=a00b727d255d45e6c52a69ea1697e97a},

doi = {10.3390/cancers16112001},

issn = {20726694},

year  = {2024},

date = {2024-01-01},

urldate = {2024-01-01},

journal = {Cancers},

volume = {16},

number = {11},

publisher = {Multidisciplinary Digital Publishing Institute (MDPI)},

abstract = {In current clinical practice, effective cancer testing and screening paradigms are limited to specific types of cancer, exhibiting varying efficiency, acceptance, and adherence. Cell-free DNA (cfDNA) methylation profiling holds promise in providing information about the presence of malignity regardless of its type and location while leveraging blood-based liquid biopsies as a method to obtain analytical samples. However, technical difficulties, costs and challenges resulting from biological variations, tumor heterogeneity, and exogenous factors persist. This method exploits the mechanisms behind cfDNA release but faces issues like fragmentation, low concentrations, and high background noise. This review explores cfDNA methylation’s origins, means of detection, and profiling for cancer diagnostics. The critical evaluation of currently available multi-cancer early detection methods (MCEDs) as well as tests targeting single genes, emphasizing their potential and limits to refine strategies for early cancer detection, are explained. The current methodology limitations, workflows, comparisons of clinically approved liquid biopsy-based methylation tests for cancer, their utilization in companion diagnostics as well as the biological limitations of the epigenetics approach are discussed, aiming to help healthcare providers as well as researchers to orient themselves in this increasingly complex and evolving field of diagnostics. © 2024 by the authors.},

keywords = {Cell-free nucleic acids, Liquid biopsy, Oncology, Review},

pubstate = {published},

tppubtype = {article}

}

@article{Pös20211,

title = {Copy number variation: Methods and clinical applications},

author = {O Pös and J Radvanszky and J Styk and Z Pös and G Buglyó and M Kajsik and J Budis and B Nagy and T Szemes},

url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-85099826325&doi=10.3390%2fapp11020819&partnerID=40&md5=bf6fb8a1dd856194a109626d3ad1f9ca},

doi = {10.3390/app11020819},

issn = {20763417},

year  = {2021},

date = {2021-01-01},

journal = {Applied Sciences (Switzerland)},

volume = {11},

number = {2},

pages = {1-16},

publisher = {MDPI AG},

abstract = {Gains and losses of large segments of genomic DNA, known as copy number variants (CNVs) gained considerable interest in clinical diagnostics lately, as particular forms may lead to inherited genetic diseases. In recent decades, researchers developed a wide variety of cytogenetic and molecular methods with different detection capabilities to detect clinically relevant CNVs. In this review, we summarize methodological progress from conventional approaches to current state of the art techniques capable of detecting CNVs from a few bases up to several megabases. Although the recent rapid progress of sequencing methods has enabled precise detection of CNVs, determining their functional effect on cellular and whole-body physiology remains a challenge. Here, we provide a comprehensive list of databases and bioinformatics tools that may serve as useful assets for researchers, laboratory diagnosticians, and clinical geneticists facing the challenge of CNV detection and interpretation. © 2021 by the authors.},

keywords = {Copy number variation, Review, Variant interpretation},

pubstate = {published},

tppubtype = {article}

}

@article{Kiani2020e2020021,

title = {Prenatal genetic diagnosis: Fetal therapy as a possible solution to a positive test},

author = {A K Kiani and S Paolacci and P Scanzano and S Michelini and N Capodicasa and L DÁgruma and A Notarangelo and G Tonini and D Piccinelli and K R Farshid and P Petralia and E Fulcheri and F Buffelli and P Chiurazzi and C Terranova and F Plotti and R Angioli and M Castori and O Pös and T Szemes and M Bertelli},

url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-85096079899&doi=10.23750%2fabm.v91i13-S.10534&partnerID=40&md5=8100ee0e6931cd1a57203e138b3cd27c},

doi = {10.23750/abm.v91i13-S.10534},

issn = {25316745},

year  = {2020},

date = {2020-01-01},

journal = {Acta bio-medica : Atenei Parmensis},

volume = {91},

number = {13S},

pages = {e2020021},

publisher = {NLM (Medline)},

abstract = {BACKGROUND: Fetal abnormalities cause 20% of perinatal deaths. Advances in prenatal genetic and other types of screening offer great opportunities for identifying high risk pregnancies. METHODS: Through a literature search, here we summarise what are the prenatal diagnostic technique that are being used and how those techniques may allow for prenatal interventions. RESULTS: Next generation sequencing and non-invasive prenatal testing are fundamental for clinical diagnostics because of their sensitivity and accuracy in identifying point mutations, aneuploidies, and microdeletions, respectively. Timely identification of genetic disorders and other fetal abnormalities enables early intervention, such as in-utero gene therapy, fetal drug therapy and prenatal surgery. CONCLUSION: Prenatal intervention is mainly focused on conditions that may cause death or lifelong disabilities, like spina bifida, congenital diaphragm hernia and sacrococcygeal teratoma; and may be an alternative therapeutic option to termination of pregnancy. However, it is not yet widely available, due to lack of specialized centers.},

keywords = {Non-invasive prenatal testing, Prenatal diagnosis, Prenatal therapy, Review},

pubstate = {published},

tppubtype = {article}

}

@article{Pös20201,

title = {Technical and methodological aspects of cell‐free nucleic acids analyzes},

author = {Z Pös and O Pös and J Styk and A Mocova and L Strieskova and J Budis and L Kadasi and J Radvanszky and T Szemes},

url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-85096148893&doi=10.3390%2fijms21228634&partnerID=40&md5=826434c64ac9dbe5f81fc0ee5b62eaa3},

doi = {10.3390/ijms21228634},

issn = {16616596},

year  = {2020},

date = {2020-01-01},

journal = {International Journal of Molecular Sciences},

volume = {21},

number = {22},

pages = {1-43},

publisher = {MDPI AG},

abstract = {Analyzes of cell‐free nucleic acids (cfNAs) have shown huge potential in many biomedical applications, gradually entering several fields of research and everyday clinical care. Many biological properties of cfNAs can be informative to gain deeper insights into the function of the organism, such as their different types (DNA, RNAs) and subtypes (gDNA, mtDNA, bacterial DNA, miRNAs, etc.), forms (naked or vesicle bound NAs), fragmentation profiles, sequence composition, epigenetic modifications, and many others. On the other hand, the workflows of their analyzes comprise many important steps, from sample collection, storage and transportation, through extraction and laboratory analysis, up to bioinformatic analyzes and statistical evaluations, where each of these steps has the potential to affect the outcome and informational value of the performed analyzes. There are, however, no universal or standard protocols on how to exactly proceed when analyzing different cfNAs for different applications, at least according to our best knowledge. We decided therefore to prepare an overview of the available literature and products commercialized for cfNAs processing, in an attempt to summarize the benefits and limitations of the currently available approaches, devices, consumables, and protocols, together with various factors influencing the workflow, its processes, and outcomes. © 2020 by the authors. Licensee MDPI, Basel, Switzerland.},

keywords = {Body fluids, Cell-free nucleic acids, Liquid biopsy, Non-invasive prenatal testing, Review},

pubstate = {published},

tppubtype = {article}

}

@article{Radvánszky2015418,

title = {Interpretation of clinical significance of sequence variants in molecular genetics [Interpretácia klinického významu sekvenčných variantov v molekulovej genetike]},

author = {J Radvánszky and G Minárik and T Szemeš and M Konečný and L Kádaši},

url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-85020271195&partnerID=40&md5=bf647ff52f306470833ee835a42d012b},

issn = {04574214},

year  = {2015},

date = {2015-01-01},

journal = {Lekarsky Obzor},

volume = {64},

number = {11},

pages = {418-427},

publisher = {Slovenska zdravotnicka univerzita},

abstract = {By applications of genomic analyses we are able to get an enormous number of different sequence variants in each analysed individual. From these only a small, although constantly growing, number of variants are already known and well characterised, while the majority of them are yet not characterised unknown variants. Their correct classification and interpretation are key factors for the understanding and usage of their informational value in clinical practice. Consistent education of professional staff able to handle, interpret and transfer the generated data to clinical workflow represents therefore a very important factor of professional practice. This article summarizes different recommendations for the evaluation and interpretation of sequence variants, from their correct nomenclature up to assigning them certain clinically relevant significance.},

keywords = {Genetic testing, Review, Single nucleotide variants, Variant interpretation},

pubstate = {published},

tppubtype = {article}

}

@article{Vlková2010b,

title = {Advances in the research of fetal DNA in maternal plasma for noninvasive prenatal diagnostics},

author = {B Vlková and T Szemes and G Minárik and J Turňa and P Celec},

url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-77954303943&partnerID=40&md5=f8502e85159556021100dec5321b7865},

issn = {12341010},

year  = {2010},

date = {2010-01-01},

journal = {Medical Science Monitor},

volume = {16},

number = {4},

pages = {RA85-RA91},

abstract = {Molecular analysis of fetal DNA present in the maternal circulation allows noninvasive, early, and precise determination of fetal genetic status in prenatal diagnostics. The most common clinical applications, i.e. prenatal gender determination and fetal RhD genotyping, are possible already in the first trimester using specialized protocols for DNA isolation from plasma and subsequent realtime PCR detection. Recent advances in molecular techniques enable other applications of fetal DNA purified from maternal plasma samples. Chromosomal abnormalities (e.g. trisomy 21) can be diagnosed by digital PCR, which offers higher accuracy in quantifying DNA sequences than standard real-time PCR. Digital PCR, but also MALDI-TOF, are suitable for detecting point mutations, widening the spectrum of applications to monogenic diseases. The ongoing lowering of costs for massively parallel sequencing might lead to replacement of most of the other currently used approaches. Adopting specialized protocols for the purification of fragmented circulating fetal DNA and improving the bioinformatic analysis of raw data can bring us closer to sequencing the fetal genome as the ultimate goal of prenatal DNA diagnostics, with wide-ranging medical applications. The discussion and solution of ethical issues beyond early fetal gender or paternity determination is hanging just behind the rapid technical progress of noninvasive prenatal DNA diagnostics. © Med Sci Monit, 2010.},

keywords = {Liquid biopsy, Non-invasive prenatal testing, Review, Validation},

pubstate = {published},

tppubtype = {article}

}