Publikácie

@article{Holesova2024,

title = {Understanding genetic variability: exploring large-scale copy number variants through non-invasive prenatal testing in European populations},

author = {Z. Holesova and O. Pös and J. Gazdarica and M. Kucharik and J. Budis and M. Hyblova and G. Minarik and T. Szemes},

url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-85190362328&doi=10.1186%2fs12864-024-10267-5&partnerID=40&md5=9db9ad228e071b255f5c759790d53c82},

doi = {10.1186/s12864-024-10267-5},

issn = {14712164},

year  = {2024},

date = {2024-01-01},

urldate = {2024-01-01},

journal = {BMC Genomics},

volume = {25},

number = {1},

publisher = {BioMed Central Ltd},

abstract = {Large-scale copy number variants (CNVs) are structural alterations in the genome that involve the duplication or deletion of DNA segments, contributing to genetic diversity and playing a crucial role in the evolution and development of various diseases and disorders, as they can lead to the dosage imbalance of one or more genes. Massively parallel sequencing (MPS) has revolutionized the field of genetic analysis and contributed significantly to routine clinical diagnosis and screening. It offers a precise method for detecting CNVs with exceptional accuracy. In this context, a non-invasive prenatal test (NIPT) based on the sequencing of cell-free DNA (cfDNA) from pregnant women’s plasma using a low-coverage whole genome MPS (WGS) approach represents a valuable source for population studies. Here, we analyzed genomic data of 12,732 pregnant women from the Slovak (9,230), Czech (1,583), and Hungarian (1,919) populations. We identified 5,062 CNVs ranging from 200 kbp and described their basic characteristics and differences between the subject populations. Our results suggest that re-analysis of sequencing data from routine WGS assays has the potential to obtain large-scale CNV population frequencies, which are not well known and may provide valuable information to support the classification and interpretation of this type of genetic variation. Furthermore, this could contribute to expanding knowledge about the central European genome without investing in additional laboratory work, as NIPTs are a relatively widely used screening method. © The Author(s) 2024.},

keywords = {Copy number variation, Non-invasive prenatal testing, Population study},

pubstate = {published},

tppubtype = {article}

}

@article{Forgacova2023,

title = {Evaluation and limitations of different approaches among COVID-19 fatal cases using whole-exome sequencing data},

author = {N. Forgacova and Z. Holesova and R. Hekel and T. Sedlackova and Z. Pos and L. Krivosikova and P. Janega and K. M. Kuracinova and P. Babal and P. Radvak and J. Radvanszky and J. Gazdarica and J. Budis and T. Szemes},

url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-85146101670&doi=10.1186%2fs12864-022-09084-5&partnerID=40&md5=d25846b50ef1ee4668a13ebd7d02bb47},

doi = {10.1186/s12864-022-09084-5},

issn = {14712164},

year  = {2023},

date = {2023-01-01},

urldate = {2023-01-01},

journal = {BMC Genomics},

volume = {24},

number = {1},

publisher = {BioMed Central Ltd},

abstract = {Background: COVID-19 caused by the SARS-CoV-2 infection may result in various disease symptoms and severity, ranging from asymptomatic, through mildly symptomatic, up to very severe and even fatal cases. Although environmental, clinical, and social factors play important roles in both susceptibility to the SARS-CoV-2 infection and progress of COVID-19 disease, it is becoming evident that both pathogen and host genetic factors are important too. In this study, we report findings from whole-exome sequencing (WES) of 27 individuals who died due to COVID-19, especially focusing on frequencies of DNA variants in genes previously associated with the SARS-CoV-2 infection and the severity of COVID-19. Results: We selected the risk DNA variants/alleles or target genes using four different approaches: 1) aggregated GWAS results from the GWAS Catalog; 2) selected publications from PubMed; 3) the aggregated results of the Host Genetics Initiative database; and 4) a commercial DNA variant annotation/interpretation tool providing its own knowledgebase. We divided these variants/genes into those reported to influence the susceptibility to the SARS-CoV-2 infection and those influencing the severity of COVID-19. Based on the above, we compared the frequencies of alleles found in the fatal COVID-19 cases to the frequencies identified in two population control datasets (non-Finnish European population from the gnomAD database and genomic frequencies specific for the Slovak population from our own database). When compared to both control population datasets, our analyses indicated a trend of higher frequencies of severe COVID-19 associated risk alleles among fatal COVID-19 cases. This trend reached statistical significance specifically when using the HGI-derived variant list. We also analysed other approaches to WES data evaluation, demonstrating its utility as well as limitations. Conclusions: Although our results proved the likely involvement of host genetic factors pointed out by previous studies looking into severity of COVID-19 disease, careful considerations of the molecular-testing strategies and the evaluated genomic positions may have a strong impact on the utility of genomic testing. © 2023, The Author(s).},

note = {cited By 0},

keywords = {Non-invasive prenatal testing, Sars-cov-2},

pubstate = {published},

tppubtype = {article}

}

@article{Hyblova2022,

title = {Maternal Copy Number Imbalances in Non-Invasive Prenatal Testing: Do They Matter?},

author = {M. Hyblova and A. Gnip and M. Kucharik and J. Budis and M. Sekelska and G. Minarik},

url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-85144618980&doi=10.3390%2fdiagnostics12123056&partnerID=40&md5=3f313608e34c3a2137159e1e157d014c},

doi = {10.3390/diagnostics12123056},

issn = {20754418},

year  = {2022},

date = {2022-01-01},

urldate = {2022-01-01},

journal = {Diagnostics},

volume = {12},

number = {12},

publisher = {MDPI},

abstract = {Non-invasive prenatal testing (NIPT) has become a routine practice in screening for common aneuploidies of chromosomes 21, 18, and 13 and gonosomes X and Y in fetuses worldwide since 2015 and has even expanded to include smaller subchromosomal events. In fact, the fetal fraction represents only a small proportion of cell-free DNA on a predominant background of maternal DNA. Unlike fetal findings that have to be confirmed using invasive testing, it has been well documented that NIPT provides information on maternal mosaicism, occult malignancies, and hidden health conditions due to copy number variations (CNVs) with diagnostic resolution. Although large duplications or deletions associated with certain medical conditions or syndromes are usually well recognized and easy to interpret, very little is known about small, relatively common copy number variations on the order of a few hundred kilobases and their potential impact on human health. We analyzed data from 6422 NIPT patient samples with a CNV detection resolution of 200 kb for the maternal genome and identified 942 distinct CNVs; 328 occurred repeatedly. We defined them as multiple occurring variants (MOVs). We scrutinized the most common ones, compared them with frequencies in the gnomAD SVs v2.1, dbVar, and DGV population databases, and analyzed them with an emphasis on genomic content and potential association with specific phenotypes. © 2022 by the authors.},

keywords = {Copy number variation, Non-invasive prenatal testing},

pubstate = {published},

tppubtype = {article}

}

@article{Forgacova2022,

title = {Non-intuitive trends of fetal fraction development related to gestational age and fetal gender, and their practical implications for non-invasive prenatal testing},

author = {N. Forgacova and J. Gazdarica and J. Budis and M. Kucharik and M. Sekelska and T. Szemes},

url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-85141451340&doi=10.1016%2fj.mcp.2022.101870&partnerID=40&md5=5f0a0eeb4603486d4288fc56950e00fe},

doi = {10.1016/j.mcp.2022.101870},

issn = {08908508},

year  = {2022},

date = {2022-01-01},

urldate = {2022-01-01},

journal = {Molecular and Cellular Probes},

volume = {66},

publisher = {Academic Press},

abstract = {Discovery of fetal cell-free DNA fragments in maternal blood revolutionized prenatal diagnostics. Although non-invasive prenatal testing (NIPT) is already a matured screening test with high specificity and sensitivity, the accurate estimation of the proportion of fetal fragments, called fetal fraction, is crucial to avoid false-negative results. In this study, we collected 6999 samples from women undergoing NIPT testing with a single male fetus to demonstrate the influence of fetal fraction by the maternal and fetal characteristics. We show several fetal fraction discrepancies that contradict the generally presented conventional view. At first, the fetal fraction is not consistently rising with the maturity of the fetus due to a drop in 15 weeks of maturation. Secondly, the male samples have a lower fetal fraction than female fetuses, arguably due to the smaller gonosomal chromosomes. Finally, we discuss not only the possible reasons why this inconsistency exists but we also outline why these differences have not yet been identified and published. We demonstrate two non-intuitive trends to better comprehend the fetal fraction development and more precise selection of patients with sufficient fetal fraction for accurate testing. © 2022 The Authors},

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

pubstate = {published},

tppubtype = {article}

}

@article{Kucharík2021,

title = {Copy number variant detection with low-coverage whole-genome sequencing represents a viable alternative to the conventional array-cgh},

author = {M Kucharík and J Budiš and M Hýblová and G Minárik and T Szemes},

url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-85109087040&doi=10.3390%2fdiagnostics11040708&partnerID=40&md5=6fdfa35027032bf889399d967bb1cce9},

doi = {10.3390/diagnostics11040708},

issn = {20754418},

year  = {2021},

date = {2021-01-01},

urldate = {2021-01-01},

journal = {Diagnostics},

volume = {11},

number = {4},

publisher = {MDPI AG},

abstract = {Copy number variations (CNVs) represent a type of structural variant involving alterations in the number of copies of specific regions of DNA that can either be deleted or duplicated. CNVs contribute substantially to normal population variability, however, abnormal CNVs cause numerous genetic disorders. At present, several methods for CNV detection are applied, ranging from the conventional cytogenetic analysis, through microarray-based methods (aCGH), to next-generation sequencing (NGS). In this paper, we present GenomeScreen, an NGS-based CNV detection method for low-coverage, whole-genome sequencing. We determined the theoretical limits of its accuracy and obtained confirmation in an extensive in silico study and in real patient samples with known genotypes. In theory, at least 6 M uniquely mapped reads are required to detect a CNV with the length of 100 kilobases (kb) or more with high confidence (Z-score > 7). In practice, the in silico analysis required at least 8 M to obtain >99% accuracy (for 100 kb deviations). We compared GenomeScreen with one of the currently used aCGH methods in diagnostic laboratories, which has mean resolution of 200 kb. GenomeScreen and aCGH both detected 59 deviations, while GenomeScreen furthermore detected 134 other (usually) smaller variations. When compared to aCGH, overall performance of the proposed GenemoScreen tool is comparable or superior in terms of accuracy, turn-around time, and cost-effectiveness, thus providing reasonable benefits, particularly in a prenatal diagnosis setting. © 2021 by the authors. Licensee MDPI, Basel, Switzerland.},

keywords = {Cell-free nucleic acids, Computational method, Copy number variation, Liquid biopsy, Non-invasive prenatal testing},

pubstate = {published},

tppubtype = {article}

}

@article{Radvanszky2021,

title = {Characterisation of non-pathogenic premutation-range myotonic dystrophy type 2 alleles},

author = {J Radvanszky and M Hyblova and E Radvanska and P Spalek and A Valachova and G Magyarova and C Bognar and E Polak and T Szemes and L Kadasi},

url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-85114043590&doi=10.3390%2fjcm10173934&partnerID=40&md5=57bc1cfc4be446edf6fbfea3c9ad284a},

doi = {10.3390/jcm10173934},

issn = {20770383},

year  = {2021},

date = {2021-01-01},

urldate = {2021-01-01},

journal = {Journal of Clinical Medicine},

volume = {10},

number = {17},

publisher = {MDPI},

abstract = {Myotonic dystrophy type 2 (DM2) is caused by expansion of a (CCTG)n repeat in the cellular retroviral nucleic acid-binding protein (CNBP) gene. The sequence of the repeat is most commonly interrupted and is stably inherited in the general population. Although expanded alleles, premutation range and, in rare cases, also non-disease associated alleles containing uninterrupted CCTG tracts have been described, the threshold between these categories is poorly characterised. Here, we describe four families with members reporting neuromuscular complaints, in whom we identified altogether nine ambiguous CNBP alleles containing uninterrupted CCTG repeats in the range between 32 and 42 repeats. While these grey-zone alleles are most likely not pathogenic themselves, since other pathogenic mutations were identified and particular family structures did not support their pathogenic role, they were found to be unstable during intergenerational transmission. On the other hand, there was no observable general microsatellite instability in the genome of the carriers of these alleles. Our results further refine the division of CNBP CCTG repeat alleles into two major groups, i.e., interrupted and uninterrupted alleles. Both interrupted and uninterrupted alleles with up to approximately 30 CCTG repeats were shown to be generally stable during intergenerational transmission, while intergenerational as well as somatic instability seems to gradually increase in uninterrupted alleles with tract length growing above this threshold. © 2021 by the authors. Licensee MDPI, Basel, Switzerland.},

keywords = {Non-invasive prenatal testing, Oncology, Single nucleotide variants},

pubstate = {published},

tppubtype = {article}

}

@article{Forgacova2021,

title = {Repurposing non‑invasive prenatal testing data: Population study of single nucleotide variants associated with Colorectal Cancer and Lynch Syndrome},

author = {N Forgacova and J Gazdarica and J Budis and J Radvanszky and T Szemes},

url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-85115197955&doi=10.3892%2fol.2021.13040&partnerID=40&md5=2e80f1d2538655ce09382de2cd0b3e20},

doi = {10.3892/ol.2021.13040},

issn = {17921074},

year  = {2021},

date = {2021-01-01},

urldate = {2021-01-01},

journal = {Oncology Letters},

volume = {22},

number = {5},

publisher = {Spandidos Publications},

abstract = {In our previous work, genomic data generated through non‑invasive prenatal testing (NIPT) based on low‑coverage massively parallel whole‑genome sequencing of totalplasmaDNAofpregnantwomeninSlovakiawasdescribed as a valuable source of population specific data. In the present study, these data were used to determine the population allele frequency of common risk variants located in genes associated with colorectal cancer (CRC) and Lynch syndrome (LS). Allele frequencies of identified variants were compared with six world populations to detect significant differences between populations. Finally, variants were interpreted, functional consequences were searched for and clinical significance of variants was investigated using publicly available databases. Although the present study did not identify any pathogenic variants associated with CRC or LS in the Slovak population using NIPT data, significant differences were observed in the allelic frequency of risk CRC variants previously reported in genome‑wide association studies and common variants located in genes associated with LS. As Slovakia is one of the leading countries with the highest incidence of CRC among male patients in the world, there is a need for studies dedicated to investigating the cause of such a high incidence of CRC in Slovakia. The present study also assumed that extensive cross‑country data aggregation of NIPT results would represent an unprecedented source of information concerning human genome variation in cancer research. © 2021 Spandidos Publications. All rights reserved.},

keywords = {Non-invasive prenatal testing, Oncology, Population study},

pubstate = {published},

tppubtype = {article}

}

@article{Kucharik2020,

title = {Non-invasive prenatal testing (NIPT) by low coverage genomic sequencing: Detection limits of screened chromosomal microdeletions},

author = {M Kucharik and A Gnip and M Hyblova and J Budis and L Strieskova and M Harsanyova and O Pös and Z Kubiritova and J Radvanszky and G Minarik and T Szemes},

url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-85089990305&doi=10.1371%2fjournal.pone.0238245&partnerID=40&md5=56850bc0c9e9e5e266a3538da3dd5bed},

doi = {10.1371/journal.pone.0238245},

issn = {19326203},

year  = {2020},

date = {2020-01-01},

journal = {PLoS ONE},

volume = {15},

number = {8 August},

publisher = {Public Library of Science},

abstract = {To study the detection limits of chromosomal microaberrations in non-invasive prenatal testing with aim for five target microdeletion syndromes, including DiGeorge, Prader-Willi/Angelman, 1p36, Cri-Du-Chat, and Wolf-Hirschhorn syndromes. We used known cases of pathogenic deletions from ISCA database to specifically define regions critical for the target syndromes. Our approach to detect microdeletions, from whole genome sequencing data, is based on sample normalization and read counting for individual bins. We performed both an in-silico study using artificially created data sets and a laboratory test on mixed DNA samples, with known microdeletions, to assess the sensitivity of prediction for varying fetal fractions, deletion lengths, and sequencing read counts. The in-silico study showed sensitivity of 79.3% for 10% fetal fraction with 20M read count, which further increased to 98.4% if we searched only for deletions longer than 3Mb. The test on laboratory-prepared mixed samples was in agreement with in-silico results, while we were able to correctly detect 24 out of 29 control samples. Our results suggest that it is possible to incorporate microaberration detection into basic NIPT as part of the offered screening/diagnostics procedure, however, accuracy and reliability depends on several specific factors. Copyright: © 2020 Kucharik et al.},

keywords = {Copy number variation, Fetal fraction, Non-invasive prenatal testing, Validation},

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{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{Hyblova2020,

title = {Validation of copy number variants detection from pregnant plasma using low-pass whole-genome sequencing in noninvasive prenatal testing-like settings},

author = {M Hyblova and M Harsanyova and D Nikulenkov-Grochova and J Kadlecova and M Kucharik and J Budis and G Minarik},

url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-85090251668&doi=10.3390%2fdiagnostics10080569&partnerID=40&md5=b34f5ed83d4c332d97149be1644573c0},

doi = {10.3390/diagnostics10080569},

issn = {20754418},

year  = {2020},

date = {2020-01-01},

journal = {Diagnostics},

volume = {10},

number = {8},

publisher = {MDPI AG},

abstract = {Detection of copy number variants as an integral part of noninvasive prenatal testing is increasingly used in clinical practice worldwide. We performed validation on plasma samples from 34 pregnant women with known aberrations using cell-free DNA sequencing to evaluate the sensitivity for copy number variants (CNV) detection using an in-house CNV fraction-based detection algorithm. The sensitivity for CNVs smaller than 3 megabases (Mb), larger than 3Mb, and overall was 78.57%, 100%, and 90.6%, respectively. Regarding the fetal fraction, detection sensitivity in the group with a fetal fraction of less than 10% was 57.14%, whereas there was 100% sensitivity in the group with fetal fraction exceeding 10%. The assay is also capable of indicating whether the origin of an aberration is exclusively fetal or fetomaternal/maternal. This validation demonstrated that a CNV fraction-based algorithm was applicable and feasible in clinical settings as a supplement to testing for common trisomies 21, 18, and 13. © 2020 by the authors. Licensee MDPI, Basel, Switzerland. This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY) license (http://creativecommons.org/licenses/by/4.0/).},

keywords = {Copy number variation, Fetal fraction, Non-invasive prenatal testing, Validation},

pubstate = {published},

tppubtype = {article}

}

@article{Sekelska2019,

title = {Result of prospective validation of the trisomy Test® for the detection of chromosomal trisomies},

author = {M Sekelska and A Izsakova and K Kubosova and P Tilandyova and E Csekes and Z Kuchova and M Hyblova and M Harsanyova and M Kucharik and J Budis and T Szemes and G Minarik},

url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-85076805864&doi=10.3390%2fdiagnostics9040138&partnerID=40&md5=ffdda3394730383358ea467fee4a90f8},

doi = {10.3390/diagnostics9040138},

issn = {20754418},

year  = {2019},

date = {2019-01-01},

journal = {Diagnostics},

volume = {9},

number = {4},

publisher = {MDPI AG},

abstract = {Noninvasive prenatal testing (NIPT) is one of the most common prenatal screening tests used worldwide. Trisomy Test® belongs to NIPT tests based on low-coverage whole-genome sequencing. In our prospective study, 7279 samples of pregnant women collected during approximately two years were analyzed. In this cohort, 117 positive cases for trisomies 21, 18, and 13 were reported. An in-house designed bioinformatic pipeline and proprietary biostatistical approach was used for the detection of trisomies. The pooled sensitivity and specificity of our test reached 99.12% and 99.94%, respectively. The proportion of repeatedly uninformative results after repeated blood draws was 1.11%. Based on the presented results, we can confirm that the Trisomy Test® is fully comparable with other commercial NIPT tests available worldwide. © 2019 by the authors.},

keywords = {Aneuploidy, Fetal fraction, Non-invasive prenatal testing, Validation},

pubstate = {published},

tppubtype = {article}

}

@article{Pös2019,

title = {Identification of structural variation from NGS-based non-invasive prenatal testing},

author = {O Pös and J Budis and Z Kubiritova and M Kucharik and F Duris and J Radvanszky and T Szemes},

url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-85071973486&doi=10.3390%2fijms20184403&partnerID=40&md5=2b201ce501881c47092d14454e2ed2a9},

doi = {10.3390/ijms20184403},

issn = {16616596},

year  = {2019},

date = {2019-01-01},

journal = {International Journal of Molecular Sciences},

volume = {20},

number = {18},

publisher = {MDPI AG},

abstract = {Copy number variants (CNVs) are an important type of human genome variation, which play a significant role in evolution contribute to population diversity and human genetic diseases. In recent years, next generation sequencing has become a valuable tool for clinical diagnostics and to provide sensitive and accurate approaches for detecting CNVs. In our previous work, we described a non-invasive prenatal test (NIPT) based on low-coverage massively parallel whole-genome sequencing of total plasma DNA for detection of CNV aberrations ≥600 kbp. We reanalyzed NIPT genomic data from 5018 patients to evaluate CNV aberrations in the Slovak population. Our analysis of autosomal chromosomes identified 225 maternal CNVs (47 deletions; 178 duplications) ranging from 600 to 7820 kbp. According to the ClinVar database, 137 CNVs (60.89%) were fully overlapping with previously annotated variants, 66 CNVs (29.33%) were in partial overlap, and 22 CNVs (9.78%) did not overlap with any previously described variant. Identified variants were further classified with the AnnotSV method. In summary, we identified 129 likely benign variants, 13 variants of uncertain significance, and 83 likely pathogenic variants. In this study, we use NIPT as a valuable source of population specific data. Our results suggest the utility of genomic data from commercial CNV analysis test as background for a population study. © 2019 by the authors. Licensee MDPI, Basel, Switzerland.},

keywords = {Copy number variation, Non-invasive prenatal testing, Population study},

pubstate = {published},

tppubtype = {article}

}

@article{Gazdarica2019,

title = {Combination of fetal fraction estimators based on fragment lengths and fragment counts in non-invasive prenatal testing},

author = {J Gazdarica and R Hekel and J Budis and M Kucharik and F Duris and J Radvanszky and J Turna and T Szemes},

url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-85071515046&doi=10.3390%2fijms20163959&partnerID=40&md5=13c0a797eeb085dba097cea3d39680a9},

doi = {10.3390/ijms20163959},

issn = {16616596},

year  = {2019},

date = {2019-01-01},

journal = {International Journal of Molecular Sciences},

volume = {20},

number = {16},

publisher = {MDPI AG},

abstract = {The reliability of non-invasive prenatal testing is highly dependent on accurate estimation of fetal fraction. Several methods have been proposed up to date, utilizing different attributes of analyzed genomic material, for example length and genomic location of sequenced DNA fragments. These two sources of information are relatively unrelated, but so far, there have been no published attempts to combine them to get an improved predictor. We collected 2454 single euploid male fetus samples from women undergoing NIPT testing. Fetal fractions were calculated using several proposed predictors and the state-of-the-art SeqFF method. Predictions were compared with the reference Y-based method. We demonstrate that prediction based on length of sequenced DNA fragments may achieve nearly the same precision as the state-of-the-art methods based on their genomic locations. We also show that combination of several sample attributes leads to a predictor that has superior prediction accuracy over any single approach. Finally, appropriate weighting of samples in the training process may achieve higher accuracy for samples with low fetal fraction and so allow more reliability for subsequent testing for genomic aberrations. We propose several improvements in fetal fraction estimation with a special focus on the samples most prone to wrong conclusion. © 2019 by the authors. Licensee MDPI, Basel, Switzerland.},

keywords = {Aneuploidy, Computational method, Fetal fraction, Non-invasive prenatal testing},

pubstate = {published},

tppubtype = {article}

}

@article{Gazdarica2019b,

title = {Adaptable model parameters in non-invasive prenatal testing lead to more stable predictions},

author = {J Gazdarica and J Budis and F Duris and J Turna and T Szemes},

url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-85070461646&doi=10.3390%2fijms20143414&partnerID=40&md5=055222c81da89a9a0300464ee09b9c1b},

doi = {10.3390/ijms20143414},

issn = {16616596},

year  = {2019},

date = {2019-01-01},

journal = {International Journal of Molecular Sciences},

volume = {20},

number = {14},

publisher = {MDPI AG},

abstract = {Recent advances in massively parallel shotgun sequencing opened up new options for affordable non-invasive prenatal testing (NIPT) for fetus aneuploidy from DNA material extracted from maternal plasma. Tests typically compare chromosomal distributions of a tested sample with a control set of healthy samples with unaffected fetuses. Deviations above certain threshold levels are concluded as positive findings. The main problem with this approach is that the variance of the control set is dependent on the number of sequenced fragments. The higher the amount, the more precise the estimation of actual chromosomal proportions is. Testing a sample with a highly different number of sequenced reads as used in training may thus lead to over- or under-estimation of their variance, and so lead to false predictions. We propose the calculation of a variance for each tested sample adaptively, based on the actual number of its sequenced fragments. We demonstrate how it leads to more stable predictions, mainly in real-world diagnostics with the highly divergent inter-sample coverage. © 2019 by the authors. Licensee MDPI, Basel, Switzerland.},

keywords = {Aneuploidy, Computational method, Non-invasive prenatal testing},

pubstate = {published},

tppubtype = {article}

}

@article{Budis201972,

title = {Non-invasive prenatal testing as a valuable source of population specific allelic frequencies},

author = {J Budis and J Gazdarica and J Radvanszky and M Harsanyova and I Gazdaricova and L Strieskova and R Frno and F Duris and G Minarik and M Sekelska and B Nagy and T Szemes},

url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-85064459936&doi=10.1016%2fj.jbiotec.2019.04.026&partnerID=40&md5=73c18a2081a2ec5ead08247b7543d15b},

doi = {10.1016/j.jbiotec.2019.04.026},

issn = {01681656},

year  = {2019},

date = {2019-01-01},

journal = {Journal of Biotechnology},

volume = {299},

pages = {72-78},

publisher = {Elsevier B.V.},

abstract = {Low-coverage massively parallel genome sequencing for non-invasive prenatal testing (NIPT)of common aneuploidies is one of the most rapidly adopted and relatively low-cost DNA tests. Since aggregation of reads from a large number of samples allows overcoming the problems of extremely low coverage of individual samples, we describe the possible re-use of the data generated during NIPT testing for genome scale population specific frequency determination of small DNA variants, requiring no additional costs except of those for the NIPT test itself. We applied our method to a data set comprising of 1501 original NIPT test results and evaluated the findings on different levels, from in silico population frequency comparisons up to wet lab validation analyses using a gold-standard method based on Sanger sequencing. The revealed high reliability of variant calling and allelic frequency determinations suggest that these NIPT data could serve as valuable alternatives to large scale population studies even for smaller countries around the world. © 2019 Elsevier B.V.},

keywords = {Non-invasive prenatal testing, Population study, Single nucleotide variants, Variant calling},

pubstate = {published},

tppubtype = {article}

}

@article{Budis20191284,

title = {Combining count- And length-based z-scores leads to improved predictions in non-invasive prenatal testing},

author = {J Budis and J Gazdarica and J Radvanszky and G Szucs and M Kucharik and L Strieskova and I Gazdaricova and M Harsanyova and F Duris and G Minarik and M Sekelska and B Nagy and J Turna and T Szemes},

url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-85067353429&doi=10.1093%2fbioinformatics%2fbty806&partnerID=40&md5=c63c304db3eb59cb922d0ca8e3a9e76a},

doi = {10.1093/bioinformatics/bty806},

issn = {13674803},

year  = {2019},

date = {2019-01-01},

journal = {Bioinformatics},

volume = {35},

number = {8},

pages = {1284-1291},

publisher = {Oxford University Press},

abstract = {Motivation: Non-invasive prenatal testing or NIPT is currently among the top researched topic in obstetric care. While the performance of the current state-of-the-art NIPT solutions achieve high sensitivity and specificity, they still struggle with a considerable number of samples that cannot be concluded with certainty. Such uninformative results are often subject to repeated blood sampling and re-analysis, usually after two weeks, and this period may cause a stress to the future mothers as well as increase the overall cost of the test. Results: We propose a supplementary method to traditional z-scores to reduce the number of such uninformative calls. The method is based on a novel analysis of the length profile of circulating cell free DNA which compares the change in such profiles when random-based and length-based elimination of some fragments is performed. The proposed method is not as accurate as the standard z-score; however, our results suggest that combination of these two independent methods correctly resolves a substantial portion of healthy samples with an uninformative result. Additionally, we discuss how the proposed method can be used to identify maternal aberrations, thus reducing the risk of false positive and false negative calls. Availability and implementation: The open-source code of the proposed methods, together with test data, is freely available for non-commercial users at github web page https://github.com/jbudis/lambda. © The Author(s) 2018. Published by Oxford University Press. All rights reserved.},

keywords = {Aneuploidy, Computational method, Fetal fraction, Non-invasive prenatal testing, Prenatal diagnosis},

pubstate = {published},

tppubtype = {article}

}

@article{Duris2018,

title = {Mean and variance of ratios of proportions from categories of a multinomial distribution},

author = {F Duris and J Gazdarica and I Gazdaricova and L Strieskova and J Budis and J Turna and T Szemes},

url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-85062689021&doi=10.1186%2fs40488-018-0083-x&partnerID=40&md5=d293ac604976bfd7c1b99a1bb71fd1f2},

doi = {10.1186/s40488-018-0083-x},

issn = {21955832},

year  = {2018},

date = {2018-01-01},

journal = {Journal of Statistical Distributions and Applications},

volume = {5},

number = {1},

publisher = {Springer},

abstract = {Ratio distribution is a probability distribution representing the ratio of two random variables, each usually having a known distribution. Currently, there are results when the random variables in the ratio follow (not necessarily the same) Gaussian, Cauchy, binomial or uniform distributions. In this paper we consider a case, where the random variables in the ratio are joint binomial components of a multinomial distribution. We derived formulae for mean and variance of this ratio distribution using a simple Taylor-series approach and also a more complex approach which uses a slight modification of the original ratio. We showed that the more complex approach yields better results with simulated data. The presented results can be directly applied in the computation of confidence intervals for ratios of multinomial proportions. AMS Subject Classification: 62E20. © 2018, The Author(s).},

keywords = {Aneuploidy, Computational method, Non-invasive prenatal testing},

pubstate = {published},

tppubtype = {article}

}

@article{Minarik2015,

title = {Utilization of benchtop next generation sequencing platforms ion torrent PGM and miseq in noninvasive prenatal testing for chromosome 21 trisomy and testing of impact of in silico and physical size selection on its analytical performance},

author = {G Minarik and G Repiska and M Hyblova and E Nagyova and K Soltys and J Budis and F Duris and R Sysak and M G Bujalkova and B Vlkova-Izrael and O Biro and B Nagy and T Szemes},

url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-84956618019&doi=10.1371%2fjournal.pone.0144811&partnerID=40&md5=ba19c1dabbdb0f2c2d3718fd27e8fc9c},

doi = {10.1371/journal.pone.0144811},

issn = {19326203},

year  = {2015},

date = {2015-01-01},

journal = {PLoS ONE},

volume = {10},

number = {12},

publisher = {Public Library of Science},

abstract = {Objectives The aims of this study were to test the utility of benchtop NGS platforms for NIPT for trisomy 21 using previously published z score calculation methods and to optimize the sample preparation and data analysis with use of in silico and physical size selection methods. Methods Samples from 130 pregnant women were analyzed by whole genome sequencing on benchtop NGS systems Ion Torrent PGM and MiSeq. The targeted yield of 3 million raw reads on each platform was used for z score calculation. The impact of in silico and physical size selection on analytical performance of the test was studied. Results Using a z score value of 3 as the cut-off, 98.11% - 100% (104-106/106) specificity and 100% (24/24) sensitivity and 99.06% - 100% (105-106/106) specificity and 100% (24/24) sensitivity were observed for Ion Torrent PGM and MiSeq, respectively. After in silico based size selection both platforms reached 100% specificity and sensitivity. Following the physical size selection z scores of tested trisomic samples increased significantlyâ€"p = 0.0141 and p = 0.025 for Ion Torrent PGM and MiSeq, respectively. Conclusions Noninvasive prenatal testing for chromosome 21 trisomy with the utilization of benchtop NGS systems led to results equivalent to previously published studies performed on highto- ultrahigh throughput NGS systems. The in silico size selection led to higher specificity of the test. Physical size selection performed on isolated DNA led to significant increase in z scores. The observed results could represent a basis for increasing of cost effectiveness of the test and thus help with its penetration worldwide. © 2015 Minarik et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.},

keywords = {Aneuploidy, Non-invasive prenatal testing, Size selection, Validation},

pubstate = {published},

tppubtype = {article}

}

@article{Repiská201558,

title = {Effect of different DNA concentration methods on performance of non-invasive fetal y-chromosomal short tandem repeat profiling from maternal plasma},

author = {G Repiská and T Sedláčková and T Szemes and G Minárik},

url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-84922410960&doi=10.1159%2f000362664&partnerID=40&md5=7c7661ed02547b6c348c02c18d1f0b51},

doi = {10.1159/000362664},

issn = {10153837},

year  = {2015},

date = {2015-01-01},

journal = {Fetal Diagnosis and Therapy},

volume = {37},

number = {1},

pages = {58-64},

publisher = {S. Karger AG},

abstract = {Background: The accuracy and reliability of detection of free fetal DNA in plasma of pregnant women can be significantly improved by increasing the overall DNA concentration following the isolation from maternal plasma. The aim of our study was to compare DNA concentration methods on samples with free fetal DNA. Materials and Methods: DNA isolated from plasma samples of pregnant women carrying a male fetus were concentrated by 3 different methods: vacuum concentration, centrifugal filters and spin columns. Their performance was evaluated using PCR-based Y-chromosomal short tandem repeat (Y-STR) genotyping of the fetus. Results: A statistically significant difference was found between the 3 tested methods (F = 15.57, p < 0.0001). Using vacuum concentration 85.3% of paternally inherited Y-STR alleles were correctly identified. A significantly smaller proportion of alleles was correctly identified in samples concentrated by centrifugal filters and spin columns - 75.9 and 66.5%, respectively. Discussion: The highest proportion of paternally inherited Y-STR alleles was found in samples concentrated with the use of vacuum concentration. This concentration procedure does not require further handling of the sample either, which is an advantage because it avoids potential sample contamination. On the other hand, when automation is considered, vacuum concentration is less suitable because of an uneven and unpredictable sample evaporation rate. © 2014 S. Karger AG, Basel.},

keywords = {Fetal fraction, Non-invasive prenatal testing, Prenatal diagnosis, Short tandem repeats},

pubstate = {published},

tppubtype = {article}

}

@article{Sedlackova20141543,

title = {Selection of an optimal method for co-isolation of circulating DNA and miRNA from the plasma of pregnant women},

author = {T Sedlackova and G Repiska and G Minarik},

url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-84908102134&doi=10.1515%2fcclm-2014-0021&partnerID=40&md5=ff635286396a625ebe2934f00e7b7772},

doi = {10.1515/cclm-2014-0021},

issn = {14346621},

year  = {2014},

date = {2014-01-01},

journal = {Clinical Chemistry and Laboratory Medicine},

volume = {52},

number = {11},

pages = {1543-1548},

publisher = {Walter de Gruyter GmbH},

abstract = {Background: Circulating nucleic acids acquired non-invasively have been confirmed as useful biomarkers in cancer and prenatal medicine. The most important molecules in the field of circulating nucleic acids research are circulating DNA and miRNA. In this study, the possibility of co-isolation of total circulating DNA, cell-free fetal DNA and miRNA from the plasma of pregnant women was tested, and the yields of co-isolated circulating nucleic acids using two commercial kits and three protocols were compared. 

Methods: Cell-free fetal DNA and miRNA from the plasma of pregnant women carrying male fetuses were co-isolated with the miRCURY™ RNA Isolation Kit according to the original protocol and the QIAamp Circulating Nucleic Acid Kit (CNA kit) according to the manufacturer's protocol for DNA isolation and miRNA isolation. For comparison of DNA isolation, the AR and DYS14 gene-based assays were used for the detection and quantification of total circulating and cell-free fetal DNA. For miRNA detection and quantification, the miR-16 and miR-451 assays were used. Results: Two different protocols for isolation using the CNA kit did not significantly differ in the yields of isolated tcDNA and cffDNA; however, the amount of isolated cffDNA using the miRCURY™ RNA Isolation Kit was significantly less (p<0.05},

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

pubstate = {published},

tppubtype = {article}

}

@article{Sedlackova2013,

title = {Fragmentation of DNA affects the accuracy of the DNA quantitation by the commonly used methods},

author = {T Sedlackova and G Repiska and P Celec and T Szemes and G Minarik},

url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-84874073176&doi=10.1186%2f1480-9222-15-5&partnerID=40&md5=723b0e9568bb2d83456bbc497a945237},

doi = {10.1186/1480-9222-15-5},

issn = {14809222},

year  = {2013},

date = {2013-01-01},

journal = {Biological Procedures Online},

volume = {15},

number = {1},

abstract = {Background: Specific applications and modern technologies, like non-invasive prenatal testing, non-invasive cancer diagnostic and next generation sequencing, are currently in the focus of researchers worldwide. These have common characteristics in use of highly fragmented DNA molecules for analysis. Hence, for the performance of molecular methods, DNA concentration is a crucial parameter; we compared the influence of different levels of DNA fragmentation on the accuracy of DNA concentration measurements. Results: In our comparison, the performance of the currently most commonly used methods for DNA concentration measurement (spectrophotometric, fluorometric and qPCR based) were tested on artificially fragmented DNA samples. In our comparison, unfragmented and three specifically fragmented DNA samples were used. According to our results, the level of fragmentation did not influence the accuracy of spectrophotometric measurements of DNA concentration, while other methods, fluorometric as well as qPCR-based, were significantly influenced and a decrease in measured concentration was observed with more intensive DNA fragmentation. Conclusions: Our study has confirmed that the level of fragmentation of DNA has significant impact on accuracy of DNA concentration measurement with two of three mostly used methods (PicoGreen and qPCR). Only spectrophotometric measurement was not influenced by the level of fragmentation, but sensitivity of this method was lowest among the three tested. Therefore if it is possible the DNA quantification should be performed with use of equally fragmented control DNA. © 2013 Sedlackova et al.; licensee BioMed Central Ltd.},

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

pubstate = {published},

tppubtype = {article}

}

@article{Repiská20131185,

title = {Selection of the optimal manual method of cell free fetal DNA isolation from maternal plasma},

author = {G Repiská and T Sedláčková and T Szemes and P Celec and G Minárik},

url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-84882355382&doi=10.1515%2fcclm-2012-0418&partnerID=40&md5=f476653212c66d4f5b9ec534582f5921},

doi = {10.1515/cclm-2012-0418},

issn = {14346621},

year  = {2013},

date = {2013-01-01},

journal = {Clinical Chemistry and Laboratory Medicine},

volume = {51},

number = {6},

pages = {1185-1189},

abstract = {Background: The cell free fetal DNA (cffDNA) present in plasma of pregnant women represents an important alternative source of DNA for non-invasive prenatal diagnosis. Due to the low quantity and increased fragmentation of cffDNA, the choice of DNA extraction method is a crucial step for downstream analyses. Methods: In our study, the three spin column-based kits for isolation of cffDNA [DNA Blood Mini Kit (DBM), DSP Virus Kit (DSP) and Circulating Nucleic Acid (CNA) Kit] were compared. Original and optimized protocol were used in comparison and applied in the two phases of the study. Results: A statistically significant difference in performance of the kits was determined based on the comparison of genomic equivalents per mL (GEq/mL) values (p < 0.0001). The GEq/mL of isolated DNA was significantly higher using CNA and DSP Kits than DBM Kit. The CNA Kit and DSP Kit did not significantly differ in the GEq/mL values, although all tested samples isolated with CNA Kit showed higher values. Conclusions: According to our results the commonly used DBM Kit could be successfully replaced with CNA or DSP Kits. The replacement could be beneficial in qualitative as well quantitative tests (e.g., gender determination, aneu ploidy detection) when the isolation yield limits subsequent analyses. However, there is an important decision to be made when switching DBM Kit for DSP or CNA Kits. The price of DBM Kit is two and six times lower than DSP and CNA Kits, respectively.},

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

pubstate = {published},

tppubtype = {article}

}

@article{Vlková2010258,

title = {Does maternal saliva contain fetal DNA usable for 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-s2.0-72449174721&doi=10.1016%2fj.mehy.2009.09.022&partnerID=40&md5=e4a8ec14001f99b11fadd011098f2c5d},

doi = {10.1016/j.mehy.2009.09.022},

issn = {03069877},

year  = {2010},

date = {2010-01-01},

journal = {Medical Hypotheses},

volume = {74},

number = {2},

pages = {258-260},

abstract = {Non-invasive molecular analysis of fetal DNA is the diagnostic goal of prenatal medicine. Circulating fetal DNA can be detected in maternal plasma. Recently, it has been detected in the urine of pregnant women. We hypothesize that fetal DNA is present also in maternal saliva and that advances in stabilization and isolation of nucleic acids from saliva enable non-invasive and repeated sampling for prenatal diagnostics. The hypothesis is testable using saliva samples of pregnant women with confirmed male fetuses. Y-specific sequences should be detectable in salivary DNA. Caution must be given to the prevention of contamination. If proved in large studies, the presence of fetal DNA fragments in maternal saliva would enable a wide range of applications in prenatal medicine. © 2009 Elsevier Ltd. All rights reserved.},

keywords = {Body fluids, Cell-free nucleic acids, Non-invasive prenatal testing, Prenatal diagnosis},

pubstate = {published},

tppubtype = {article}

}

@article{Vlková20101030,

title = {Circulating free fetal nucleic acids in maternal plasma and preeclampsia},

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-s2.0-77951621628&doi=10.1016%2fj.mehy.2010.01.003&partnerID=40&md5=2fc0136f965402efa4d19525338fde3c},

doi = {10.1016/j.mehy.2010.01.003},

issn = {03069877},

year  = {2010},

date = {2010-01-01},

journal = {Medical Hypotheses},

volume = {74},

number = {6},

pages = {1030-1032},

abstract = {Although preeclampsia represents a major threat for many pregnant women, the pathogenesis of this complication is far from being clear. Recent studies suggest that preeclampsia is an autoimmune disorder. Auto-antibodies against angiotensin receptor might explain some of the pathologic findings associated with preeclampsia. However, the origin of the autoimmune reaction is unknown. Here we hypothesize that circulating fetal RNA in maternal plasma might transfect maternal cells. Expression of fetal specific sequences could lead to an immune reaction breaking the immune tolerance against some antigens. Male fetus bearing pregnancies could be at higher risk of preeclampsia due to expression of Y-specific transcripts. This hypothesis is testable by analyzing antibodies and T-lymphocytes of pregnant women with male and female fetuses. © 2010 Elsevier Ltd.},

keywords = {Cell-free nucleic acids, Non-invasive prenatal testing, Preeclampsia},

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}

}

@article{Vlková2010806,

title = {Testosterone and estradiol in maternal plasma and their relation to fetal sex},

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

url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-77955104417&doi=10.1002%2fpd.2535&partnerID=40&md5=6b4caf352bcd6bfd2674ead44ea48db1},

doi = {10.1002/pd.2535},

issn = {01973851},

year  = {2010},

date = {2010-01-01},

journal = {Prenatal Diagnosis},

volume = {30},

number = {8},

pages = {806-807},

keywords = {Fetal sex determination, Non-invasive prenatal testing, Prenatal diagnosis},

pubstate = {published},

tppubtype = {article}

}