Publikácie

@article{Maronek2021,

title = {Extracellular DNA Correlates with Intestinal Inflammation in Chemically Induced Colitis in Mice},

author = {M Maronek and B Gromova and R Liptak and B Konecna and M Pastorek and B Cechova and M Harsanyova and J Budis and D Smolak and J Radvanszky and T Szemes and J Harsanyiova and A Kralova Trancikova and R Gardlik},

url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-85099721641&doi=10.3390%2fcells10010081&partnerID=40&md5=e2a2d57bcd02c36a1091367862022bb1},

doi = {10.3390/cells10010081},

issn = {20734409},

year  = {2021},

date = {2021-01-01},

journal = {Cells},

volume = {10},

number = {1},

publisher = {NLM (Medline)},

abstract = {Circulating extracellular DNA (ecDNA) is known to worsen the outcome of many diseases. ecDNA released from neutrophils during infection or inflammation is present in the form of neutrophil extracellular traps (NETs). It has been shown that higher ecDNA concentration occurs in a number of inflammatory diseases including inflammatory bowel disease (IBD). Enzymes such as peptidyl arginine deiminases (PADs) are crucial for NET formation. We sought to describe the dynamics of ecDNA concentrations and fragmentation, along with NETosis during a mouse model of chemically induced colitis. Plasma ecDNA concentration was highest on day seven of dextran sulfate sodium (DSS) intake and the increase was time-dependent. This increase correlated with the percentage of cells undergoing NETosis and other markers of disease activity. Relative proportion of nuclear ecDNA increased towards more severe colitis; however, absolute amount decreased. In colon explant medium, the highest concentration of ecDNA was on day three of DSS consumption. Early administration of PAD4 inhibitors did not alleviate disease activity, but lowered the ecDNA concentration. These results uncover the biological characteristics of ecDNA in IBD and support the role of ecDNA in intestinal inflammation. The therapeutic intervention aimed at NETs and/or nuclear ecDNA has yet to be fully investigated.},

keywords = {Body fluids, Cell-free nucleic acids},

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{Misova20211914,

title = {Repression of a large number of genes requires interplay between homologous recombination and HIRA},

author = {I Misova and A Pitelova and J Budis and J Gazdarica and T Sedlackova and A Jordakova and Z Benko and M Smondrkova and N Mayerova and K Pichlerova and L Strieskova and M Prevorovsky and J Gregan and L Cipak and T Szemes and S B Polakova},

url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-85102408904&doi=10.1093%2fnar%2fgkab027&partnerID=40&md5=77d6eafd60e9cb1a1c3c8237566b8cc1},

doi = {10.1093/nar/gkab027},

issn = {03051048},

year  = {2021},

date = {2021-01-01},

urldate = {2021-01-01},

journal = {Nucleic Acids Research},

volume = {49},

number = {4},

pages = {1914-1934},

publisher = {Oxford University Press},

abstract = {During homologous recombination, Dbl2 protein is required for localisation of Fbh1, an F-box helicase that efficiently dismantles Rad51-DNA filaments. RNA-seq analysis of dbl2Δtranscriptome showed that the dbl2 deletion results in upregulation of more than 500 loci in Schizosaccharomyces pombe. Compared with the loci with no change in expression, the misregulated loci in dbl2Δare closer to long terminal and long tandem repeats. Furthermore, the misregulated loci overlap with antisense transcripts, retrotransposons, meiotic genes and genes located in subtelomeric regions. A comparison of the expression profiles revealed that Dbl2 represses the same type of genes as the HIRA histone chaperone complex. Although dbl2 deletion does not alleviate centromeric or telomeric silencing, it suppresses the silencing defect at the outer centromere caused by deletion of hip1 and slm9 genes encoding subunits of the HIRA complex. Moreover, our analyses revealed that cells lacking dbl2 show a slight increase of nucleosomes at transcription start sites and increased levels of methylated histone H3 (H3K9me2) at centromeres, subtelomeres, rDNA regions and long terminal repeats. Finally, we show that other proteins involved in homologous recombination, such as Fbh1, Rad51, Mus81 and Rad54, participate in the same gene repression pathway. © 2021 The Author(s) 2021. Published by Oxford University Press on behalf of Nucleic Acids Research.},

keywords = {Epigenetics, Transcriptomics},

pubstate = {published},

tppubtype = {article}

}

@article{Ženišová202187,

title = {Effects of co-fermentation with lachancea thermotolerans or metschnikowia pulcherrima on concentration of aroma compounds in pinot blanc wine},

author = {K Ženišová and T Cabicarová and R Sidari and E Kolek and D Pangallo and T Szemes and T Kuchta},

url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-85103857742&partnerID=40&md5=d4693544a7b1a478503ed67094155402},

issn = {13368672},

year  = {2021},

date = {2021-01-01},

journal = {Journal of Food and Nutrition Research},

volume = {60},

number = {1},

pages = {87-91},

publisher = {Food Reseach Institute},

abstract = {Slovakian strains of Lachancea thermotolerans and Metschnikowia pulcherrima were used in sequential co-fermentation with Saccharomyces cerevisiae in small-scale production of Pinot Blanc wine from the Small Carpathian wine region in Slovakia. Aroma compounds of the produced wines were analysed using solid-phase microextraction coupled to gas chromatography-mass spectrometry. Thirty-six aroma compounds were quantified, demonstrating no significant differences in concentrations of almost half of them, including acetic acid, ethyl acetate, 2,3-butanediol and butanoic acid. Wines produced with non-Saccharomyces yeasts did not contain increased concentrations of aroma-active esters, but contained increased concentrations of methionol and decreased concentrations of furfural. Wine produced with L. thermotolerans contained increased concentrations of 2-phenylethanol, diethyl succinate and phenylethyl acetate, together with an increased concentration of 3-methylbutanoic acid. Wine produced with M. pulcherrima contained increased concentrations of 2-phenylethanol and diethyl succinate, together with a decreased concentration of acet-aldehyde. Results of the study demonstrate that L. thermotolerans and M. pulcherrima, when used in a co-culture with S. cerevisiae, can modulate the composition of Pinot Blanc wine regarding aroma compounds, thereby positively con-tributing to its quality. © 2021 National Agricultural and Food Centre (Slovakia).},

keywords = {Bacteria, Food microbiome, Fungi},

pubstate = {published},

tppubtype = {article}

}

@article{BágeľováPoláková2021,

title = {Mitochondrial DNA duplication, recombination, and introgression during interspecific hybridization},

author = {S Bágeľová Poláková and Ž Lichtner and T Szemes and M Smolejová and P Sulo},

url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-85108161297&doi=10.1038%2fs41598-021-92125-y&partnerID=40&md5=6bc31d15f4fb89003df9c7623ab3db19},

doi = {10.1038/s41598-021-92125-y},

issn = {20452322},

year  = {2021},

date = {2021-01-01},

journal = {Scientific Reports},

volume = {11},

number = {1},

publisher = {Nature Research},

abstract = {mtDNA recombination events in yeasts are known, but altered mitochondrial genomes were not completed. Therefore, we analyzed recombined mtDNAs in six Saccharomyces cerevisiae × Saccharomyces paradoxus hybrids in detail. Assembled molecules contain mostly segments with variable length introgressed to other mtDNA. All recombination sites are in the vicinity of the mobile elements, introns in cox1, cob genes and free standing ORF1, ORF4. The transplaced regions involve co-converted proximal exon regions. Thus, these selfish elements are beneficial to the host if the mother molecule is challenged with another molecule for transmission to the progeny. They trigger mtDNA recombination ensuring the transfer of adjacent regions, into the progeny of recombinant molecules. The recombination of the large segments may result in mitotically stable duplication of several genes. © 2021, The Author(s).},

keywords = {Fungi, Mitochondria},

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{Pecimonova2021e26136,

title = {Admixed phenotype of NEDD4L associated periventricular nodular heterotopia: A case report},

author = {M Pecimonova and J Radvanszky and D Smolak and J Budis and M Lichvar and D Kristinova and I Rozova and J Turna and T Szemes},

url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-85107796467&doi=10.1097%2fMD.0000000000026136&partnerID=40&md5=6d8eac607b0de5b1897c2cee34a64ec9},

doi = {10.1097/MD.0000000000026136},

issn = {15365964},

year  = {2021},

date = {2021-01-01},

urldate = {2021-01-01},

journal = {Medicine},

volume = {100},

number = {22},

pages = {e26136},

publisher = {NLM (Medline)},

abstract = {RATIONALE: Periventricular nodular heterotopia-7 (PVNH7) is a neurodevelopmental disorder associated with improper neuronal migration during neurogenesis in cortex development caused by pathogenic variants in the NEDD4L gene. PATIENT CONCERNS: We report the case of a polystigmatized 2-year-old boy having significant symptomatologic overlap with PVNH7, such as delayed psychomotor and mental development, seizures and infantile spasms, periventricular nodular heterotopia, polymicrogyria, cleft palate, 2 to 3 toe syndactyly, hypotonia, microretrognathia, strabismus, and absent speech and walking. The patient showed also distinct symptoms falling outside PVNH7 symptomatology, also present in the proband's older brother, such as blue sclerae, hydronephrosis, transversal palmar crease (found also in their father), and bilateral talipes equinovarus. In addition, the patient suffered from many other symptoms. DIAGNOSES: The boy, his brother and their parents were subjected to whole-exome sequencing. Because of uncertainties in symptomatology and inheritance pattern, the top-down approach was hard to apply. Using the bottom-up approach, we identified a known pathogenic variant, NM_001144967.2(NEDD4L):c.2677G>A:p.Glu893Lys, in the proband's genome that absented in any other analyzed family member, suggesting its de novo origin. INTERVENTIONS AND OUTCOMES: The patient was treated with Convulex 300 mg/mL for the successful seizure control and Euthyrox 25mg for the treatment of thyroid malfunction. He also took various supplements for the metabolism support and digestion regulation. Moreover, the patient underwent the corrective surgeries of cleft palate and talipes equinovarus. LESSONS: We successfully identified the causative mutation NM_001144967.2(NEDD4L):c.2677G>A:p.Glu893Lys explaining symptoms overlapping those reported for PVNH7. Symptoms shared with the brother were not explained by this variant, since he was not a carrier of the pathogenic NEDD4L variant. These are most likely not extended phenotypes of PVNH7, rather an independent clinical entity caused by a yet unidentified genetic factor in the family, highlighting thus the importance of thorough evaluation of symptomatology and genomic findings in affected and unaffected family members, when such data are available. Copyright © 2021 the Author(s). Published by Wolters Kluwer Health, Inc.},

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

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{Hekel2021,

title = {Privacy-preserving storage of sequenced genomic data},

author = {R. Hekel and J. Budis and M. Kucharik and J. Radvanszky and Z. Pös and T. Szemes},

url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-85116340115&doi=10.1186%2fs12864-021-07996-2&partnerID=40&md5=d65889f16bf2c9525f7bf6a7c6d8a129},

doi = {10.1186/s12864-021-07996-2},

issn = {14712164},

year  = {2021},

date = {2021-01-01},

journal = {BMC Genomics},

volume = {22},

number = {1},

publisher = {BioMed Central Ltd},

abstract = {Background: The current and future applications of genomic data may raise ethical and privacy concerns. Processing and storing of this data introduce a risk of abuse by potential offenders since the human genome contains sensitive personal information. For this reason, we have developed a privacy-preserving method, named Varlock providing secure storage of sequenced genomic data. We used a public set of population allele frequencies to mask the personal alleles detected in genomic reads. Each personal allele described by the public set is masked by a randomly selected population allele with respect to its frequency. Masked alleles are preserved in an encrypted confidential file that can be shared in whole or in part using public-key cryptography. Results: Our method masked the personal variants and introduced new variants detected in a personal masked genome. Alternative alleles with lower population frequency were masked and introduced more often. We performed a joint PCA analysis of personal and masked VCFs, showing that the VCFs between the two groups cannot be trivially mapped. Moreover, the method is reversible and personal alleles in specific genomic regions can be unmasked on demand. Conclusion: Our method masks personal alleles within genomic reads while preserving valuable non-sensitive properties of sequenced DNA fragments for further research. Personal alleles in the desired genomic regions may be restored and shared with patients, clinics, and researchers. We suggest that the method can provide an additional security layer for storing and sharing of the raw aligned reads. © 2021, The Author(s).},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Böhmer20201,

title = {Identification of bacterial and fungal communities in the roots of orchids and surrounding soil in heavy metal contaminated area of mining heaps},

author = {M Böhmer and D Ozdín and M Račko and M Lichvár and J Budiš and T Szemes},

url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-85093967272&doi=10.3390%2fapp10207367&partnerID=40&md5=a65386928d7c2f6f118d18ce7a0e4bb3},

doi = {10.3390/app10207367},

issn = {20763417},

year  = {2020},

date = {2020-01-01},

journal = {Applied Sciences (Switzerland)},

volume = {10},

number = {20},

pages = {1-18},

publisher = {MDPI AG},

abstract = {Orchids represent a unique group of plants that are well adapted to extreme conditions. In our study, we aimed to determine if different soil contamination and pH significantly change fungal and bacterial composition. We identified bacterial and fungal communities from the roots and the surrounding soil of the family Orchidaceae growing on different mining sites in Slovakia. These communities were detected from the samples of Cephalanthera longifolia and Epipactis pontica from Fe deposit Sirk, E. atrorubens from Ni-Co deposit Dobšiná and Pb-Zn deposit Jasenie and Platanthera bifolia by 16S rRNA gene and ITS next-generation sequencing method. A total of 171 species of fungi and 30 species of bacteria were detected from five samples of orchids. In summary, slight differences in pH of the initial soils do not significantly affect the presence of fungi and bacteria and thus the presence of the studied orchids in these localities. Similarly, the toxic elements in the studied localities, do not affect the occurrence of fungi, bacteria, and orchids. Moreover, Cortinarius saturatus, as a dominant fungus, and Candidatus Udaeobacter as a dominant bacterium were present in all soil samples and some root samples. Finally, many of these fungal and bacterial communities have the potential to be used in the bioremediation of the mining areas. © 2020 by the authors. Licensee MDPI, Basel, Switzerland.},

keywords = {Bacteria, Environmental microbiome, Metagenomics, Plants},

pubstate = {published},

tppubtype = {article}

}

@article{Böhmer2020b,

title = {Comparison of microbial diversity during two different wine fermentation processes},

author = {M Böhmer and D Smoľak and K Ženišová and Z Čaplová and D Pangallo and A Puškárová and M Bučková and T Cabicarová and J Budiš and K Šoltýs and D Rusňáková and T Kuchta and T Szemes},

url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-85091808679&doi=10.1093%2ffemsle%2ffnaa150&partnerID=40&md5=bc04ad6a27036f5f7562c73abecb183f},

doi = {10.1093/femsle/fnaa150},

issn = {15746968},

year  = {2020},

date = {2020-01-01},

journal = {FEMS microbiology letters},

volume = {367},

number = {18},

publisher = {NLM (Medline)},

abstract = {Wine production is a complex procedure in which an important role is played by many microorganisms, particularly yeasts and bacteria. In modern wineries, alcoholic fermentation is usually carried out by adding microbial starter cultures of Saccharomyces cerevisiae strains for precisely controlled production. Nowadays, in the Slovak Republic, autochthonous vinification is getting more popular. The present article deals with the comparison of two vinification approaches, namely spontaneous fermentation and fermentation controlled by a standard commercial S. cerevisiae starter, from the point of view of microbiota dynamics and the chemical characteristics of the wines produced. The dynamics of microbial populations were determined during the fermentation process by a 16S and 28S rRNA next-generation sequencing approach. A profile of the volatile compounds during these fermentation processes was identified by solid-phase microextraction (SPME) coupled to gas chromatography-mass spectrometry (GC-MS). In summary, the microbial diversity in the m1 phase (initial must) was higher, despite the presence of the starter culture. In the m3 phase (young wine), the microbiome profiles of both batches were very similar. It seems that the crucial phase in order to study the relationship of the microbiome and the resulting product should be based on the m2 phase (fermented must), where the differences between the autochthonous and inoculated batches were more evident. © The Author(s) 2020. Published by Oxford University Press on behalf of FEMS.},

keywords = {Bacteria, Food microbiome, Fungi, Metagenomics, Plants},

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{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{Šubr2020,

title = {Comparative transcriptome analysis of two cucumber cultivars with different sensitivity to cucumber mosaic virus infection},

author = {Z Šubr and L Predajňa and K Šoltys and B Bokor and J Budiš and M Glasa},

url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-85079843504&doi=10.3390%2fpathogens9020145&partnerID=40&md5=c92697bfc9481af2a87da1aae35966e1},

doi = {10.3390/pathogens9020145},

issn = {20760817},

year  = {2020},

date = {2020-01-01},

journal = {Pathogens},

volume = {9},

number = {2},

publisher = {MDPI AG},

abstract = {Cucumber mosaic virus (CMV), with extremely broad host range including both monocots and dicots around the world, belongs to most important viral crop threats. Either natural or genetically constructed sources of resistance are being intensively investigated; for this purpose, exhaustive knowledge of molecular virus-host interaction during compatible and incompatible infection is required. New technologies and computer-based “omics” on various levels contribute markedly to this topic. In this work, two cucumber cultivars with different response to CMV challenge were tested, i.e., sensitive cv. Vanda and resistant cv. Heliana. The transcriptomes were prepared from both cultivars at 18 days after CMV or mock inoculation. Subsequently, four independent comparative analyses of obtained data were performed, viz. mock-and CMV-inoculated samples within each cultivar, samples from mock-inoculated cultivars to each other and samples from virus-inoculated cultivars to each other. A detailed picture of CMV-influenced genes, as well as constitutive differences in cultivar-specific gene expression was obtained. The compatible CMV infection of cv. Vanda caused downregulation of genes involved in photosynthesis, and induction of genes connected with protein production and modification, as well as components of signaling pathways. CMV challenge caused practically no change in the transcription profile of the cv. Heliana. The main differences between constitutive transcription activity of the two cultivars relied in the expression of genes responsible for methylation, phosphorylation, cell wall organization and carbohydrate metabolism (prevailing in cv. Heliana), or chromosome condensation and glucan biosynthesis (prevailing in cv. Vanda). Involvement of several genes in the resistant cucumber phenotype was predicted; this can be after biological confirmation potentially applied in breeding programs for virus-resistant crops. © 2020 by the authors. Licensee MDPI, Basel, Switzerland.},

keywords = {Plants, Transcriptomics, Viruses},

pubstate = {published},

tppubtype = {article}

}

@article{Bielik2020,

title = {Gut microbiota diversity in lean athletes is associated with positive energy balance},

author = {V Bielik and I Hric and V BalᎠand A Penesová and S Vávrová and J Grones and B Bokor and J Budiš and M Bohmer and G Minárik and D Augustovičová and K Šoltys},

url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-85091307627&doi=10.1159%2f000509833&partnerID=40&md5=4461653fb07e53dc12411cda7d4cb566},

doi = {10.1159/000509833},

issn = {02506807},

year  = {2020},

date = {2020-01-01},

journal = {Annals of Nutrition and Metabolism},

publisher = {S. Karger AG},

abstract = {Introduction: In contrast to obesity, little is known about the human lean phenotype associated with gut microbiota composition. Objective: We aimed to investigate whether the bacterial composition of lean athletes with a positive energy balance differs from the equal-calorie food group. Methods: Twenty-four male participants were included in this cross-sectional study: lean athletes with a positive energy balance (LA, n 12) and control group athletes (CTRLs, n 12). Nutritional data, resting and total energy expenditure, and body composition were determined. DNA was extracted from stool samples and subjected to 16S rRNA gene analysis. Results: We found 7 differentially abundant bacterial taxa between the LA and CTRL groups. Of those, 5 were significantly less abundant and 2 were enriched in the LA group. The following categories significantly associated with the community structure were identified: body fat parameters, BMI, energy intake and expenditure, oxygen consumption, and respiratory exchange ratio. Conclusions: Although we are far from a detailed interpretation of lean human body maintenance, the primary findings of our study suggest that gut microbial composition may be a factor influencing the regulation of weight gain in lean athletes with a positive energy balance. © 2020 Cambridge University Press. All rights reserved.},

keywords = {Bacteria, Gut microbiome, Metagenomics},

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{Soltysova20201,

title = {Monosomy 3 influences epithelial-mesenchymal transition gene expression in uveal melanoma patients; consequences for liquid biopsy},

author = {A Soltysova and T Sedlackova and D Dvorska and K Jasek and P C Baradaran and V H Kajabova and L Demkova and V Buocikova and T Kurucova and D Lyskova and A Furdova and G Minarik and P Babal and Z Dankova and B Smolkova},

url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-85097833518&doi=10.3390%2fijms21249651&partnerID=40&md5=133b8d5d56ebac3bf7a09024f007273e},

doi = {10.3390/ijms21249651},

issn = {16616596},

year  = {2020},

date = {2020-01-01},

journal = {International Journal of Molecular Sciences},

volume = {21},

number = {24},

pages = {1-24},

publisher = {MDPI AG},

abstract = {Despite outstanding advances in diagnosis and the treatment of primary uveal melanoma (UM), nearly 50% of UM patients develop metastases via hematogenous dissemination, driven by the epithelial-mesenchymal transition (EMT). Despite the failure in UM to date, a liquid biopsy may offer a feasible non-invasive approach for monitoring metastatic disease progression and addressing protracted dormancy. To detect circulating tumor cells (CTCs) in UM patients, we evaluated the mRNA expression of EMT-associated transcription factors in CD45-depleted blood fraction, using qRT-PCR. ddPCR was employed to assess UM-specific GNA11, GNAQ, PLCβ4, and CYSLTR2 mutations in plasma DNA. Moreover, microarray analysis was performed on total RNA isolated from tumor tissues to estimate the prognostic value of EMT-associated gene expression. In total, 42 primary UM and 11 metastatic patients were enrolled. All CD45-depleted samples were negative for CTC when compared to the peripheral blood fraction of 60 healthy controls. Tumor-specific mutations were detected in the plasma of 21.4% patients, merely, in 9.4% of primary UM, while 54.5% in metastatic patients. Unsupervised hierarchical clustering of differentially expressed EMT genes showed significant differences between monosomy 3 and disomy 3 tumors. Newly identified genes can serve as non-invasive prognostic biomarkers that can support therapeutic decisions. © 2020 by the authors. Licensee MDPI, Basel, Switzerland.},

keywords = {Aneuploidy, Body fluids, Circulating tumor cells, Liquid biopsy, Oncology},

pubstate = {published},

tppubtype = {article}

}

@article{Smolkova20201,

title = {Increased stromal infiltrating lymphocytes are associated with the risk of disease progression in mesenchymal circulating tumor cell-positive primary breast cancer patients},

author = {B Smolkova and Z Cierna and K Kalavska and S Miklikova and J Plava and G Minarik and T Sedlackova and D Cholujova and P Gronesova and M Cihova and K Majerova and M Karaba and J Benca and D Pindak and J Mardiak and M Mego},

url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-85097678410&doi=10.3390%2fijms21249460&partnerID=40&md5=8dd0aa352be241f64188de23774ac3c4},

doi = {10.3390/ijms21249460},

issn = {16616596},

year  = {2020},

date = {2020-01-01},

journal = {International Journal of Molecular Sciences},

volume = {21},

number = {24},

pages = {1-16},

publisher = {MDPI AG},

abstract = {Circulating tumor cells (CTCs) and the immune infiltration of tumors are closely related to clinical outcomes. This study aimed to verify the influence of stromal lymphocyte infiltration and the immune context of tumor microenvironment on the hematogenous spread and prognosis of 282 chemotherapy naïve primary BC patients. To detect the presence of mesenchymal CTCs, RNA extracted from CD45-depleted peripheral blood was interrogated for the expression of mesenchymal gene transcripts. Tumor-infiltrating lymphocytes (TILs) were detected in the stromal areas by immunohistochemistry, using CD3, CD8, and CD45RO antibodies. The concentrations of 51 plasma cytokines were measured by multiplex bead arrays. TILs infiltration in mesenchymal CTC-positive patients significantly decreased their progression-free survival (HR = 4.88, 95% CI 2.30–10.37, p < 0.001 for CD3high; HR = 6.17, 95% CI 2.75–13.80, p < 0.001 for CD8high; HR = 6.93, 95% CI 2.86–16.81, p < 0.001 for CD45ROhigh). Moreover, the combination of elevated plasma concentrations of transforming growth factor beta-3 (cut-off 662 pg/mL), decreased monocyte chemotactic protein-3 (cut-off 52.5 pg/mL) and interleukin-15 (cut-off 17.1 pg/mL) significantly increased the risk of disease recurrence (HR = 4.838, 95% CI 2.048–11.427, p < 0.001). Our results suggest a strong impact of the immune tumor microenvironment on BC progression, especially through influencing the dissemination and survival of more aggressive, mesenchymal CTC subtypes. © 2020 by the authors. Licensee MDPI, Basel, Switzerland.},

keywords = {Body fluids, Circulating tumor cells, Liquid biopsy, Oncology},

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{Pangallo2019416,

title = {Transcription activity of lactic acid bacterial proteolysis-related genes during cheese maturation},

author = {D Pangallo and L Kraková and A Puškárová and K Šoltys and M Bučková and J Koreňová and J Budiš and T Kuchta},

url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-85063597246&doi=10.1016%2fj.fm.2019.03.015&partnerID=40&md5=ebfc8c9f9e3d1955df5b867600b581a5},

doi = {10.1016/j.fm.2019.03.015},

issn = {07400020},

year  = {2019},

date = {2019-01-01},

journal = {Food Microbiology},

volume = {82},

pages = {416-425},

publisher = {Academic Press},

abstract = {The catabolism of milk protein in cheese is one way how the microorganisms influence the sensorial characteristics of the final product. In this investigation, we paid attention to four genes [prtP (cell-envelope proteinase gene), pepX (X-prolyl dipeptidyl aminopeptidase gene), pepN (aminopeptidase gene) and bcaT (branched chain aminotransferase gene)] responsible for the production of volatile aroma-active compounds from milk proteins by lactic acid bacteria (LAB). We studied the dynamics of these genes and their corresponding LAB host, during the maturation of a raw ewes’ milk-based cheese, using metagenomics and metatranscriptomics approaches. The transcriptome-oriented experiments included the analysis of total RNA (at three stages of cheese maturation) and also the construction of specific cDNA sub-libraries of the abovementioned genes. The proteolytic transcriptome analysis was supported by following the transcription activity of 16S rRNA gene and by metagenomic investigation. The combination of the described methods permitted to screen the dynamics of targeted genes throughout the cheese production. Lactococci were the major players in the LAB group, but the analysis provided also information on the role and properties of members of the genus Lactobacillus, such as Lb. rhamnosus, Lb. helveticus, Lb. pentosus, Lb. curvatus, Lb. parabuchneri, Lb. plantarum, Lb. brevis, Lb. delbrueckii, Lb. paracasei, Lb. fermentum and Lb. heilongjiangensis, proteolysis-related genes of which were active during cheese ripening. © 2019 Elsevier Ltd},

keywords = {Bacteria, Food microbiome, Metagenomics, Transcriptomics},

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{Planý20191151,

title = {Biogas production: evaluation of the influence of K2FeO4 pretreatment of maple leaves (Acer platanoides) on microbial consortia composition},

author = {M Planý and M Czolderová and L Kraková and A Puškárová and M Bučková and K Šoltys and J Budiš and T Szemes and T Mackulak and J -H Wu and D Pangallo},

url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-85064487903&doi=10.1007%2fs00449-019-02112-x&partnerID=40&md5=49c72565995160169ee6d43ac9524510},

doi = {10.1007/s00449-019-02112-x},

issn = {16157591},

year  = {2019},

date = {2019-01-01},

journal = {Bioprocess and Biosystems Engineering},

volume = {42},

number = {7},

pages = {1151-1163},

publisher = {Springer Verlag},

abstract = {The potential of K2FeO4 as a pretreatment agent of a lignocellulosic material was examined on leaves of Acer platanodides as the sole substrate for biogas production by anaerobic digestion carried out through modelling laboratory-scaled semi-continuous reactors differing in loading rates and substrate (pretreated and untreated leaves). The quality of bioagas produced by K2FeO4-pretreated leaves was significantly better in terms of higher methane content and lower content of H2S. K2FeO4 had no crucial influence on growth inhibition of biogas-producing bacteria, which were analysed by comprehensive culture-independent methods utilising high-throughput sequencing of specific genes [bacterial and archaeal 16S rRNA, formyltetrahydrofolate synthetase gene (fhs), methyl-coenzyme M reductase α subunit gene (mcrA) and fungal internal transcribed spacers (ITS)]. The higher amount of CH4 in biogas utilising pretreated leaves as substrate could be caused by a shift to acetoclastic methanogenesis pathway, which was indicated by the higher amount of homoacetogenic bacteria and acetotrophic methanogens detected in those reactors. © 2019, Springer-Verlag GmbH Germany, part of Springer Nature.},

keywords = {Bacteria, Biogas production, Fungi, Metagenomics, Plants},

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{Strieskova20198,

title = {Ultracentrifugation enrichment protocol followed by total RNA sequencing allows assembly of the complete mitochondrial genome},

author = {L Strieskova and I Gazdaricova and M Kajsik and K Soltys and J Budis and O Pos and M Lickova and B Klempa and T Szemes},

url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-85064954323&doi=10.1016%2fj.jbiotec.2019.04.019&partnerID=40&md5=90856f6a0fd40fd7eeaf877edfdbdeb3},

doi = {10.1016/j.jbiotec.2019.04.019},

issn = {01681656},

year  = {2019},

date = {2019-01-01},

journal = {Journal of Biotechnology},

volume = {299},

pages = {8-12},

publisher = {Elsevier B.V.},

abstract = {The mitochondrial genome is an independent genetic system in each eukaryotic cell outside the nuclear genome. Mitochondrial DNA (mtDNA) appears in high copy number within one cell, unlike nuclear DNA, which exists in two copies. But nevertheless, mtDNA represent only small part of total cellular DNA what causes problematic analysis and identification of relevant mutations. While most researchers tend to overlook it because of its small size, the mitochondrial genome contains genes that are essential for cellular energetics and survival. Because of the increased awareness on the importance of metabolism and bioenergetics in a wide variety of human diseases, more and more mtDNA studies were performed. Mitochondrial genome research has established the connection between mtDNA and a wide variety of diseases such as cancer or neurodegenerative disorders. At the present time, several methods are known, that allow sequencing of mtDNA. However, genomic analysis is often complicated due to the low content of mtDNA compared to nuclear DNA. For this reason, we have designed a new approach to obtaining the genomic mitochondrial sequence. We chose RNA based sequencing. Since human mtDNA does not contain introns, the reconstruction of whole mitochondrial genome through RNA sequencing seems to be effective. Our method is based on total RNA sequencing coupled with simple ultracentrifugation protocol and de novo assembly. Following our protocol, we were able to assemble a complete mammalian mitochondrial genome with a length of 16,505 bp and an average coverage of 156. The method is a relatively simple and inexpensive which could help in the further research or diagnostics of mtDNA-based diseases. © 2019 Elsevier B.V.},

keywords = {Assembly, Mitochondria, Single nucleotide variants, Transcriptomics},

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{Kubiritova201964,

title = {On the critical evaluation and confirmation of germline sequence variants identified using massively parallel sequencing},

author = {Z Kubiritova and M Gyuraszova and E Nagyova and M Hyblova and M Harsanyova and J Budis and R Hekel and J Gazdarica and F Duris and L Kadasi and T Szemes and J Radvanszky},

url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-85064435175&doi=10.1016%2fj.jbiotec.2019.04.013&partnerID=40&md5=175358cc48df08933da3da830780ad66},

doi = {10.1016/j.jbiotec.2019.04.013},

issn = {01681656},

year  = {2019},

date = {2019-01-01},

journal = {Journal of Biotechnology},

volume = {298},

pages = {64-75},

publisher = {Elsevier B.V.},

abstract = {Although massively parallel sequencing (MPS) is becoming common practice in both research and routine clinical care, confirmation requirements of identified DNA variants using alternative methods are still topics of debate. When evaluating variants directly from MPS data, different read depth statistics, together with specialized genotype quality scores are, therefore, of high relevance. Here we report results of our validation study performed in two different ways: 1) confirmation of MPS identified variants using Sanger sequencing; and 2) simultaneous Sanger and MPS analysis of exons of selected genes. Detailed examination of false-positive and false-negative findings revealed typical error sources connected to low read depth/coverage, incomplete reference genome, indel realignment problems, as well as microsatellite associated amplification errors leading to base miss-calling. However, all these error types were identifiable with thorough manual revision of aligned reads according to specific patterns of distributions of variants and their corresponding reads. Moreover, our results point to dependence of both basic quantitative metrics (such as total read counts, alternative allele read counts and allelic balance) together with specific genotype quality scores on the used bioinformatics pipeline, stressing thus the need for establishing of specific thresholds for these metrics in each laboratory and for each involved pipeline independently. © 2019 Elsevier B.V.},

keywords = {Genetic testing, Single nucleotide variants, Validation, Variant calling},

pubstate = {published},

tppubtype = {article}

}

@article{Budiš20191310,

title = {Dante: Genotyping of known complex and expanded short tandem repeats},

author = {J Budiš and M Kucharík and F Duriš and J Gazdarica and M Zrubcová and A Ficek and T Szemes and B Brejová and J Radvanszky},

url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-85064435619&doi=10.1093%2fbioinformatics%2fbty791&partnerID=40&md5=7e873f64aff7726aeb724a3a0c37237f},

doi = {10.1093/bioinformatics/bty791},

issn = {13674803},

year  = {2019},

date = {2019-01-01},

journal = {Bioinformatics},

volume = {35},

number = {8},

pages = {1310-1317},

publisher = {Oxford University Press},

abstract = {Motivation: Short tandem repeats (STRs) are stretches of repetitive DNA in which short sequences, typically made of 2-6 nucleotides, are repeated several times. Since STRs have many important biological roles and also belong to the most polymorphic parts of the human genome, they became utilized in several molecular-genetic applications. Precise genotyping of STR alleles, therefore, was of high relevance during the last decades. Despite this, massively parallel sequencing (MPS) still lacks the analysis methods to fully utilize the information value of STRs in genome scale assays. Results: We propose an alignment-free algorithm, called Dante, for genotyping and characterization of STR alleles at user-specified known loci based on sequence reads originating from STR loci of interest. The method accounts for natural deviations from the expected sequence, such as variation in the repeat count, sequencing errors, ambiguous bases and complex loci containing several different motifs. In addition, we implemented a correction for copy number defects caused by the polymerase induced stutter effect as well as a prediction of STR expansions that, according to the conventional view, cannot be fully captured by inherently short MPS reads. We tested Dante on simulated datasets and on datasets obtained by targeted sequencing of protein coding parts of thousands of selected clinically relevant genes. In both these datasets, Dante outperformed HipSTR and GATK genotyping tools. Furthermore, Dante was able to predict allele expansions in all tested clinical cases. Availability and implementation: Dante is open source software, freely available for download at https://github.com/jbudis/dante. © The Author(s) 2018. Published by Oxford University Press. All rights reserved.},

keywords = {Computational method, Genetic testing, Short tandem repeats, Variant calling},

pubstate = {published},

tppubtype = {article}

}

@article{Sádecká2019382,

title = {Microorganisms and volatile aroma-active compounds in bryndza cheese produced and marketed in Slovakia},

author = {J Sádecká and Z Čaplová and M Tomáška and K Šoltys and M Kopuncová and J Budiš and M Drončovský and E I Kolek and J Koreňová and T Kuchta},

url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-85076215677&partnerID=40&md5=462a79588febfb4630b304b476f04a07},

issn = {13368672},

year  = {2019},

date = {2019-01-01},

journal = {Journal of Food and Nutrition Research},

volume = {58},

number = {4},

pages = {382-392},

publisher = {Food Reseach Institute},

abstract = {Ten industrially and traditionally produced versions of bryndza, a typical Slovakian ewes’ cheese, covering the dominating offer in the market in Slovakia, were studied regarding the contents of microorganisms and key volatile aromaactive compounds. Culture-based microbiological analysis was complemented by culture-independent analysis by high throughput sequencing on Illumina MiSeq platform using 16S rDNA and internal transcribed spacer amplicons. Aroma-active compounds extracted by headspace solid-phase microextraction were analysed by gas chromatographyolfactometry supported by gas chromatography-mass spectrometry. Bacterial microflora was found to be dominated by lactic acid bacteria, mostly lactococci, followed by streptococci, lactobacilli and leuconostocs. A portion of cheeses contained Enterobacteriaceae, pseudomonads or Chryseobacterium spp. and, exceptionally, coagulase-positive staphylococci at a legally acceptable level. Eukaryotic microflora was dominated by Dipodascaceae in most samples. Certain samples contained contaminants such as Mucor spp. Key aroma-active compounds comprised butanoic acid, δ-decalactone, acetic acid, diacetyl and guaiacol. Further significant aroma-active compounds were 3-methylbutanol, 3-methylbutanoic acid, 2-phenylethanol, octanoic acid and p-cresol. The results demonstrated that geographical location, involvement of pasteurization or admixture of the cows’ milk-based component do not entirely determine the aroma profile of bryndza cheese, but it appears to be the result of a complex interplay of the production technology and microorganisms. © 2019 National Agricultural and Food Centre (Slovakia).},

keywords = {Bacteria, Food microbiome, Fungi, Metagenomics},

pubstate = {published},

tppubtype = {article}

}

@article{Tomáška2019187,

title = {Microorganisms and volatile aroma-active compounds in “nite“and “vojky” cheeses},

author = {M Tomáška and Z Čaplová and J Sádecká and K Šoltys and M Kopuncová and J Budiš and M Drončovský and E Kolek and J Koreňová and T Kuchta},

url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-85070496049&partnerID=40&md5=62737878bddf81c54e9649a0583d4e54},

issn = {13368672},

year  = {2019},

date = {2019-01-01},

journal = {Journal of Food and Nutrition Research},

volume = {58},

number = {2},

pages = {187-200},

publisher = {Food Reseach Institute},

abstract = {“Nite“and “vojky“are various string-like forms of a traditional cheese in Slovakia. These products are manufactured by shaping of pasteurized or raw cows’ or ewes’ milk-based lump cheeses after melting in hot water. Unsmoked versions of these cheeses from three producers were studied regarding the contents of microorganisms and volatile aroma-active compounds in four seasons during a year. Culture-based microbiological analysis was carried out using selective media. Because eukaryotic microflora was found to be negligible, culture-independent analysis was focused to prokaryotes, using 16S rDNA amplification coupled to high throughput sequencing on Illumina MiSeq platform (Illumina, San Diego, California, USA). Aroma-active compounds were extracted by headspace solid-phase microextraction and subsequently analysed by gas chromatography-olfactometry supported by gas chromatography-mass spectrometry. Microflora was found to be dominated by Lactococcus spp. with significant levels of Streptococcus spp., Lactobacillus spp. and Enterococcus spp. Dominant aroma-active compounds comprised butanoic acid, diacetyl and 3-methylbutanoic acid, the latter being profound in “nite“produced from unpasteurized ewes’ milk. Traditionally produced cheeses contained a more diverse prokaryotic microflora and had a stronger aroma profile containing a rich complex of volatile aroma-active compounds, while “nite“produced from pasteurized cows’ milk by industrial process contained a uniform microflora and had a weaker aroma profile. © 2019, Food Reseach Institute. All rights reserved.},

keywords = {Bacteria, Food microbiome, Fungi, Metagenomics},

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{Nagyova201946,

title = {Targeted next-generation sequencing in Slovak cardiomyopathy patients},

author = {E Nagyova and J Radvanszky and M Hyblova and V Simovicova and E Goncalvesova and F W Asselbergs and L Kadasi and T Szemes and G Minarik},

url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-85060659545&doi=10.4149%2fBLL_2019_007&partnerID=40&md5=4242fb0c864e6c82fe2565c6cc094102},

doi = {10.4149/BLL_2019_007},

issn = {00069248},

year  = {2019},

date = {2019-01-01},

journal = {Bratislava Medical Journal},

volume = {120},

number = {1},

pages = {46-51},

publisher = {Comenius University},

abstract = {OBJECTIVES: For the first time we used targeted next-generation sequencing to detect candidate pathogenic variants in Slovak cardiomyopathy patients. BACKGROUND: Targeted next-generation sequencing is considered to be the best practice in genetic diagnostics of cardiomyopathies. However, in Slovakia, with high cardiomyopathies prevalence of 1/440, the current diagnostic tests are still based on Sanger sequencing of a few genes. Consequently, little is known about the exact contribution of pathogenic variants in known cardiomyopathy genes in Slovak patients. METHODS: We used a panel of 46 known cardiomyopathy-associated genes to detect genetic variants in 16 Slovak cardiomyopathy patients (6 dilated, 8 hypertrophic, 2 non-compaction subtypes). RESULTS: We identified candidate pathogenic variants in 11 of 16 patients (69 %). Genes with higher count of candidate pathogenic variants were MYBPC3, MYH and TTN, each with 3 different variants. Seven variants ACTC1 (c.329C > T), ANKRD1 (c.683G > T), MYH7 (c.1025C > T), PKP2 (c.2003delA), TTN (c.51655C > T, c.84841G > T, c.101874_101881delAGAATTTG) have been detected for the first time and might represent Slovak- specific genetic cause. CONCLUSIONS: We have performed genetic testing of previously untested Slovak cardiomyopathy patients using next-generation sequencing cardiomyopathy gene panel. Given the high percentage of candidate pathogenic variants it should be recommended to implement this method into routine genetic diagnostic practice in Slovakia. © AEPress s.r.o.},

keywords = {Genetic testing, Single nucleotide variants, Variant calling},

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{Kraková20183294,

title = {The microbiomes of a XVIII century mummy from the castle of Krásna Hôrka (Slovakia) and its surrounding environment},

author = {L Kraková and K Šoltys and A Puškárová and M Bučková and L Jeszeová and M Kucharík and J Budiš and L Orovčík and T Szemes and D Pangallo},

url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-85053249745&doi=10.1111%2f1462-2920.14312&partnerID=40&md5=31ee6742ce17089e12cc092f5dc64938},

doi = {10.1111/1462-2920.14312},

issn = {14622912},

year  = {2018},

date = {2018-01-01},

journal = {Environmental Microbiology},

volume = {20},

number = {9},

pages = {3294-3308},

publisher = {Blackwell Publishing Ltd},

abstract = {This microbiological survey was performed to determine the conservation state of a mummy in the Slovak castle of Krásna Hôrka and its surrounding environment. Culture-dependent identification was coupled with biodegradation assays on keratin, gelatin and cellulose. Next Generation Sequencing (NGS) using Illumina platform was used for a deeper microbial investigation. Three environmental samples were collected: from the glass of the sarcophagus, from the air inside it, and from the air of the chapel where the mummy is located. Seven different samples were taken from mummy's surface: from the left ear, left-hand palm, left-hand nail, left instep, right hand, abdomen and mineral crystals embedded within the skin. Three internal organ samples, from the lung, pleura and stomach, were also included in this study. Together, the culture-dependent and culture-independent analyses revealed that the bacterial communities present had fewer taxa than the fungal ones. The mycobiome showed the largest variability and included Epicoccum nigrum, Penicillium spp., Alternaria spp., Aspergillus spp., Cladosporium spp. and Aureobasidium pullulans; many other Ascomycota and Basidiomycota genera were detected by NGS. The most interesting results came from the skin mineral crystals and the internal organs. The hydrolytic assays revealed those microorganisms which might be considered dangerous ‘mummy pathogens’. © 2018 Society for Applied Microbiology and John Wiley & Sons Ltd. © 2018 Society for Applied Microbiology and John Wiley & Sons Ltd},

keywords = {Bacteria, Biodeterioration, Fungi, Metagenomics},

pubstate = {published},

tppubtype = {article}

}

@article{Soltys2018,

title = {Draft genome sequence of Escherichia coli KL53},

author = {K Soltys and S Vavrova and J Budis and L Palkova and G Minarik and J Grones},

url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-85044840002&doi=10.1128%2fgenomeA.00220-18&partnerID=40&md5=b7145569beb42e97a74d2c434287004d},

doi = {10.1128/genomeA.00220-18},

issn = {21698287},

year  = {2018},

date = {2018-01-01},

journal = {Genome Announcements},

volume = {6},

number = {13},

publisher = {American Society for Microbiology},

abstract = {Here, we report the draft genome sequence of a clinical isolate of the uropathogenic strain Escherichia coli KL53. A total of 5,083,632 bp was de novo assembled into 170 contigs containing 89 RNAs and 5,034 protein-coding genes. Remarkable is the presence of the tellurite resistance (ter) operon on a plasmid. © 2018 Soltys et al.},

keywords = {Assembly, Bacteria},

pubstate = {published},

tppubtype = {article}

}

@article{Radvanszky2017339,

title = {Complex phenotypes blur conventional borders between Say–Barber–Biesecker–Young–Simpson syndrome and genitopatellar syndrome},

author = {J Radvanszky and M Hyblova and D Durovcikova and M Hikkelova and E Fiedler and L Kadasi and J Turna and G Minarik and T Szemes},

url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-84989325626&doi=10.1111%2fcge.12840&partnerID=40&md5=f3981a3dbb893dceec013f830ecf68f6},

doi = {10.1111/cge.12840},

issn = {00099163},

year  = {2017},

date = {2017-01-01},

journal = {Clinical Genetics},

volume = {91},

number = {2},

pages = {339-343},

publisher = {Blackwell Publishing Ltd},

abstract = {Say–Barber–Biesecker–Young–Simpson syndrome (SBBYSS) and genitopatellar syndrome (GTPTS) are clinically similar disorders with some overlapping features. Although they are currently considered to be distinct clinical entities, both were found to be caused by de novo truncating sequence variants in the KAT6B (lysine acetyltransferase 6B) gene, strongly suggesting that they are allelic disorders. Herein, we report the clinical and genetic findings in a girl presenting with a serious multiple congenital anomaly syndrome with phenotypic features overlapping both SBBYSS and GTPTS; pointing out that the clinical distinction between these disorders is not exact and there do exist patients, in whom conventional clinical classification is problematic. Genetic analyses revealed a truncating c.4592delA (p.Asn1531Thrfs*18) variant in the last KAT6B exon. Our findings support that phenotypes associated with typical KAT6B disease-causing variants should be referred to as ‘KAT6B spectrum disorders’ or ‘KAT6B related disorders’, rather than their current SBBYSS and GTPTS classification. © 2016 John Wiley & Sons A/S. Published by John Wiley & Sons Ltd},

keywords = {Case study, Genetic testing, Single nucleotide variants, Variant calling},

pubstate = {published},

tppubtype = {article}

}

@article{Sulo2017571,

title = {The evolutionary history of Saccharomyces species inferred fromcompleted mitochondrial genomes and revision in the 'yeast mitochondrial genetic code'},

author = {P Sulo and D Szabóová and P Bielik and S Poláková and K Soltys and K Jatzová and T Szemes},

url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-85043997344&doi=10.1093%2fdnares%2fdsx026&partnerID=40&md5=06765f8bce0a85c0d5b881f73efb11f8},

doi = {10.1093/dnares/dsx026},

issn = {13402838},

year  = {2017},

date = {2017-01-01},

journal = {DNA Research},

volume = {24},

number = {6},

pages = {571-583},

publisher = {Oxford University Press},

abstract = {The yeast Saccharomyces are widely used to test ecological and evolutionary hypotheses. A large number of nuclear genomic DNA sequences are available, but mitochondrial genomic data are insufficient. We completed mitochondrial DNA (mtDNA) sequencing from Illumina MiSeq reads for all Saccharomyces species. All are circularly mapped molecules decreasing in size with phylogenetic distance from Saccharomyces cerevisiae but with similar gene content including regulatory and selfish elements like origins of replication, introns, free-standing open reading frames or GC clusters. Their most profound feature is species-specific alteration in gene order. The genetic code slightly differs from well-established yeast mitochondrial code as GUG is used rarely as the translation start and CGA and CGC code for arginine. The multilocus phylogeny, inferred from mtDNA, does not correlate with the trees derived from nuclear genes. mtDNA data demonstrate that Saccharomyces cariocanus should be assigned as a separate species and Saccharomyces bayanus CBS 380T should not be considered as a distinct species due to mtDNA nearly identical to Saccharomyces uvarum mtDNA. Apparently, comparison of mtDNAs should not be neglected in genomic studies as it is an important tool to understand the origin and evolutionary history of some yeast species. © The Author 2017.},

keywords = {Assembly, Fungi, Mitochondria, Phylogeny},

pubstate = {published},

tppubtype = {article}

}

@article{Cierna2017449,

title = {The first reported case of meckel-gruber syndrome associated with abnormal karyotype mosaic trisomy 17},

author = {Z Cierna and P Janega and F Grochal and V Ferianec and T Braxatorisova and L Strieskova and J Malova and P Jungova and T Szemes},

url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-85032002622&doi=10.1177%2f1093526616689184&partnerID=40&md5=8458f3e2bde61a3a4f9694e41e605a73},

doi = {10.1177/1093526616689184},

issn = {10935266},

year  = {2017},

date = {2017-01-01},

journal = {Pediatric and Developmental Pathology},

volume = {20},

number = {5},

pages = {449-454},

publisher = {SAGE Publications Ltd},

abstract = {Meckel-Gruber syndrome (MKS) is a rare lethal autosomal recessive disorder with typical anomalies including encephalocele, multicystic renal dysplasia, congenital liver fibrosis, and polydactyly. MKS is caused by mutations of genes localized on different chromosomes. Karyotypes of published Meckel-Gruber syndrome cases are without any aberrations. We present a male fetus with meningoencephalocele, multicystic renal dysplasia, congenital liver fibrosis, and other anomalies. Standard cytogenetic examination of cultured fetal skin and muscle fibroblasts showed mosaic trisomy 17. Homozygous deletion in CC2D2A gene was found by Sanger sequencing. This is to our knowledge the first case of genetically confirmed Meckel- Gruber syndrome with incidental cofinding of mosaic trisomy 17. Abnormal karyotype does not exclude diagnosis of MKS with risk of recurrence 25% in next pregnancy. In the case of anomalies typical for Meckel-Gruber syndrome, genetic analysis is indicated. © 2017, Society for Pediatric Pathology.},

keywords = {Aneuploidy, Case study, Genetic testing},

pubstate = {published},

tppubtype = {article}

}

@article{Kraková2016795,

title = {Investigation of bacterial and archaeal communities: novel protocols using modern sequencing by Illumina MiSeq and traditional DGGE-cloning},

author = {L Kraková and K Šoltys and J Budiš and T Grivalský and F Ďuriš and D Pangallo and T Szemes},

url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-84976272674&doi=10.1007%2fs00792-016-0855-5&partnerID=40&md5=a73c4e305f7b0f97139840b4328bff01},

doi = {10.1007/s00792-016-0855-5},

issn = {14310651},

year  = {2016},

date = {2016-01-01},

journal = {Extremophiles},

volume = {20},

number = {5},

pages = {795-808},

publisher = {Springer Tokyo},

abstract = {Different protocols based on Illumina high-throughput DNA sequencing and denaturing gradient gel electrophoresis (DGGE)-cloning were developed and applied for investigating hot spring related samples. The study was focused on three target genes: archaeal and bacterial 16S rRNA and mcrA of methanogenic microflora. Shorter read lengths of the currently most popular technology of sequencing by Illumina do not allow analysis of the complete 16S rRNA region, or of longer gene fragments, as was the case of Sanger sequencing. Here, we demonstrate that there is no need for special indexed or tailed primer sets dedicated to short variable regions of 16S rRNA since the presented approach allows the analysis of complete bacterial 16S rRNA amplicons (V1–V9) and longer archaeal 16S rRNA and mcrA sequences. Sample augmented with transposon is represented by a set of approximately 300 bp long fragments that can be easily sequenced by Illumina MiSeq. Furthermore, a low proportion of chimeric sequences was observed. DGGE-cloning based strategies were performed combining semi-nested PCR, DGGE and clone library construction. Comparing both investigation methods, a certain degree of complementarity was observed confirming that the DGGE-cloning approach is not obsolete. Novel protocols were created for several types of laboratories, utilizing the traditional DGGE technique or using the most modern Illumina sequencing. © 2016, Springer Japan.},

keywords = {Bacteria, Environmental microbiome, Metagenomics},

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{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{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{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{Minárik2013539,

title = {Spectrum of mutations in gastrointestinal stromal tumor patients - a population-based study from Slovakia},

author = {G Minárik and L Plank and Z Lasabová and T Szemes and T Burjanivová and P Szépe and V Buzalková and D Porubský and J Šufliarsky},

url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-84878263424&doi=10.1111%2fapm.12019&partnerID=40&md5=dbaf848510fcae4f4e67f5505c875199},

doi = {10.1111/apm.12019},

issn = {09034641},

year  = {2013},

date = {2013-01-01},

journal = {APMIS},

volume = {121},

number = {6},

pages = {539-548},

abstract = {Gastrointestinal stromal tumors (GISTs) are the most common mesenchymal neoplasms of gastrointestinal tract and are characterized by presence of mutations in tyrosine kinases cKIT (KIT) and PDGFRα (PDGFRA). Mutations identified are highly heterogeneous, but some mutations are associated with specific clinical features of the tumor. Samples from 278 GIST patients collected during the period 2004-2011 were screened for mutations in exons 9, 11, 13, and 17 of KIT and 12, 14 and 18 of PDGFRA. Results of mutation screening were summarized and tested for possible association with clinical parameters of tumors. Mutations were identified in 83.81% of patients. Most frequent mutations were found in KIT exon 11 reaching frequency of 62.95%. Other exons contributed to the mutation pool with frequencies 8.27%, 7.55%, 2.52%, 1.44%, 1.08%, and 0.00%, in decreasing order KIT exon 9, PDGRFA exons 18 and 12, KIT exon 13, PDGFRA exon 14, and KIT exon 17. General linear model analysis showed no effect of any individual analyzed mutation on the phenotypic variables, but we confirmed association between mutations KIT exon 9 p. 503-504_dup2, and PDGFRA exon 18 p. D842V and intestinal and gastric localization of tumors. © 2012 APMIS.},

keywords = {Oncology, Population study, Single nucleotide variants},

pubstate = {published},

tppubtype = {article}

}