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1.

001-es BibID:BIBFORM078672
035-os BibID:(WoS)000468162100011 (Scopus)85064459936
Első szerző:Budis, Jaroslav
Cím:Non-invasive prenatal testing as a valuable source of population specific allelic frequencies / Jaroslav Budis, Juraj Gazdarica, Jan Radvanszky, Maria Harsanyova, Iveta Gazdaricova, Lucia Strieskova, Richard Frno, Frantisek Duris, Gabriel Minarik, Martina Sekelska, Balint Nagy, Tomas Szemes
Dátum:2019
ISSN:0168-1656 1873-4863
Megjegyzések: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 1,548 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. 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.
Tárgyszavak:Orvostudományok Klinikai orvostudományok idegen nyelvű folyóiratközlemény külföldi lapban
folyóiratcikk
allelic
frequencies
non-invasive
prenatal
Megjelenés:Journal of Biotechnology. - 299 (2019), p. 72-78. -
További szerzők:Gazdarica, Juraj Radvanszky, Jan Harsanyova, Maria Gazdaricova, Iveta Strieskova, Lucia Frno, Richard Duris, Frantisek Minarik, Gabriel Sekelska, Martina Nagy Bálint (1956-) (molekuláris genetikus) Szemes, Tomas (1980-) (biológus)
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2.

001-es BibID:BIBFORM075319
035-os BibID:(WoS)000473691900004 (Scopus)85067353429
Első szerző:Budis, Jaroslav
Cím:Combining count- and length-based z-scores leads to improved predictions in non-invasive prenatal testing / Budis Jaroslav, Gazdarica Juraj, Radvanszky Jan, Szucs Gabor, Kucharik Marcel, Strieskova Lucia, Gazdaricova Iveta, Harsanyova Maria, Duris Frantisek, Minarik Gabriel, Sekelska Martina, Nagy Balint, Turna Jan, Szemes Tomas
Dátum:2019
ISSN:1367-4803
Megjegyzések: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: 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.
Tárgyszavak:Orvostudományok Klinikai orvostudományok idegen nyelvű folyóiratközlemény külföldi lapban
folyóiratcikk
non-invasive
prenatal
testing
improved
Megjelenés:Bioinformatics. - 35 : 8 (2019), p. 1284-1291. -
További szerzők:Gazdarica, Juraj Radvanszky, Jan Szűcs Gábor Kucharik, Marcel Strieskova, Lucia Gazdaricova, Iveta Harsanyova, Maria Duris, Frantisek Minarik, Gabriel Sekelska, Martina Nagy Bálint (1956-) (molekuláris genetikus) Turna, Jan Szemes, Tomas (1980-) (biológus)
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3.

001-es BibID:BIBFORM065208
Első szerző:Minarik, Gabriel
Cím: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 / Gabriel Minarik, Gabriela Repiska, Michaela Hyblova, Emilia Nagyova, Katarina Soltys, Jaroslav Budis, Frantisek Duris, Rastislav Sysak, Maria Gerykova Bujalkova, Barbora Vlkova-Izrael, Orsolya Biro, Balint Nagy, Tomas Szemes
Dátum:2015
ISSN:1932-6203
Megjegyzések:ObjectivesThe 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 silicoand physical size selection methods.MethodsSamples 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 ofin silico and physical size selection on analytical performance of the test was studied.ResultsUsing 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 physical size selection z scores of tested trisomic samples increased significantly ? p= 0.0141 and p = 0.025 for Ion Torrent PGM and MiSeq, respectively.ConclusionsNoninvasive prenatal testing for chromosome 21 trisomy with the utilization of benchtop NGS systems led to results equivalent to previously published studies performed on high-to-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
Tárgyszavak:Orvostudományok Klinikai orvostudományok idegen nyelvű folyóiratközlemény külföldi lapban
next generation sequencing
trisomy 21
non-invasive
free DNA
Megjelenés:Plos One. - 10 (2015), p. 1-12. -
További szerzők:Repiska, Gabriela Hyblova, Michaela Nagyova Emilia Soltys, Katarina Budis, Jaroslav Duris, Frantisek Sysak, Rastislav Bujalkova, Maria Gerykova Vlkova-Izrael, Barbora Biró Orsolya (molekuláris biológus) Nagy Bálint (1956-) (molekuláris genetikus) Szemes, Tomas (1980-) (biológus)
Internet cím:DOI
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4.

001-es BibID:BIBFORM090548
035-os BibID:(Scopus)85099826325 (WOS)000610904200001 (cikkazonosító)819
Első szerző:Pös, Ondrej (biológus)
Cím:Copy Number Variation : methods and Clinical Applications / Ondrej Pös, Jan Radvanszky, Jakub Styk, Zuzana Pös, Gergely Buglyó, Michal Kajsik, Jaroslav Budis, Bálint Nagy, Tomas Szemes
Dátum:2021
ISSN:2076-3417
Megjegyzések: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.
Tárgyszavak:Orvostudományok Elméleti orvostudományok idegen nyelvű folyóiratközlemény külföldi lapban
folyóiratcikk
copy number variants
CNV detection
CNV interpretation
bioinformatics tools
molecular methods
Megjelenés:Applied Sciences-Basel. - 11 : 2 (2021), p. 1-16. -
További szerzők:Radvanszky, Jan Styk, Jakub Pös, Zuzana Buglyó Gergely (1980-) (genetikus) Kajsik, Michal Budis, Jaroslav Nagy Bálint (1956-) (molekuláris genetikus) Szemes, Tomas (1980-) (biológus)
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5.

001-es BibID:BIBFORM105554
035-os BibID:(cikkazonosító)101875
Első szerző:Soltész Beáta (molekuláris biológus)
Cím:Mitochondrial DNA copy number changes, heteroplasmy, and mutations in plasma-derived exosomes and brain tissue of glioblastoma patients / Soltész Beáta, Pös Ondrej, Wlachovska Zuzana, Budis Jaroslav, Hekel Rastislav, Strieskova Lucia, Liptak Jana Bozenka, Krampl Werner, Styk Jakub, Németh Nikolett, Keserű Judit Sz., Jenei Adrienn, Buglyó Gergely, Klekner Álmos, Nagy Bálint, Szemes Tomas
Dátum:2022
ISSN:0890-8508
Tárgyszavak:Orvostudományok Klinikai orvostudományok idegen nyelvű folyóiratközlemény külföldi lapban
folyóiratcikk
Megjelenés:Molecular And Cellular Probes. - 66 (2022), p. 1-6. -
További szerzők:Pös, Ondrej (1990-) (biológus) Wlachovska, Zuzana Budis, Jaroslav Hekel, Rastislav Strieskova, Lucia Liptak, Jana Bozenka Krampl, Werner Styk, Jakub Németh Nikolett (1995-) (biológus) Keserű Judit (1976-) (molekuláris genetikus) Jenei Adrienn (1978-) (biológus, kémikus) Buglyó Gergely (1980-) (genetikus) Klekner Álmos (1970-) (idegsebész) Nagy Bálint (1956-) (molekuláris genetikus) Szemes, Tomas (1980-) (biológus)
Pályázati támogatás:2.0-2017-1.2.1-NKP-2017-00002
Egyéb
ITMS: 313011V446 (LISPER)
Egyéb
ITMS: 313011W428 (BIOMEDIRES II.)
Egyéb
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6.

001-es BibID:BIBFORM107654
035-os BibID:(Scopus)85146857319 (WoS)000920608400001
Első szerző:Styk, Jakub
Cím:Microsatellite instability assessment is instrumental for Predictive, Preventive and Personalised Medicine : status quo and outlook / Styk Jakub, Pös Zuzana, Pös Ondrej, Radvanszky Jan, Turnova Evelina Hrckova, Buglyó Gergely, Klimova Daniela, Budis Jaroslav, Repiska Vanda, Nagy Bálint, Szemes Tomas
Dátum:2023
ISSN:1878-5077 1878-5085
Megjegyzések:A form of genomic alteration called microsatellite instability (MSI) occurs in a class of tandem repeats (TRs) called microsatellites (MSs) or short tandem repeats (STRs) due to the failure of a post-replicative DNA mismatch repair (MMR) system. Traditionally, the strategies for determining MSI events have been low-throughput procedures that typically require assessment of tumours as well as healthy samples. On the other hand, recent large-scale pan-tumour studies have consistently highlighted the potential of massively parallel sequencing (MPS) on the MSI scale. As a result of recent innovations, minimally invasive methods show a high potential to be integrated into the clinical routine and delivery of adapted medical care to all patients. Along with advances in sequencing technologies and their ever-increasing cost-effectiveness, they may bring about a new era of Predictive, Preventive and Personalised Medicine (3PM). In this paper, we offered a comprehensive analysis of high-throughput strategies and computational tools for the calling and assessment of MSI events, including whole-genome, whole-exome and targeted sequencing approaches. We also discussed in detail the detection of MSI status by current MPS blood-based methods and we hypothesised how they may contribute to the shift from conventional medicine to predictive diagnosis, targeted prevention and personalised medical services. Increasing the efficacy of patient stratification based on MSI status is crucial for tailored decision-making. Contextually, this paper highlights drawbacks both at the technical level and those embedded deeper in cellular/molecular processes and future applications in routine clinical testing.
Tárgyszavak:Orvostudományok Elméleti orvostudományok idegen nyelvű folyóiratközlemény külföldi lapban
folyóiratcikk
Microsatellite instability
Cancer
Screening
Massively parallel sequencing
Liquid biopsy
Patient stratification
Predictive Preventive Personalised Medicine (PPPM / 3PM)
Megjelenés:EPMA Journal. - 14 : 1 (2023), p. 143-165. -
További szerzők:Pös, Zuzana Pös, Ondrej (1990-) (biológus) Radvanszky, Jan Turnova, Evelina Hrckova Buglyó Gergely (1980-) (genetikus) Klimova, Daniela Budis, Jaroslav Repiska Vanda Nagy Bálint (1956-) (molekuláris genetikus) Szemes, Tomas (1980-) (biológus)
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7.

001-es BibID:BIBFORM084977
Első szerző:Szemes, Tomas (biológus)
Cím:The utilization of MiSeq platform for noninvasive prenatal testing of trisomy 21 and evaluation of size selection methods on analytical performance / Tomas Szemes, Michaela Hyblova, Barbora Vlkova-Izrael, Jaroslav Budis, Frantisek Duris, Biró Orsolya Brigitta, Nagy Bálint, Gabriel Minarik
Dátum:2016
Tárgyszavak:Orvostudományok Klinikai orvostudományok idézhető absztrakt
folyóiratcikk
Megjelenés:Paediatria Croatica. - 60 : Suppl. 2 (2016), p. 19. -
További szerzők:Hyblova, Michaela Vlkova-Izrael, Barbora Budis, Jaroslav Duris, Frantisek Biró Orsolya (molekuláris biológus) Nagy Bálint (1956-) (molekuláris genetikus) Minarik, Gabriel
Internet cím:Intézményi repozitóriumban (DEA) tárolt változat
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8.

001-es BibID:BIBFORM074288
Első szerző:Szemes, Tomas (biológus)
Cím:Are phages part of our immunity? / Tomas Szemes, Andrej Balaz, Michal Kajsik, Iveta Gazdaricova, Orsolya Biro, Balint Nagy, Jan Turna, Jaroslav Budis
Dátum:2018
Megjegyzések:Introduction: Several non-invasive prenatal tests (NIPT) use total DNA massively parallel sequencing. A portion of sequences are not mapped to human genome reference sequence and is filtered out in the NIPT analysis. Our aim was to determine source of unmapped reads. Preliminary data suggests presence of bacteriophage DNA in human circulation. Materials and methods: We carried out massively parallel sequencing of total DNA from plasma from group of healthy individuals and individuals undergoing antiviral treatment. DNA fragments which mapped to the human reference genome (version hg38) were filtered. We assigned each unmapped fragment a taxonomic label using metagenomic classifier Clark. Taxonomic composition of samples was compared and visualized using Krona graphs. We assembled filtered reads using assembler specialized for assembly of viral genomes called Savage.Results: We identified presence of phage sequences in a small number of reads in studied samples of healthy individuals. In addition, we observed significant drop in phage sequences in individuals undergoing antiviral treatment. In the results we present breakdown of the identified phage data.Conclusions: Preliminary data suggest presence of phage DNA in circulating free nucleic acids. We hypothesize that host immune system tolerates phages to assist in control and stabilization of microenvironment. More rigorous analysis needs to be carried out and supportive experiments are needed to confirm the finding as well as to study our hypotheses.
Tárgyszavak:Orvostudományok Klinikai orvostudományok idézhető absztrakt
DNA
phage
MPS
Megjelenés:Biomedical Papers. - 162 : Suppl. 1 (2018), p. S14. -
További szerzők:Balaz, Andrej Kajsik, Michal Gazdaricova, Iveta Biró Orsolya (molekuláris biológus) Nagy Bálint (1956-) (molekuláris genetikus) Turna, Jan Budis, Jaroslav
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