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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)
Internet cím:	DOI Intézményi repozitóriumban (DEA) tárolt változat
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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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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 Intézményi repozitóriumban (DEA) tárolt változat
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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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