CCL

Összesen 3 találat.
#/oldal:
Részletezés:
Rendezés:

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

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)
Internet cím:Szerző által megadott URL
DOI
Intézményi repozitóriumban (DEA) tárolt változat
Borító:

3.

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
Internet cím:Intézményi repozitóriumban (DEA) tárolt változat
Borító:
Rekordok letöltése1