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001-es BibID:BIBFORM072517
035-os BibID:(cikkazonosító)158 (WoS)000426305200003 (Scopus)85042425048
Első szerző:Ivády Gergely (laboratóriumi szakorvos)
Cím:Analytical parameters and validation of homopolymer detection in a pyrosequencing-based next generation sequencing system / Ivády Gergely, Madar László, Dzsudzsák Erika, Koczok Katalin, Kappelmayer János, Krulisova Veronika, Macek Milan, Horváth Attila, Balogh István
Dátum:2018
ISSN:1471-2164
Megjegyzések:BackgroundCurrent technologies in next-generation sequencing are offering high throughput reads at low costs, but still suffer from various sequencing errors. Although pyro- and ion semiconductor sequencing both have the advantage of delivering long and high quality reads, problems might occur when sequencing homopolymer-containing regions, since the repeating identical bases are going to incorporate during the same synthesis cycle, which leads to uncertainty in base calling. The aim of this study was to evaluate the analytical performance of a pyrosequencing-based next-generation sequencing system in detecting homopolymer sequences using homopolymer-preintegrated plasmid constructs and human DNA samples originating from patients with cystic fibrosis.ResultsIn the plasmid system average correct genotyping was 95.8% in 4-mers, 87.4% in 5-mers and 72.1% in 6-mers. Despite the experienced low genotyping accuracy in 5- and 6-mers, it was possible to generate amplicons with more than a 90% adequate detection rate in every homopolymer tract. When homopolymers in the CFTR gene were sequenced average accuracy was 89.3%, but varied in a wide range (52.2 ? 99.1%). In all but one case, an optimal amplicon-sequencing primer combination could be identified. In that single case (7A tract in exon 14 (c.2046_2052)), none of the tested primer sets produced the required analytical performance.ConclusionsOur results show that pyrosequencing is the most reliable in case of 4-mers and as homopolymer length gradually increases, accuracy deteriorates. With careful primer selection, the NGS system was able to correctly genotype all but one of the homopolymers in the CFTR gene. In conclusion, we configured a plasmid test system that can be used to assess genotyping accuracy of NGS devices and developed an accurate NGS assay for the molecular diagnosis of CF using self-designed primers for amplification and sequencing.
Tárgyszavak:Orvostudományok Elméleti orvostudományok idegen nyelvű folyóiratközlemény külföldi lapban
folyóiratcikk
Pyrosequencing
Homopolymer detection
Cystic fibrosis
Megjelenés:BMC Genomics. - 19 (2018), p. 1-8. -
További szerzők:Madar László (1972-) (klinikai laboratóriumi kutató) Dzsudzsák Erika Koczok Katalin (1979-) (labororvos) Kappelmayer János (1960-) (laboratóriumi szakorvos) Krulisova, Veronika Macek Jr., Milan Horváth Attila (1988-) (programtervező informatikus) Balogh István (1972-) (molekuláris biológus, genetikus)
Pályázati támogatás:K109076
OTKA
GINOP-2.3.2-15-2016-00039
GINOP
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DOI
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001-es BibID:BIBFORM054463
Első szerző:Ivády Gergely (laboratóriumi szakorvos)
Cím:Molecular Analysis of Cystic Fibrosis Patients in Hungary - an Update to the Mutational Spectrum / Gergely Ivády, Katalin Koczok, Laszlo Madar, Eva Gombos, Izabella Toth, Klaudia Gyori, István Balogh
Dátum:2015
Megjegyzések:Background: In this study the authors present an update tothe CFTR mutation profile in Hungary, utilizing data froma selected cohort of 45 cystic fibrosis (CF) patients from differentregions of the country.Methods: Depending on the preceding analysis, four differentmutation detection methods were used. A commercialassay targeting the most common CF-causing mutationswas performed as the first test followed by an allele spe cificPCR for CFTRdele2,3(21kb), Sanger sequencing andMLPA analysis of the coding region of the CFTR gene.Results: In our recent study 27 different mutations weredetected, including 2 novel ones (c.1037_1038insA andc.1394C>T). Besides F508del (c.1521_1523delCTT), thefollowing mutations were found at a frequency of ? 4.0%:W1282X (c.3846G>A), N1303K (c.3909C>G),CFTRdele2,3(21kb) (c.54-5940_273+10250del21kb)and 2184insA (c.2052_2053insA). In addition, four mutations(G542X, Y1092X, 621+1G>T, and 2143delT) werefound in more than one allele.Conclusions: The updated database of Hungarian mutationsnot only enables to increase the efficiency of the existingdiagnostic approach, but also provides a further refinedbasis for the introduction of the molecular newborn screening(NBS) program in Hungary.
Tárgyszavak:Orvostudományok Klinikai orvostudományok idegen nyelvű folyóiratközlemény külföldi lapban
cystic fibrosis
mutational spectrum
newborn screening
Megjelenés:Journal of Medical Biochemistry. - 34 (2015), p. 1-6. -
További szerzők:Koczok Katalin (1979-) (labororvos) Madar László (1972-) (klinikai laboratóriumi kutató) Gombos Éva (1966-) (orvosdiagnosztikai laboratóriumi analitikus) Tóth Izabella Győri Klaudia Balogh István (1972-) (molekuláris biológus, genetikus)
Internet cím:Intézményi repozitóriumban (DEA) tárolt változat
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