CCL

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

1.

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

2.

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
Borító:

3.

001-es BibID:BIBFORM016396
Első szerző:Ivády Gergely (laboratóriumi szakorvos)
Cím:Distribution of CFTR mutations in Eastern Hungarians : relevance to genetic testing and to the introduction of newborn screening for cystic fibrosis? / Ivady Gergely, Madar Laszlo, Nagy Bela, Gonczi Ferenc, Ajzner Eva, Dzsudzsak Erika, Dvoráková Lenka, Gombos Eva, Kappelmayer Janos, Macek Milan Jr., Balogh Istvan
Dátum:2011
ISSN:1569-1993
Megjegyzések:The aim of this study was characterization of an updated distribution of CFTR mutations in a representative cohort of 40 CF patients with the classical form of the disease drawn from Eastern Hungary. Due to the homogeneity of the Hungarian population our data are generally applicable to other regions of the country, including the sizeable diaspora. Methods: We utilized the recommended "cascade" CFTR mutation screening approach, initially using a commercial assay, followed by examination of the common "Slavic" deletion CFTRdele2,3(21 kb). Subsequently, the entire CFTR coding region of the CFTR gene was sequenced in patients with yet unidentified mutations. Results: The Elucigene CF29Tm v2 assay detected 81.25% of all CF causing mutations. An addition of the CFTRdele2,3(21 kb) increased the mutation detection rate to 86.25%. DNA sequencing enabled us to identify mutations on 79/80 CF alleles. Mutations [CFTRdele2,3(21 kb), p.Gln685ThrfsX4 (2184insA) were found at an unusually high frequency, each comprising 5.00% of all CF alleles. Conclusion: We have identified common CF causing mutations in the Hungarian population with the most common mutations (p.Phe508del, p.Asn1303Lys, CFTRdele2,3(21 kb), 2184insA, p.Gly542X, and p.Leu101X), comprising over 93.75% of all CF alleles. Obtained data are applicable to the improvement of DNA diagnostics in Hungary and beyond, and are the necessary prerequisite for the introduction of a nationwide "two tier" CF newborn screening program.
Tárgyszavak:Orvostudományok Klinikai orvostudományok idegen nyelvű folyóiratközlemény külföldi lapban
Molekuláris Medicina
Megjelenés:Journal of Cystic Fibrosis 10 : 3 (2011), p. 217-220. -
További szerzők:Madar László (1972-) (klinikai laboratóriumi kutató) Nagy Béla (1949-) (csecsemő- és gyermekgyógyász, gyermek-tüdőgyógyász) Gönczi Ferenc (Kenézy Gyula Kórház) Ajzner Éva (1968-) (laboratóriumi szakorvos) Dzsudzsák Erika Dvorakova, Lenka Gombos Éva (1966-) (orvosdiagnosztikai laboratóriumi analitikus) Kappelmayer János (1960-) (laboratóriumi szakorvos) Macek Jr., Milan Balogh István (1972-) (molekuláris biológus, genetikus)
Pályázati támogatás:TÁMOP-4.2.1/B-09/1/KONV-2010-0007
TÁMOP
Celluláris hematológia - immunológia
Internet cím:Szerző által megadott URL
DOI
Intézményi repozitóriumban (DEA) tárolt változat
Borító:
Rekordok letöltése1