Comparison of VCFs Generated from Different Software in the Evaluation of Variants in Genes Responsible for Rare Thrombophilic Conditions

Kód výsledku v IS VaVaI

<a href="https://www.isvavai.cz/riv?ss=detail&h=RIV%2F00098892%3A_____%2F23%3A10158266" target="_blank" >RIV/00098892:_____/23:10158266 - isvavai.cz</a>

Výsledek na webu

<a href="https://link.springer.com/chapter/10.1007/978-3-031-34960-7_32" target="_blank" >https://link.springer.com/chapter/10.1007/978-3-031-34960-7_32</a>

DOI - Digital Object Identifier

<a href="http://dx.doi.org/10.1007/978-3-031-34960-7_32" target="_blank" >10.1007/978-3-031-34960-7_32</a>

Jazyk výsledku

angličtina

Název v původním jazyce

Comparison of VCFs Generated from Different Software in the Evaluation of Variants in Genes Responsible for Rare Thrombophilic Conditions

Popis výsledku v původním jazyce

As part of the inplementation and validation of an optimal diagnostic approach based on high-throughput sequencing by Ion Torrent platform in the diagnosis of the rare trombophilic conditions of protein S (PS), protein C (PC) and antithrombin (AT) deficiency, we compared data from three different software tools – Torrent Suite, Ion Reporter and NextGene – to compare their performance and accuracy in the analysis of each sequence variant detected. A cohort of 31 patients was selected for PS (7), PC (13) and AT (11) deficiency based on defined indication criteria. Within these patient groups, a mutation detection rate of 67,7% was observed. In a cohort of 10 patients who were sequenced in a single sequencing run the three evaluated software detected 16, 19, and 27 variants in the PROS1 gen; 17,17, 19 variants in the PROC gene; and 15, 15, 16 variants for the SERPINC1 gene in their baseline settings. For data generated from the Ion Torrent platform, software from the same provider seems to be more suitable, mainly because of the quality of the false positive filtering. For further evaluation of the validity of the software used, it will be necessary to expand the cohort of patient examined.

Název v anglickém jazyce

Comparison of VCFs Generated from Different Software in the Evaluation of Variants in Genes Responsible for Rare Thrombophilic Conditions

Popis výsledku anglicky

As part of the inplementation and validation of an optimal diagnostic approach based on high-throughput sequencing by Ion Torrent platform in the diagnosis of the rare trombophilic conditions of protein S (PS), protein C (PC) and antithrombin (AT) deficiency, we compared data from three different software tools – Torrent Suite, Ion Reporter and NextGene – to compare their performance and accuracy in the analysis of each sequence variant detected. A cohort of 31 patients was selected for PS (7), PC (13) and AT (11) deficiency based on defined indication criteria. Within these patient groups, a mutation detection rate of 67,7% was observed. In a cohort of 10 patients who were sequenced in a single sequencing run the three evaluated software detected 16, 19, and 27 variants in the PROS1 gen; 17,17, 19 variants in the PROC gene; and 15, 15, 16 variants for the SERPINC1 gene in their baseline settings. For data generated from the Ion Torrent platform, software from the same provider seems to be more suitable, mainly because of the quality of the false positive filtering. For further evaluation of the validity of the software used, it will be necessary to expand the cohort of patient examined.

Druh

D - Stať ve sborníku

CEP obor

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OECD FORD obor

20602 - Medical laboratory technology (including laboratory samples analysis; diagnostic technologies) (Biomaterials to be 2.9 [physical characteristics of living material as related to medical implants, devices, sensors])

Projekt

—

Návaznosti

I - Institucionalni podpora na dlouhodoby koncepcni rozvoj vyzkumne organizace

Rok uplatnění

2023

Kód důvěrnosti údajů

S - Úplné a pravdivé údaje o projektu nepodléhají ochraně podle zvláštních právních předpisů

Název statě ve sborníku

Bioinformatics and Biomedical Engineering

ISBN

978-3-031-34959-1

ISSN

0302-9743

e-ISSN

1611-3349

Počet stran výsledku

7

Strana od-do

456-462

Název nakladatele

Springer Cham

Místo vydání

Cham

Místo konání akce

Meloneras

Datum konání akce

12. 7. 2023

Typ akce podle státní příslušnosti

WRD - Celosvětová akce

Kód UT WoS článku

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