Next Generation Sequencing Data Analysis Evaluation in Patients with Parkinsonism from a Genetically Isolated Population

Kód výsledku v IS VaVaI

<a href="https://www.isvavai.cz/riv?ss=detail&h=RIV%2F61989592%3A15110%2F17%3A73582208" target="_blank" >RIV/61989592:15110/17:73582208 - isvavai.cz</a>

Výsledek na webu

<a href="http://dx.doi.org/10.18547/gcb.2017.vol3.iss3.e44" target="_blank" >http://dx.doi.org/10.18547/gcb.2017.vol3.iss3.e44</a>

DOI - Digital Object Identifier

<a href="http://dx.doi.org/10.18547/gcb.2017.vol3.iss3.e44" target="_blank" >10.18547/gcb.2017.vol3.iss3.e44</a>

Jazyk výsledku

angličtina

Název v původním jazyce

Next Generation Sequencing Data Analysis Evaluation in Patients with Parkinsonism from a Genetically Isolated Population

Popis výsledku v původním jazyce

Parkinson´s disease (PD) can be caused by genetic changes in a lot of genes. The effect of these changes is determined by the nature of the mutation and ranges from weak associations to pathogenic mutation which leads to loss of protein function. Our study is based on epidemiological data which show significantly increased prevalence of PD (2,9 %) in an isolated population of South-Eastern Moravia in the Czech Republic. We compared two different Next Generation Sequencing (NGS) data analysis approaches in DNA from 28 PD patients in the genes responsible for Parkinsonism (ADH1C, ATP13A2, EIF4G1, FBXO7, GBA + GBAP1, GIGYF2, HTRA2, LRRK2, MAPT, PARK2, PARK7, PINK1, PLA2G6, SNCA, UCHL1 and VPS35) using: 1) already described missense rare variants or pathogenic mutations 2) twelve control DNA samples from the same isolated population. Ion Torrent NGS data processing and trimming from Fastaq through &quot;bam&quot; to &quot;vcf&quot; files was done parallely by Torrent Suite/Ion Reporter and NextGENe software. After filtering out, three missense mutations were found in LRRK2 gene: rs33995883 in 6/0 patients/control (p/c); rs33958906 in 1/1 p/c; rs781737269 in 3/0p/c; one missense mutation in MAPT gene rs63750072 in 6/1p/c; and one mutation in HTRA2 gene rs72470545 in 3/1p/c. Both the results from NextGENe with Ion Torrent adaptation and from Ion Reporter significantly correlated in variant calling. Our study may contribute to further explain the genetic background of Parkinsonism.

Název v anglickém jazyce

Next Generation Sequencing Data Analysis Evaluation in Patients with Parkinsonism from a Genetically Isolated Population

Popis výsledku anglicky

Parkinson´s disease (PD) can be caused by genetic changes in a lot of genes. The effect of these changes is determined by the nature of the mutation and ranges from weak associations to pathogenic mutation which leads to loss of protein function. Our study is based on epidemiological data which show significantly increased prevalence of PD (2,9 %) in an isolated population of South-Eastern Moravia in the Czech Republic. We compared two different Next Generation Sequencing (NGS) data analysis approaches in DNA from 28 PD patients in the genes responsible for Parkinsonism (ADH1C, ATP13A2, EIF4G1, FBXO7, GBA + GBAP1, GIGYF2, HTRA2, LRRK2, MAPT, PARK2, PARK7, PINK1, PLA2G6, SNCA, UCHL1 and VPS35) using: 1) already described missense rare variants or pathogenic mutations 2) twelve control DNA samples from the same isolated population. Ion Torrent NGS data processing and trimming from Fastaq through &quot;bam&quot; to &quot;vcf&quot; files was done parallely by Torrent Suite/Ion Reporter and NextGENe software. After filtering out, three missense mutations were found in LRRK2 gene: rs33995883 in 6/0 patients/control (p/c); rs33958906 in 1/1 p/c; rs781737269 in 3/0p/c; one missense mutation in MAPT gene rs63750072 in 6/1p/c; and one mutation in HTRA2 gene rs72470545 in 3/1p/c. Both the results from NextGENe with Ion Torrent adaptation and from Ion Reporter significantly correlated in variant calling. Our study may contribute to further explain the genetic background of Parkinsonism.

Druh

J_ost - Ostatní články v recenzovaných periodicích

CEP obor

—

OECD FORD obor

10603 - Genetics and heredity (medical genetics to be 3)

Projekt

—

Návaznosti

I - Institucionalni podpora na dlouhodoby koncepcni rozvoj vyzkumne organizace

Rok uplatnění

2017

Kód důvěrnosti údajů

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

Název periodika

Genomics and Computational Biology

ISSN

2365-7154

e-ISSN

—

Svazek periodika

3

Číslo periodika v rámci svazku

3

Stát vydavatele periodika

DE - Spolková republika Německo

Počet stran výsledku

6

Strana od-do

1-6

Kód UT WoS článku

—

EID výsledku v databázi Scopus

—