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

Radek Vodicka, Radek Vrtel, Katerina Mensikova, Petr Kanovsky, Iva Dolinova, Kristyna Kolarikova, Martin Prochazka

GCB, Vol. 3, No. 3 (2017): e44


Abstract


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 “bam” to “vcf” 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 1/1p/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.

Keywords


Parkinsonism; Next Generation Sequencing; LRRK2 gene; MAPT gene; HTRA2 gene

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DOI: http://dx.doi.org/10.18547/gcb.2017.vol3.iss3.e44

Copyright (c) 2017 Radek Vodicka, Kristyna Kolarikova, Radek Vrtel, Katerina Mensikova, Petr Kanovsky, Iva Dolinova, Martin Prochazka

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