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Parkinsons 2016
December 05-07, 2016
Volume 6 Issue 6(Suppl) J Alzheimers Dis Parkinsonism
ISSN: 2161-0460 JADP, an open access journal
conferenceseries .com
December 05-07, 2016 Phoenix, USA
2nd International Conference on
Parkinson’s Disease & Movement Disorders
Radek Vodicka et al., J Alzheimers Dis Parkinsonism 2016, 6:6(Suppl)
Next generation sequencing data analysis evaluation in patients with Parkinsonism from genetically
isolated population
Radek Vodicka1, Radek Vrtel1, Katerina Mensikova1, Petr Kanovsky1, Iva Dolinova2, Kristyna Kolarikova1 and Martin Prochazka1
1Palacky University, Czech Republic
2Technical University of Liberec, Czech Republic
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 and 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 parallel
by Torrent Suite/Ion Reporter and NextGene software. Variants were than filtered using following parameters: AQ>20; Read
coverage >20; MAF<0,01; SIFT: 0 - 0,05 and/or PolyPhen-2: 0,2 -1. 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 explanation of genetic background of Parkinsonism.
Biography
Radek Vodicka obtained his degree in Biology from the Faculty of Science, Masaryk University, Brno, Czech Republic, specializing in Genetics and Molecular
Biology. He joined the DNA laboratory of the Department of Medical Genetics and Foetal Medicine, the University Hospital, Olomouc, where he obtained a post-
graduate qualification in the Laboratory Method of Medical Genetics (2002). He defended his PhD thesis ‘Y-chromosomal sequences in Turner syndrome patients’
in 2003 and habilitated in 2013. His main research and clinical interest is a quantitative analysis of Human DNA sequences in relation to genetic diseases, infertility
and cancerogensis.