High-Throughput Sequencing Haplotype Analysis Indicates in <i>LRRK2</i> Gene a Potential Risk Factor for Endemic Parkinsonism in Southeastern Moravia, Czech Republic
Parkinson’s disease and parkinsonism are relatively common neurodegenerative disorders. This study aimed to assess potential genetic risk factors of haplotypes in genes associated with parkinsonism in a population in which endemic parkinsonism and atypical parkinsonism have recently been found. The...
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MDPI AG
2022-01-01
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| Series: | Life |
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| Online Access: | https://www.mdpi.com/2075-1729/12/1/121 |
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| author | Kristyna Kolarikova Radek Vodicka Radek Vrtel Julia Stellmachova Martin Prochazka Katerina Mensikova Tereza Bartonikova Tomas Furst Petr Kanovsky Jan Geryk |
| author_facet | Kristyna Kolarikova Radek Vodicka Radek Vrtel Julia Stellmachova Martin Prochazka Katerina Mensikova Tereza Bartonikova Tomas Furst Petr Kanovsky Jan Geryk |
| author_sort | Kristyna Kolarikova |
| collection | DOAJ |
| description | Parkinson’s disease and parkinsonism are relatively common neurodegenerative disorders. This study aimed to assess potential genetic risk factors of haplotypes in genes associated with parkinsonism in a population in which endemic parkinsonism and atypical parkinsonism have recently been found. The genes <i>ADH1C, EIF4G1, FBXO7, GBA, GIGYF2, HTRA2, LRRK2, MAPT, PARK2, PARK7, PINK1 PLA2G6, SNCA, UCHL1,</i> and <i>VPS35</i> were analyzed in 62 patients (P) and 69 age-matched controls from the researched area (C1). Variants were acquired by high-throughput sequencing using Ion Torrent workflow. As another set of controls, the whole genome sequencing data from 100 healthy non-related individuals from the Czech population were used (C2); the results were also compared with the Genome Project data (C3). We observed shared findings of four intron (rs11564187, rs36220738, rs200829235, and rs3789329) and one exon variant (rs33995883) in the <i>LRRK2</i> gene in six patients. A comparison of the C1–C3 groups revealed significant differences in haplotype frequencies between ratio of 2.09 for C1, 1.65 for C2, and 6.3 for C3, and odds ratios of 13.15 for C1, 2.58 for C2, and 7.6 for C3 were estimated. The co-occurrence of five variants in the <i>LRRK2</i> gene (very probably in haplotype) could be an important potential risk factor for the development of parkinsonism, even outside the recently described pedigrees in the researched area where endemic parkinsonism is present. |
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| institution | Directory Open Access Journal |
| issn | 2075-1729 |
| language | English |
| last_indexed | 2024-03-10T01:06:44Z |
| publishDate | 2022-01-01 |
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| series | Life |
| spelling | doaj.art-b5971695dbe7497280991f88cd222b472023-11-23T14:25:22ZengMDPI AGLife2075-17292022-01-0112112110.3390/life12010121High-Throughput Sequencing Haplotype Analysis Indicates in <i>LRRK2</i> Gene a Potential Risk Factor for Endemic Parkinsonism in Southeastern Moravia, Czech RepublicKristyna Kolarikova0Radek Vodicka1Radek Vrtel2Julia Stellmachova3Martin Prochazka4Katerina Mensikova5Tereza Bartonikova6Tomas Furst7Petr Kanovsky8Jan Geryk9Department of Medical Genetics, Faculty of Medicine and Dentistry, Palacky University, 779 00 Olomouc, Czech RepublicDepartment of Medical Genetics, Faculty of Medicine and Dentistry, Palacky University, 779 00 Olomouc, Czech RepublicDepartment of Medical Genetics, Faculty of Medicine and Dentistry, Palacky University, 779 00 Olomouc, Czech RepublicDepartment of Medical Genetics, Faculty of Medicine and Dentistry, Palacky University, 779 00 Olomouc, Czech RepublicDepartment of Medical Genetics, Faculty of Medicine and Dentistry, Palacky University, 779 00 Olomouc, Czech RepublicDepartment of Neurology, Faculty of Medicine and Dentistry, Palacky University, 779 00 Olomouc, Czech RepublicDepartment of Neurology, Faculty of Medicine and Dentistry, Palacky University, 779 00 Olomouc, Czech RepublicDepartment of Mathematical Analysis and Applications of Mathematics, Faculty of Science, Palacky University, 779 00 Olomouc, Czech RepublicDepartment of Neurology, Faculty of Medicine and Dentistry, Palacky University, 779 00 Olomouc, Czech RepublicFirst Faculty of Medicine, Institute of Biology and Medical Genetics, Charles University and General University Hospital in Prague, 128 00 Prague, Czech RepublicParkinson’s disease and parkinsonism are relatively common neurodegenerative disorders. This study aimed to assess potential genetic risk factors of haplotypes in genes associated with parkinsonism in a population in which endemic parkinsonism and atypical parkinsonism have recently been found. The genes <i>ADH1C, EIF4G1, FBXO7, GBA, GIGYF2, HTRA2, LRRK2, MAPT, PARK2, PARK7, PINK1 PLA2G6, SNCA, UCHL1,</i> and <i>VPS35</i> were analyzed in 62 patients (P) and 69 age-matched controls from the researched area (C1). Variants were acquired by high-throughput sequencing using Ion Torrent workflow. As another set of controls, the whole genome sequencing data from 100 healthy non-related individuals from the Czech population were used (C2); the results were also compared with the Genome Project data (C3). We observed shared findings of four intron (rs11564187, rs36220738, rs200829235, and rs3789329) and one exon variant (rs33995883) in the <i>LRRK2</i> gene in six patients. A comparison of the C1–C3 groups revealed significant differences in haplotype frequencies between ratio of 2.09 for C1, 1.65 for C2, and 6.3 for C3, and odds ratios of 13.15 for C1, 2.58 for C2, and 7.6 for C3 were estimated. The co-occurrence of five variants in the <i>LRRK2</i> gene (very probably in haplotype) could be an important potential risk factor for the development of parkinsonism, even outside the recently described pedigrees in the researched area where endemic parkinsonism is present.https://www.mdpi.com/2075-1729/12/1/121Parkinson’s diseaseatypical Parkinson syndrome<i>LRRK2</i> genehaplotypehigh-throughput sequencing |
| spellingShingle | Kristyna Kolarikova Radek Vodicka Radek Vrtel Julia Stellmachova Martin Prochazka Katerina Mensikova Tereza Bartonikova Tomas Furst Petr Kanovsky Jan Geryk High-Throughput Sequencing Haplotype Analysis Indicates in <i>LRRK2</i> Gene a Potential Risk Factor for Endemic Parkinsonism in Southeastern Moravia, Czech Republic Life Parkinson’s disease atypical Parkinson syndrome <i>LRRK2</i> gene haplotype high-throughput sequencing |
| title | High-Throughput Sequencing Haplotype Analysis Indicates in <i>LRRK2</i> Gene a Potential Risk Factor for Endemic Parkinsonism in Southeastern Moravia, Czech Republic |
| title_full | High-Throughput Sequencing Haplotype Analysis Indicates in <i>LRRK2</i> Gene a Potential Risk Factor for Endemic Parkinsonism in Southeastern Moravia, Czech Republic |
| title_fullStr | High-Throughput Sequencing Haplotype Analysis Indicates in <i>LRRK2</i> Gene a Potential Risk Factor for Endemic Parkinsonism in Southeastern Moravia, Czech Republic |
| title_full_unstemmed | High-Throughput Sequencing Haplotype Analysis Indicates in <i>LRRK2</i> Gene a Potential Risk Factor for Endemic Parkinsonism in Southeastern Moravia, Czech Republic |
| title_short | High-Throughput Sequencing Haplotype Analysis Indicates in <i>LRRK2</i> Gene a Potential Risk Factor for Endemic Parkinsonism in Southeastern Moravia, Czech Republic |
| title_sort | high throughput sequencing haplotype analysis indicates in i lrrk2 i gene a potential risk factor for endemic parkinsonism in southeastern moravia czech republic |
| topic | Parkinson’s disease atypical Parkinson syndrome <i>LRRK2</i> gene haplotype high-throughput sequencing |
| url | https://www.mdpi.com/2075-1729/12/1/121 |
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