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Kušíková K, Šoltýsová A, Ficek A, Feichtinger RG, Mayr JA, Škopková M, Gašperíková D, Kolníková M, Ornig K, Kalev O, Weis S, Weis D. Prognostic Value of Genotype-Phenotype Correlations in X-Linked Myotubular Myopathy and the Use of the Face2Gene Application as an Effective Non-Invasive Diagnostic Tool. Genes (Basel) 2023; 14:2174. [PMID: 38136996 PMCID: PMC10742680 DOI: 10.3390/genes14122174] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2023] [Revised: 11/27/2023] [Accepted: 11/29/2023] [Indexed: 12/24/2023] Open
Abstract
BACKGROUND X-linked myotubular myopathy (XLMTM) is a rare congenital myopathy resulting from dysfunction of the protein myotubularin encoded by the MTM1 gene. XLMTM has a high neonatal and infantile mortality rate due to a severe myopathic phenotype and respiratory failure. However, in a minority of XLMTM cases, patients present with milder phenotypes and achieve ambulation and adulthood. Notable facial dysmorphia is also present. METHODS We investigated the genotype-phenotype correlations in newly diagnosed XLMTM patients in a patients' cohort (previously published data plus three novel variants, n = 414). Based on the facial gestalt difference between XLMTM patients and unaffected controls, we investigated the use of the Face2Gene application. RESULTS Significant associations between severe phenotype and truncating variants (p < 0.001), frameshift variants (p < 0.001), nonsense variants (p = 0.006), and in/del variants (p = 0.036) were present. Missense variants were significantly associated with the mild and moderate phenotype (p < 0.001). The Face2Gene application showed a significant difference between XLMTM patients and unaffected controls (p = 0.001). CONCLUSIONS Using genotype-phenotype correlations could predict the disease course in most XLMTM patients, but still with limitations. The Face2Gene application seems to be a practical, non-invasive diagnostic approach in XLMTM using the correct algorithm.
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Affiliation(s)
- Katarína Kušíková
- Department of Pediatric Neurology, Faculty of Medicine, Comenius University Bratislava and National Institute of Children’s Diseases, 83340 Bratislava, Slovakia; (K.K.)
| | - Andrea Šoltýsová
- Department of Molecular Biology, Faculty of Natural Sciences, Comenius University, 84215 Bratislava, Slovakia
- Institute for Clinical and Translational Research, Biomedical Research Center, Slovak Academy of Sciences, 84505 Bratislava, Slovakia
| | - Andrej Ficek
- Department of Molecular Biology, Faculty of Natural Sciences, Comenius University, 84215 Bratislava, Slovakia
| | - René G. Feichtinger
- University Children’s Hospital, SalzburgerLandeskliniken (SALK), Paracelsus Medical University Salzburg, 5020 Salzburg, Austria; (R.G.F.)
| | - Johannes A. Mayr
- University Children’s Hospital, SalzburgerLandeskliniken (SALK), Paracelsus Medical University Salzburg, 5020 Salzburg, Austria; (R.G.F.)
| | - Martina Škopková
- Department of Metabolic Disorders, Institute of Experimental Endocrinology, Biomedical Research Center, Slovak Academy of Science, 84505 Bratislava, Slovakia
| | - Daniela Gašperíková
- Department of Metabolic Disorders, Institute of Experimental Endocrinology, Biomedical Research Center, Slovak Academy of Science, 84505 Bratislava, Slovakia
| | - Miriam Kolníková
- Department of Pediatric Neurology, Faculty of Medicine, Comenius University Bratislava and National Institute of Children’s Diseases, 83340 Bratislava, Slovakia; (K.K.)
| | - Karoline Ornig
- Division of Neuropathology, Department of Pathology and Molecular Pathology, Neuromed Campus, Kepler University Hospital, Johannes Kepler University, 4020 Linz, Austria
| | - Ognian Kalev
- Division of Neuropathology, Department of Pathology and Molecular Pathology, Neuromed Campus, Kepler University Hospital, Johannes Kepler University, 4020 Linz, Austria
| | - Serge Weis
- Division of Neuropathology, Department of Pathology and Molecular Pathology, Neuromed Campus, Kepler University Hospital, Johannes Kepler University, 4020 Linz, Austria
| | - Denisa Weis
- Department of Medical Genetics, Kepler University Hospital Med Campus IV, Johannes Kepler University, 4020 Linz, Austria
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Hulinkova I, Medova V, Soltysova A, Dobsinska V, Ficek A, Ciznar P. Severe congenital T-lymphocytopenia may affect the outcome of neonatal intensive care. Biomed Pap Med Fac Univ Palacky Olomouc Czech Repub 2023. [PMID: 37431618 DOI: 10.5507/bp.2023.028] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/12/2023] Open
Abstract
AIM Circular DNA segments TREC (T-cell receptor excision circles) formed during T-lymphocyte maturation in the thymus, are a sensitive marker of thymic lymphocyte production in a broader manner. Quantification using qPCR is proposed as a surrogate marker of T cell malfunction in various primary and secondary conditions in a non-SCID selected risk newborn population. METHODS We collected 207 dry blood spot samples during the years 2015-2018, from newly admitted risk newborns. TREC values calculated per 106 cells were determined and a cut-off values of 5th percentile was set. The positive control group consisted of patients (n=13) with genetically confirmed SCID. RESULTS The median TREC value was 34,591.56 (18,074.08-60,228.58) for girls resp. 28,391.20 (13,835.01-51,835.93) per 106 cells for boys, P=0.046. Neonates born by C-section have been found to have higher TREC levels compared to neonates born by spontaneous delivery (P=0.018). In the group of preterm newborns (n=104), 3.8% had TREC value < 5th percentile, half of them died due to sepsis as opposed to no fatalities in preterm newborns with sepsis and TREC value > 5th percentile. In the group of term newborns (n=103) 9 children (8.7%) had TREC < 5th percentile, half of them were treated for asphyxia, with no fatal complications. CONCLUSION TREC levels calculated for the 5th percentile of a risk neonatal group is suggested as a surrogate marker for increased risk of fatal septic complication. Early recognition of these newborns within a risk scoring system using TREC levels could lead to potentially lifesaving interventions.
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Affiliation(s)
- Ivana Hulinkova
- Department of Paediatrics, Faculty of Medicine, Comenius University and National Institute of Children's Diseases, Bratislava, Slovak Republic
| | - Veronika Medova
- Institute for Clinical and Translational Research, Biomedical Research Centre, Slovak Academy of Sciences, Bratislava, Slovak Republic
| | - Andrea Soltysova
- Institute for Clinical and Translational Research, Biomedical Research Centre, Slovak Academy of Sciences, Bratislava, Slovak Republic
- Department of Molecular Biology, Faculty of Natural Sciences, Comenius University, Bratislava, Slovak Republic
| | - Veronika Dobsinska
- Department of Paediatric Haematology and Oncology, Bone Marrow Transplantation Unit, Faculty of Medicine, Comenius University and National Institute of Children's Diseases, Bratislava, Slovak Republic
| | - Andrej Ficek
- Department of Molecular Biology, Faculty of Natural Sciences, Comenius University, Bratislava, Slovak Republic
| | - Peter Ciznar
- Department of Paediatrics, Faculty of Medicine, Comenius University and National Institute of Children's Diseases, Bratislava, Slovak Republic
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Soltysova A, Dvorska D, Kajabova VH, Pecimonova M, Cepcekova K, Ficek A, Demkova L, Buocikova V, Babal P, Juras I, Janikova K, Kasubova I, Samec M, Brany D, Lyskova D, Valaskova J, Dankova Z, Smolkova B, Furdova A. Uncovering accurate prognostic markers for high-risk uveal melanoma through DNA methylation profiling. Clin Transl Med 2023; 13:e1317. [PMID: 37478301 PMCID: PMC10361544 DOI: 10.1002/ctm2.1317] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2023] [Revised: 06/13/2023] [Accepted: 06/19/2023] [Indexed: 07/23/2023] Open
Affiliation(s)
- Andrea Soltysova
- Department of Molecular Biology, Faculty of Natural Sciences, Comenius University in Bratislava, Bratislava, Slovakia
- Institute for Clinical and Translational Research, Biomedical Research Center, Slovak Academy of Sciences, Bratislava, Slovakia
| | - Dana Dvorska
- Biomedical Centre Martin, Jessenius Faculty of Medicine in Martin, Comenius University in Bratislava, Martin, Slovakia
| | - Viera Horvathova Kajabova
- Department of Molecular Oncology, Cancer Research Institute, Biomedical Research Center of the Slovak Academy of Sciences, Bratislava, Slovakia
| | - Martina Pecimonova
- Department of Molecular Biology, Faculty of Natural Sciences, Comenius University in Bratislava, Bratislava, Slovakia
| | - Klaudia Cepcekova
- Department of Molecular Biology, Faculty of Natural Sciences, Comenius University in Bratislava, Bratislava, Slovakia
| | - Andrej Ficek
- Department of Molecular Biology, Faculty of Natural Sciences, Comenius University in Bratislava, Bratislava, Slovakia
| | - Lucia Demkova
- Department of Molecular Oncology, Cancer Research Institute, Biomedical Research Center of the Slovak Academy of Sciences, Bratislava, Slovakia
| | - Verona Buocikova
- Department of Molecular Oncology, Cancer Research Institute, Biomedical Research Center of the Slovak Academy of Sciences, Bratislava, Slovakia
| | - Pavel Babal
- Department of Pathology, Faculty of Medicine, Comenius University in Bratislava, Bratislava, Slovakia
| | | | - Katarina Janikova
- Biomedical Centre Martin, Jessenius Faculty of Medicine in Martin, Comenius University in Bratislava, Martin, Slovakia
| | - Ivana Kasubova
- Biomedical Centre Martin, Jessenius Faculty of Medicine in Martin, Comenius University in Bratislava, Martin, Slovakia
| | - Marek Samec
- Department of Pathophysiology, Jessenius Faculty of Medicine in Martin, Comenius University in Bratislava, Martin, Slovakia
| | - Dusan Brany
- Biomedical Centre Martin, Jessenius Faculty of Medicine in Martin, Comenius University in Bratislava, Martin, Slovakia
| | - Darina Lyskova
- Department of Ophthalmology, Faculty of Medicine, Comenius University in Bratislava, Bratislava, Slovakia
| | - Jela Valaskova
- Department of Ophthalmology, Faculty of Medicine, Comenius University in Bratislava, Bratislava, Slovakia
| | - Zuzana Dankova
- Biomedical Centre Martin, Jessenius Faculty of Medicine in Martin, Comenius University in Bratislava, Martin, Slovakia
| | - Bozena Smolkova
- Department of Molecular Oncology, Cancer Research Institute, Biomedical Research Center of the Slovak Academy of Sciences, Bratislava, Slovakia
| | - Alena Furdova
- Department of Pathophysiology, Jessenius Faculty of Medicine in Martin, Comenius University in Bratislava, Martin, Slovakia
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Medova V, Hulinkova I, Laiferova N, Urdova V, Ciznar P, Dolnikova D, Krasnanova V, Fabri O, Ficek A, Soltysova A. The importance of defining the age-specific TREC/KREC levels for detection of various inborn errors of immunity in pediatric and adult patients. Clin Immunol 2022; 245:109155. [DOI: 10.1016/j.clim.2022.109155] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2022] [Revised: 10/01/2022] [Accepted: 10/07/2022] [Indexed: 11/26/2022]
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Krivoňáková N, Šoltýsová A, Tamáš M, Takáč Z, Krahulec J, Ficek A, Gál M, Gall M, Fehér M, Krivjanská A, Horáková I, Belišová N, Bímová P, Škulcová AB, Mackuľak T. Mathematical modeling based on RT-qPCR analysis of SARS-CoV-2 in wastewater as a tool for epidemiology. Sci Rep 2021; 11:19456. [PMID: 34593871 PMCID: PMC8484274 DOI: 10.1038/s41598-021-98653-x] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2021] [Accepted: 09/09/2021] [Indexed: 02/06/2023] Open
Abstract
Coronavirus disease 2019 (COVID-19) pandemic caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) emerges to scientific research and monitoring of wastewaters to predict the spread of the virus in the community. Our study investigated the COVID-19 disease in Bratislava, based on wastewater monitoring from September 2020 until March 2021. Samples were analyzed from two wastewater treatment plants of the city with reaching 0.6 million monitored inhabitants. Obtained results from the wastewater analysis suggest significant statistical dependence. High correlations between the number of viral particles in wastewater and the number of reported positive nasopharyngeal RT-qPCR tests of infected individuals with a time lag of 2 weeks/12 days (R2 = 83.78%/R2 = 52.65%) as well as with a reported number of death cases with a time lag of 4 weeks/27 days (R2 = 83.21%/R2 = 61.89%) was observed. The obtained results and subsequent mathematical modeling will serve in the future as an early warning system for the occurrence of a local site of infection and, at the same time, predict the load on the health system up to two weeks in advance.
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Affiliation(s)
- Naďa Krivoňáková
- Institute of Information Engineering, Automation, and Mathematics, Department of Mathematics, Faculty of Chemical and Food Technology, Slovak University of Technology in Bratislava, Radlinského 9, 812 37, Bratislava, Slovakia
| | - Andrea Šoltýsová
- Department of Molecular Biology, Faculty of Natural Sciences, Comenius University, Ilkovičova 6, 842 15, Bratislava, Slovakia
- Institute for Clinical and Translational Research, Biomedical Research Center, Slovak Academy of Sciences, Dúbravska Cesta 9, 84505, Bratislava, Slovakia
| | - Michal Tamáš
- Department of Environmental Engineering, Faculty of Chemistry and Food Technology, Slovak University of Technology in Bratislava, Radlinského 9, 812 37, Bratislava, Slovak Republic.
| | - Zdenko Takáč
- Institute of Information Engineering, Automation, and Mathematics, Department of Mathematics, Faculty of Chemical and Food Technology, Slovak University of Technology in Bratislava, Radlinského 9, 812 37, Bratislava, Slovakia
| | - Ján Krahulec
- Department of Molecular Biology, Faculty of Natural Sciences, Comenius University, Ilkovičova 6, 842 15, Bratislava, Slovakia
| | - Andrej Ficek
- Department of Molecular Biology, Faculty of Natural Sciences, Comenius University, Ilkovičova 6, 842 15, Bratislava, Slovakia
| | - Miroslav Gál
- Department of Inorganic Technology, Faculty of Chemical and Food Technology, Slovak University of Technology in Bratislava, Radlinského 9, 812 37, Bratislava, Slovakia
| | - Marián Gall
- Institute of Information Engineering, Automation, and Mathematics, Department of Mathematics, Faculty of Chemical and Food Technology, Slovak University of Technology in Bratislava, Radlinského 9, 812 37, Bratislava, Slovakia
| | - Miroslav Fehér
- Department of Environmental Engineering, Faculty of Chemistry and Food Technology, Slovak University of Technology in Bratislava, Radlinského 9, 812 37, Bratislava, Slovak Republic
| | - Anna Krivjanská
- Department of Environmental Engineering, Faculty of Chemistry and Food Technology, Slovak University of Technology in Bratislava, Radlinského 9, 812 37, Bratislava, Slovak Republic
| | - Ivana Horáková
- Department of Environmental Engineering, Faculty of Chemistry and Food Technology, Slovak University of Technology in Bratislava, Radlinského 9, 812 37, Bratislava, Slovak Republic
| | - Noemi Belišová
- Department of Environmental Engineering, Faculty of Chemistry and Food Technology, Slovak University of Technology in Bratislava, Radlinského 9, 812 37, Bratislava, Slovak Republic
| | - Paula Bímová
- Department of Environmental Engineering, Faculty of Chemistry and Food Technology, Slovak University of Technology in Bratislava, Radlinského 9, 812 37, Bratislava, Slovak Republic
| | - Andrea Butor Škulcová
- Department of Environmental Engineering, Faculty of Chemistry and Food Technology, Slovak University of Technology in Bratislava, Radlinského 9, 812 37, Bratislava, Slovak Republic
| | - Tomáš Mackuľak
- Department of Environmental Engineering, Faculty of Chemistry and Food Technology, Slovak University of Technology in Bratislava, Radlinského 9, 812 37, Bratislava, Slovak Republic
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Lundy L, Fatta-Kassinos D, Slobodnik J, Karaolia P, Cirka L, Kreuzinger N, Castiglioni S, Bijlsma L, Dulio V, Deviller G, Lai FY, Alygizakis N, Barneo M, Baz-Lomba JA, Béen F, Cíchová M, Conde-Pérez K, Covaci A, Donner E, Ficek A, Hassard F, Hedström A, Hernandez F, Janská V, Jellison K, Hofman J, Hill K, Hong PY, Kasprzyk-Hordern B, Kolarević S, Krahulec J, Lambropoulou D, de Llanos R, Mackuľak T, Martinez-García L, Martínez F, Medema G, Micsinai A, Myrmel M, Nasser M, Niederstätter H, Nozal L, Oberacher H, Očenášková V, Ogorzaly L, Papadopoulos D, Peinado B, Pitkänen T, Poza M, Rumbo-Feal S, Sánchez MB, Székely AJ, Soltysova A, Thomaidis NS, Vallejo J, van Nuijs A, Ware V, Viklander M. Making Waves: Collaboration in the time of SARS-CoV-2 - rapid development of an international co-operation and wastewater surveillance database to support public health decision-making. Water Res 2021; 199:117167. [PMID: 34015748 PMCID: PMC8060897 DOI: 10.1016/j.watres.2021.117167] [Citation(s) in RCA: 34] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/03/2021] [Revised: 03/24/2021] [Accepted: 04/17/2021] [Indexed: 05/19/2023]
Abstract
The presence of SARS-CoV-2 RNA in wastewater was first reported in March 2020. Over the subsequent months, the potential for wastewater surveillance to contribute to COVID-19 mitigation programmes has been the focus of intense national and international research activities, gaining the attention of policy makers and the public. As a new application of an established methodology, focused collaboration between public health practitioners and wastewater researchers is essential to developing a common understanding on how, when and where the outputs of this non-invasive community-level approach can deliver actionable outcomes for public health authorities. Within this context, the NORMAN SCORE "SARS-CoV-2 in sewage" database provides a platform for rapid, open access data sharing, validated by the uploading of 276 data sets from nine countries to-date. Through offering direct access to underpinning meta-data sets (and describing its use in data interpretation), the NORMAN SCORE database is a resource for the development of recommendations on minimum data requirements for wastewater pathogen surveillance. It is also a tool to engage public health practitioners in discussions on use of the approach, providing an opportunity to build mutual understanding of the demand and supply for data and facilitate the translation of this promising research application into public health practice.
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Affiliation(s)
- Lian Lundy
- DRIZZLE Centre of Excellence, Luleå University of Technology, VA-Teknik, 971 87, Luleå, Sweden.
| | - Despo Fatta-Kassinos
- Department of Civil and Environmental Engineering and Nireas-International Water Research Centre, School of Engineering, University of Cyprus, PO Box 20537, 1678, Nicosia, Cyprus
| | | | - Popi Karaolia
- Department of Civil and Environmental Engineering and Nireas-International Water Research Centre, School of Engineering, University of Cyprus, PO Box 20537, 1678, Nicosia, Cyprus
| | - Lubos Cirka
- Environmental Institute, Okruzna 784/42, 97241, Kos, Slovakia; Faculty of Chemical and Food Technology, Slovak University of Technology in Bratislava, Radlinskeho 9, 81237, Bratislava, Slovakia
| | - Norbert Kreuzinger
- Technische Universität Wien, Institute for Water Quality and Resources Management, Karlsplatz 13/226-1, 1040, Vienna, Austria
| | - Sara Castiglioni
- Istituto di Ricerche Farmacologiche Mario Negri IRCCS, Department of Environmental Sciences, Via Mario Negri 2, 20156, Milan, Italy
| | - Lubertus Bijlsma
- Environmental and Public Health Analytical Chemistry, Research Institute for Pesticides and Water, University Jaume I, Castellón, Spain
| | - Valeria Dulio
- National Institute for Environment and Industrial Risks, Rue Jacques Taffanel, Parc Technologique ALATA, Verneuil-en-Halatte, 60550, France
| | | | - Foon Yin Lai
- Department of Aquatic Sciences and Assessment, Swedish University of Agricultural Sciences (SLU), SE-75007, Uppsala, Sweden
| | - Nikiforos Alygizakis
- Environmental Institute, Okruzna 784/42, 97241, Kos, Slovakia; Laboratory of Analytical Chemistry, Department of Chemistry, National and Kapodistrian University of Athens, Greece
| | - Manuela Barneo
- Unidad Predepartamental de Medicina (Facultad de Salud), Universitat Jaume I, 12071, Castellón, Spain
| | | | - Frederic Béen
- KWR Water Research Institute, Groningenhaven 7, 3430, BB Nieuwegein, The Netherlands
| | - Marianna Cíchová
- Water Research Institute, Nábrežie arm. gen. L. Svobodu 5, 812 49, Bratislava, Slovak Republic
| | - Kelly Conde-Pérez
- Microbiology Service, University Hospital-Biomedical Research Institute-University of A Coruña, Spain
| | - Adrian Covaci
- Toxicological Center, University of Antwerp Universiteitsplein 1, 2610, Wilrijk, Belgium
| | - Erica Donner
- Future Industries Institute (FII), University of South Australia, Building X, University Boulevard, Mawson Lakes, 5095, South Australia, Australia
| | - Andrej Ficek
- Department of Molecular Biology, Faculty of Natural Sciences, Comenius University, Bratislava, Slovakia
| | - Francis Hassard
- School of Water, Energy and Environment, Cranfield University, Cranfield, Bedfordshire MK43 0AL, UK
| | - Annelie Hedström
- DRIZZLE Centre of Excellence, Luleå University of Technology, VA-Teknik, 971 87, Luleå, Sweden
| | - Félix Hernandez
- Environmental and Public Health Analytical Chemistry, Research Institute for Pesticides and Water, University Jaume I, Castellón, Spain
| | - Veronika Janská
- Water Research Institute, Nábrežie arm. gen. L. Svobodu 5, 812 49, Bratislava, Slovak Republic
| | - Kristen Jellison
- Department of Civil and Environmental Engineering, Lehigh University, 1 West Packer Avenue, Bethlehem, PA 18015, USA
| | - Jan Hofman
- University of Bath, Department of Chemical Engineering, Water Innovation and Research Centre, Claverton Down, Bath, BA2 7AY, UK
| | - Kelly Hill
- Water Research Australia Limited | Level 2, 250 Victoria Square / Tarntanyangga Adelaide SA 5000 | GPO Box 1751, Adelaide SA 5001, Australia
| | - Pei-Ying Hong
- Division of Biological and Environmental Science and Engineering, Water Desalination and Reuse Center, King Abdullah University of Science and Technology (KAUST), Thuwal, 23955-6900, Saudi Arabia
| | | | - Stoimir Kolarević
- University of Belgrade, Institute for Biological Research "Siniša Stanković", National Institute of Republic of Serbia, Department for Hydroecology and Water Protection, Bulevar despota Stefana 142, 11000, Belgrade, Serbia
| | - Jan Krahulec
- Department of Molecular Biology, Faculty of Natural Sciences, Comenius University, Bratislava, Slovakia
| | - Dimitra Lambropoulou
- Laboratory of Environmental Pollution Control, Department of Chemistry, Aristotle University of Thessaloniki, GR-541 24, Thessaloniki, Greece; Center for Interdisciplinary Research and Innovation (CIRI-AUTH), Balkan Center, Thessaloniki, GR-57001
| | - Rosa de Llanos
- Unidad Predepartamental de Medicina (Facultad de Salud), Universitat Jaume I, 12071, Castellón, Spain
| | - Tomáš Mackuľak
- Institute of Chemical and Environmental Engineering, Faculty of Chemical and Food Technology, Slovak University of Technology, Radlinského 9, 812 37, Bratislava, Slovakia
| | - Lorena Martinez-García
- IMDEA Water Institute, Science and Technology Campus of the University of Alcalá, Avenida Punto Com 2, 28805, Alcalá de Henares, Spain
| | - Francisco Martínez
- IMDEA Water Institute, Science and Technology Campus of the University of Alcalá, Avenida Punto Com 2, 28805, Alcalá de Henares, Spain
| | - Gertjan Medema
- KWR Water Research Institute, Groningenhaven 7, 3430, BB Nieuwegein, The Netherlands
| | | | - Mette Myrmel
- Norwegian University of Life Sciences, Faculty of Veterinary Medicine, Virology Unit, P.O. Box 8146 Dep., N-0033, Oslo, Norway
| | - Mohammed Nasser
- Microbiology Service, University Hospital-Biomedical Research Institute-University of A Coruña, Spain
| | - Harald Niederstätter
- Institute of Legal Medicine and Core Facility Metabolomics, Medical University of Innsbruck, Muellerstrasse 44, A-6020, Innsbruck, Austria
| | - Leonor Nozal
- Norwegian University of Life Sciences, Faculty of Veterinary Medicine, Virology Unit, P.O. Box 8146 Dep., N-0033, Oslo, Norway
| | - Herbert Oberacher
- Institute of Legal Medicine and Core Facility Metabolomics, Medical University of Innsbruck, Muellerstrasse 44, A-6020, Innsbruck, Austria
| | - Věra Očenášková
- T. G. Masaryk Water Research Institute, p.r.i., Branch of Analysis and Assessment of Environmental Components, Podbabská 2582/30, 160 00, Prague 6, Czech Republic
| | - Leslie Ogorzaly
- Luxembourg Institute of Science and Technology (LIST), Environmental Research & Innovation department, 41 rue du Brill L-4422, Belvaux, Luxembourg
| | - Dimitrios Papadopoulos
- Laboratory of Environmental Pollution Control, Department of Chemistry, Aristotle University of Thessaloniki, GR-541 24, Thessaloniki, Greece
| | - Beatriz Peinado
- IMDEA Water Institute, Science and Technology Campus of the University of Alcalá, Avenida Punto Com 2, 28805, Alcalá de Henares, Spain
| | - Tarja Pitkänen
- Finnish Institute for Health and Welfare, Expert Microbiology Unit, Neulaniementie 4, FI-70701, Kuopio, Finland; University of Helsinki, Faculty of Veterinary Medicine, Dept. Food Hygiene and Environmental Health, Agnes Sjöbergin katu 2, FI-00014, Helsingin yliopisto, Finland
| | - Margarita Poza
- Microbiology Service, University Hospital-Biomedical Research Institute-University of A Coruña, Spain
| | - Soraya Rumbo-Feal
- Microbiology Service, University Hospital-Biomedical Research Institute-University of A Coruña, Spain
| | - Maria Blanca Sánchez
- IMDEA Water Institute, Science and Technology Campus of the University of Alcalá, Avenida Punto Com 2, 28805, Alcalá de Henares, Spain
| | - Anna J Székely
- Evolutionary Biology Centre, Limnology, Uppsala University, Norbyvägen 18 D, SE-752 36, Uppsala, Sweden
| | - Andrea Soltysova
- Department of Molecular Biology, Faculty of Natural Sciences, Comenius University, Bratislava, Slovakia; Institute for Clinical and Translational Research, Biomedical Research Center, Slovak Academy of Sciences, Dubravska Cesta 9, 84505, Bratislava, Slovakia
| | - Nikolaos S Thomaidis
- Laboratory of Analytical Chemistry, Department of Chemistry, National and Kapodistrian University of Athens, Greece
| | - Juan Vallejo
- Microbiology Service, University Hospital-Biomedical Research Institute-University of A Coruña, Spain
| | - Alexander van Nuijs
- Toxicological Center, University of Antwerp Universiteitsplein 1, 2610, Wilrijk, Belgium
| | - Vassie Ware
- Department of Civil and Environmental Engineering, Lehigh University, 1 West Packer Avenue, Bethlehem, PA 18015, USA
| | - Maria Viklander
- DRIZZLE Centre of Excellence, Luleå University of Technology, VA-Teknik, 971 87, Luleå, Sweden
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Kluckova D, Kolnikova M, Medova V, Bognar C, Foltan T, Svecova L, Gnip A, Kadasi L, Soltysova A, Ficek A. Clinical manifestation of CDKL5 deficiency disorder and identified mutations in a cohort of Slovak patients. Epilepsy Res 2021; 176:106699. [PMID: 34229227 DOI: 10.1016/j.eplepsyres.2021.106699] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2021] [Revised: 06/06/2021] [Accepted: 06/17/2021] [Indexed: 11/16/2022]
Abstract
CDKL5 deficiency disorder (CDD) is an independent clinical entity associated with early-onset encephalopathy, which is often considered the type of epileptic encephalopathy with CDKL5 mutation also found in children diagnosed with early-onset seizure (Hanefeld) type of Rett syndrome, epileptic spasms, West syndrome, Lennox-Gastaut syndrome, or autism. Since early seizure onset is a prominent feature, in this study, a cohort of 54 unrelated patients consisting of 26 males and 28 females was selected for CDKL5 screening, with seizures presented before 12 months of age being the only clinical criterion. Five patients were found to have pathogenic or likely pathogenic variants in CDKL5 while 1 was found to have a variant of uncertain significance (p.L522V). Although CDKL5 variants are more frequently identified in female patients, we identified three male and three female patients (11.1 %, 6/54) in this study. Missense variant with unknown inheritance (p.L522V), de novo missense variant (p.E60 K), two de novo splicing (IVS15 + 1G > A, IVS16 + 2 T > A), and one de novo nonsense variant p.W125* were identified using Sanger sequencing. Whole exome analysis approach revealed de novo frameshift variant c.1247_1248delAG in a mosaic form in one of the males. Patient clinical features are reviewed and compared to those previously described in related literature. Variable clinical features were presented in CDKL5 positive patients characterised in this study. In addition to more common features, such as early epileptic seizures, severe intellectual disability, and gross motor impairment, inappropriate laughing/screaming spells and hypotonia appeared at the age of 1 year in all patients, regardless of the type of CDKL5 mutation or sex. All three CDKL5 positive males from our cohort were initially diagnosed with West syndrome, which suggests that the CDKL5 gene mutations are a significant cause of West syndrome phenotype, and also indicate the overlapping characteristics of these two clinical entities.
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Affiliation(s)
- Daniela Kluckova
- Department of Molecular Biology, Faculty of Natural Sciences, Comenius University, Ilkovicova 6, Bratislava, 842 15, Slovakia
| | - Miriam Kolnikova
- Department of Paediatric Neurology, Faculty of Medicine, Comenius University and National Institute of Children's Diseases, Limbova 1, 833 40, Bratislava, Slovakia
| | - Veronika Medova
- Institute for Clinical and Translational Research, Biomedical Research Centre, Slovak Academy of Sciences, Dubravska cesta 9, 845 05, Bratislava, Slovakia
| | - Csaba Bognar
- Department of Molecular Biology, Faculty of Natural Sciences, Comenius University, Ilkovicova 6, Bratislava, 842 15, Slovakia
| | - Tomas Foltan
- Department of Paediatric Neurology, Faculty of Medicine, Comenius University and National Institute of Children's Diseases, Limbova 1, 833 40, Bratislava, Slovakia
| | - Lucia Svecova
- Department of Paediatric Neurology, Faculty of Medicine, Comenius University and National Institute of Children's Diseases, Limbova 1, 833 40, Bratislava, Slovakia
| | - Andrej Gnip
- Medirex a.s., MEDIREX GROUP, Holubyho 35, 902 01, Pezinok, Slovakia
| | - Ludevit Kadasi
- Department of Molecular Biology, Faculty of Natural Sciences, Comenius University, Ilkovicova 6, Bratislava, 842 15, Slovakia; Institute for Clinical and Translational Research, Biomedical Research Centre, Slovak Academy of Sciences, Dubravska cesta 9, 845 05, Bratislava, Slovakia
| | - Andrea Soltysova
- Department of Molecular Biology, Faculty of Natural Sciences, Comenius University, Ilkovicova 6, Bratislava, 842 15, Slovakia; Institute for Clinical and Translational Research, Biomedical Research Centre, Slovak Academy of Sciences, Dubravska cesta 9, 845 05, Bratislava, Slovakia
| | - Andrej Ficek
- Department of Molecular Biology, Faculty of Natural Sciences, Comenius University, Ilkovicova 6, Bratislava, 842 15, Slovakia.
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Kluckova D, Kolnikova M, Lacinova L, Jurkovicova-Tarabova B, Foltan T, Demko V, Kadasi L, Ficek A, Soltysova A. A Study among the Genotype, Functional Alternations, and Phenotype of 9 SCN1A Mutations in Epilepsy Patients. Sci Rep 2020; 10:10288. [PMID: 32581296 PMCID: PMC7314844 DOI: 10.1038/s41598-020-67215-y] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2020] [Accepted: 05/26/2020] [Indexed: 12/14/2022] Open
Abstract
Mutations in the voltage-gated sodium channel Nav1.1 (SCN1A) are linked to various epileptic phenotypes with different severities, however, the consequences of newly identified SCN1A variants on patient phenotype is uncertain so far. The functional impact of nine SCN1A variants, including five novel variants identified in this study, was studied using whole-cell patch-clamp recordings measurement of mutant Nav1.1 channels expressed in HEK293T mammalian cells. E78X, W384X, E1587K, and R1596C channels failed to produce measurable sodium currents, indicating complete loss of channel function. E788K and M909K variants resulted in partial loss of function by exhibiting reduced current density, depolarizing shifts of the activation and hyperpolarizing shifts of the inactivation curves, and slower recovery from inactivation. Hyperpolarizing shifts of the activation and inactivation curves were observed in D249E channels along with slower recovery from inactivation. Slower recovery from inactivation was observed in E78D and T1934I with reduced current density in T1934I channels. Various functional effects were observed with the lack of sodium current being mainly associated with severe phenotypes and milder symptoms with less damaging channel alteration. In vitro functional analysis is thus fundamental for elucidation of the molecular mechanisms of epilepsy, to guide patients' treatment, and finally indicate misdiagnosis of SCN1A related epilepsies.
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Affiliation(s)
- Daniela Kluckova
- Department of Molecular Biology, Faculty of Natural Sciences, Comenius University, Ilkovicova 6, Bratislava, 842 15, Slovakia
| | - Miriam Kolnikova
- Department of Pediatric Neurology, Comenius University Medical School and National Institute of Children's Diseases, Limbova 1, Bratislava, 833 40, Slovakia
| | - Lubica Lacinova
- Center of Biosciences, Institute of Molecular Physiology and Genetics, Slovak Academy of Sciences, Dubravská cesta 9, Bratislava, 840 05, Slovakia
| | - Bohumila Jurkovicova-Tarabova
- Center of Biosciences, Institute of Molecular Physiology and Genetics, Slovak Academy of Sciences, Dubravská cesta 9, Bratislava, 840 05, Slovakia
| | - Tomas Foltan
- Department of Pediatric Neurology, Comenius University Medical School and National Institute of Children's Diseases, Limbova 1, Bratislava, 833 40, Slovakia
| | - Viktor Demko
- Department of Plant Physiology, Faculty of Natural Sciences, Comenius University, Ilkovicova 6, Bratislava, 842 15, Slovakia
| | - Ludevit Kadasi
- Department of Molecular Biology, Faculty of Natural Sciences, Comenius University, Ilkovicova 6, Bratislava, 842 15, Slovakia.,Institute for Clinical and Translational Research, Biomedical Research Center, Slovak Academy of Sciences, Dubravska cesta 9, 845 05, Bratislava, Slovakia
| | - Andrej Ficek
- Department of Molecular Biology, Faculty of Natural Sciences, Comenius University, Ilkovicova 6, Bratislava, 842 15, Slovakia
| | - Andrea Soltysova
- Department of Molecular Biology, Faculty of Natural Sciences, Comenius University, Ilkovicova 6, Bratislava, 842 15, Slovakia. .,Institute for Clinical and Translational Research, Biomedical Research Center, Slovak Academy of Sciences, Dubravska cesta 9, 845 05, Bratislava, Slovakia.
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Budiš J, Kucharík M, Ďuriš F, Gazdarica J, Zrubcová M, Ficek A, Szemes T, Brejová B, Radvanszky J. Dante: genotyping of known complex and expanded short tandem repeats. Bioinformatics 2020; 35:1310-1317. [PMID: 30203023 DOI: 10.1093/bioinformatics/bty791] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2018] [Revised: 08/23/2018] [Accepted: 09/06/2018] [Indexed: 01/31/2023] Open
Abstract
MOTIVATION Short tandem repeats (STRs) are stretches of repetitive DNA in which short sequences, typically made of 2-6 nucleotides, are repeated several times. Since STRs have many important biological roles and also belong to the most polymorphic parts of the human genome, they became utilized in several molecular-genetic applications. Precise genotyping of STR alleles, therefore, was of high relevance during the last decades. Despite this, massively parallel sequencing (MPS) still lacks the analysis methods to fully utilize the information value of STRs in genome scale assays. RESULTS We propose an alignment-free algorithm, called Dante, for genotyping and characterization of STR alleles at user-specified known loci based on sequence reads originating from STR loci of interest. The method accounts for natural deviations from the expected sequence, such as variation in the repeat count, sequencing errors, ambiguous bases and complex loci containing several different motifs. In addition, we implemented a correction for copy number defects caused by the polymerase induced stutter effect as well as a prediction of STR expansions that, according to the conventional view, cannot be fully captured by inherently short MPS reads. We tested Dante on simulated datasets and on datasets obtained by targeted sequencing of protein coding parts of thousands of selected clinically relevant genes. In both these datasets, Dante outperformed HipSTR and GATK genotyping tools. Furthermore, Dante was able to predict allele expansions in all tested clinical cases. AVAILABILITY AND IMPLEMENTATION Dante is open source software, freely available for download at https://github.com/jbudis/dante. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Jaroslav Budiš
- Department of Computer Science, Faculty of Mathematics, Physics and Informatics, Comenius University in Bratislava, Bratislava, Slovakia
- Geneton Ltd., Bratislava, Slovakia
- Slovak Centre of Scientific and Technical Information, Bratislava, Slovakia
| | | | - František Ďuriš
- Geneton Ltd., Bratislava, Slovakia
- Slovak Centre of Scientific and Technical Information, Bratislava, Slovakia
| | - Juraj Gazdarica
- Geneton Ltd., Bratislava, Slovakia
- Slovak Centre of Scientific and Technical Information, Bratislava, Slovakia
- Department of Molecular Biology, Faculty of Natural Sciences, Comenius University, Bratislava, Slovakia
| | - Michaela Zrubcová
- Department of Molecular Biology, Faculty of Natural Sciences, Comenius University, Bratislava, Slovakia
| | - Andrej Ficek
- Department of Molecular Biology, Faculty of Natural Sciences, Comenius University, Bratislava, Slovakia
| | - Tomáš Szemes
- Geneton Ltd., Bratislava, Slovakia
- Slovak Centre of Scientific and Technical Information, Bratislava, Slovakia
- Department of Molecular Biology, Faculty of Natural Sciences, Comenius University, Bratislava, Slovakia
| | - Broňa Brejová
- Department of Computer Science, Faculty of Mathematics, Physics and Informatics, Comenius University in Bratislava, Bratislava, Slovakia
| | - Jan Radvanszky
- Geneton Ltd., Bratislava, Slovakia
- Institute for Clinical and Translational Research, Biomedical Research Centre, Slovak Academy of Sciences, Bratislava, Slovakia
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Soltysova A, Tothova Tarova E, Ficek A, Baldovic M, Polakova H, Kayserova H, Kadasi L. Comprehensive genetic study of cystic fibrosis in Slovak patients in 25 years of genetic diagnostics. Clin Respir J 2017; 12:1197-1206. [PMID: 28544683 DOI: 10.1111/crj.12651] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/16/2016] [Revised: 03/25/2017] [Accepted: 05/02/2017] [Indexed: 11/29/2022]
Abstract
INTRODUCTION Cystic fibrosis (CF) has one of the longest histories in hereditary disease molecular diagnostics. However, identification of causative mutations in the CFTR gene is complicated by over 2000 currently identified mutations; with more still being discovered. Knowledge of mutation spectrum may improve effective routine diagnostics and is obligatory in mutation-specific treatment. OBJECTIVES This study presents comprehensive mutation screening of the CFTR gene; with 275 unrelated, clinically confirmed and treated cystic fibrosis (CF) patients diagnosed in 25 years genetic testing in Slovakia. METHODS Detection of the most common CFTR mutations was performed by ELUCIGENE 29 and ELUCIGENE CF EU2 kits. HRM and dHPLC mutation screening methods with subsequent Sanger sequencing were applied for minor mutation screening, and MLPA analysis for deletion/duplication detection. RESULTS A total of 70 different mutations were identified, from which the most common mutation F508del accounted for 60.36% of all disease alleles and 8 mutations have currently been observed only in Slovak patients. Two large deletions identified on chromosomes 2 and 22 were further characterized to identify breakpoints. Based on mutation screening results and neonatal screening we estimated incidence in Slovakian newborns at approximately 1:6000-7000. CONCLUSION In our study, we identified mutations in 98.54% of all disease chromosomes, while 86.54% were identified using ELUCIGENE kits, 0.54% by MLPA analysis and 11.46% by sequencing analysis. Knowledge of the mutation spectrum in genetically diagnosed patients improves possibilities of genetic counseling and cascade screening in the affected families and Slovak population.
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Affiliation(s)
- Andrea Soltysova
- Department of Molecular Biology, Faculty of Natural Sciences, Comenius University, Mlynska dolina Bratislava 842 15, Slovakia.,Institute for Clinical and Translational Research, Biomedical Research Center, Slovak Academy of Sciences, Dubravska cesta 9, Bratislava 845 05, Slovakia.,Institute of Virology, Biomedical Research Center, Slovak Academy of Sciences, Dubravska cesta 9, Bratislava 845 05, Slovakia
| | - Eva Tothova Tarova
- Department of Molecular Biology, Faculty of Natural Sciences, Comenius University, Mlynska dolina Bratislava 842 15, Slovakia
| | - Andrej Ficek
- Department of Molecular Biology, Faculty of Natural Sciences, Comenius University, Mlynska dolina Bratislava 842 15, Slovakia
| | - Marian Baldovic
- Department of Molecular Biology, Faculty of Natural Sciences, Comenius University, Mlynska dolina Bratislava 842 15, Slovakia
| | - Helena Polakova
- Institute for Clinical and Translational Research, Biomedical Research Center, Slovak Academy of Sciences, Dubravska cesta 9, Bratislava 845 05, Slovakia
| | - Hana Kayserova
- Center for Cystic Fibrosis, Department of Pediatric Pneumology Slovak Medical University, Krajinska 91, Bratislava 825 56, Slovakia
| | - Ludevit Kadasi
- Department of Molecular Biology, Faculty of Natural Sciences, Comenius University, Mlynska dolina Bratislava 842 15, Slovakia.,Institute for Clinical and Translational Research, Biomedical Research Center, Slovak Academy of Sciences, Dubravska cesta 9, Bratislava 845 05, Slovakia.,Institute of Virology, Biomedical Research Center, Slovak Academy of Sciences, Dubravska cesta 9, Bratislava 845 05, Slovakia
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Ficek A, Soltysova A, Tarova ET, Baldovic M, Kayserova H, Radasi L. 7 Twenty-five years' experience in genetic testing of cystic fibrosis in Slovakia – update on mutation spectrum. J Cyst Fibros 2016. [DOI: 10.1016/s1569-1993(16)30247-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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Surovy M, Soltysova A, Kolnikova M, Sykora P, Ilencikova D, Ficek A, Radvanszky J, Kadasi L. Novel SCN1A variants in Dravet syndrome and evaluating a wide approach of patient selection. Gen Physiol Biophys 2016; 35:333-42. [PMID: 27045673 DOI: 10.4149/gpb_2016002] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2015] [Accepted: 01/18/2016] [Indexed: 11/08/2022]
Abstract
Voltage-gated sodium channels are essential for generation and propagation of the action potential mainly in nerve and muscle cells. Causative variants in SCN1A gene which codes the main, pore-forming subunit of the channel expressed in central nervous system are associated predominantly with Dravet syndrome (DS), as well as with generalized epilepsy with febrile seizures plus (GEFS+) making it one of the most significant epilepsy gene. Our goal was to determine whether SCN1A screening is relevant in patients with a broad range of epileptic syndromes. 52 patients diagnosed with DS, generalized epilepsy with GEFS+ or similar types of epileptic syndromes were included. Sequencing of the protein coding parts of the gene complemented with MLPA analysis was carried out. One already described nonsense variant, four novel protein truncating variants and a deletion encompassing the whole SCN1A gene were revealed, all in heterozygous state. All identified variants were found in DS patients with 85.7% sensitivity, thus supporting the role of profound SCN1A gene variants in etiology of DS phenotype. No causative variants were identified in any of non-DS epileptic patients in our cohort, suggesting a minor, but not irrelevant role for SCN1A in patients with other types of childhood epilepsy.
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Affiliation(s)
- Milan Surovy
- Department of Molecular Biology, Faculty of Natural Sciences, Comenius University, Mlynska dolina Bratislava, 842 15 Slovak Republic.
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Mašindová I, Šoltýsová A, Varga L, Mátyás P, Ficek A, Hučková M, Sůrová M, Šafka-Brožková D, Anwar S, Bene J, Straka S, Janicsek I, Ahmed ZM, Seeman P, Melegh B, Profant M, Klimeš I, Riazuddin S, Kádasi Ľ, Gašperíková D. MARVELD2 (DFNB49) mutations in the hearing impaired Central European Roma population--prevalence, clinical impact and the common origin. PLoS One 2015; 10:e0124232. [PMID: 25885414 PMCID: PMC4401708 DOI: 10.1371/journal.pone.0124232] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2014] [Accepted: 02/27/2015] [Indexed: 01/26/2023] Open
Abstract
Background In the present study we aimed: 1) To establish the prevalence and clinical impact of DFNB49 mutations in deaf Roma from 2 Central European countries (Slovakia and Hungary), and 2) to analyze a possible common origin of the c.1331+2T>C mutation among Roma and Pakistani mutation carriers identified in the present and previous studies. Methods We sequenced 6 exons of the MARVELD2 gene in a group of 143 unrelated hearing impaired Slovak Roma patients. Simultaneously, we used RFLP to detect the c.1331+2T>C mutation in 85 Hungarian deaf Roma patients, control groups of 702 normal hearing Romanies from both countries and 375 hearing impaired Slovak Caucasians. We analyzed the haplotype using 21 SNPs spanning a 5.34Mb around the mutation c.1331+2T>C. Results One pathogenic mutation (c.1331+2T>C) was identified in 12 homozygous hearing impaired Roma patients. Allele frequency of this mutation was higher in Hungarian (10%) than in Slovak (3.85%) Roma patients. The identified common haplotype in Roma patients was defined by 18 SNP markers (3.89 Mb). Fourteen common SNPs were also shared among Pakistani and Roma homozygotes. Biallelic mutation carriers suffered from prelingual bilateral moderate to profound sensorineural hearing loss. Conclusions We demonstrate different frequencies of the c.1331+2T>C mutation in hearing impaired Romanies from 3 Central European countries. In addition, our results provide support for the hypothesis of a possible common ancestor of the Slovak, Hungarian and Czech Roma as well as Pakistani deaf patients. Testing for the c.1331+2T>C mutation may be recommended in GJB2 negative Roma cases with early-onset sensorineural hearing loss.
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Affiliation(s)
- Ivica Mašindová
- Laboratory of Diabetes and Metabolic Disorders & DIABGENE, Institute of Experimental Endocrinology, Slovak Academy of Sciences, Bratislava, Slovakia
| | - Andrea Šoltýsová
- Department of Molecular Biology, Faculty of Natural Sciences, Comenius University, Bratislava, Slovakia
- Institute of Molecular Physiology and Genetics, Slovak Academy of Sciences, Bratislava, Slovakia
| | - Lukáš Varga
- Laboratory of Diabetes and Metabolic Disorders & DIABGENE, Institute of Experimental Endocrinology, Slovak Academy of Sciences, Bratislava, Slovakia
- Department of Otorhinolaryngology—Head and Neck Surgery, Faculty of Medicine and University Hospital, Comenius University, Bratislava, Slovakia
| | - Petra Mátyás
- Department of Medical Genetics, University of Pécs, Clinical Centre, Pécs, Hungary
| | - Andrej Ficek
- Department of Molecular Biology, Faculty of Natural Sciences, Comenius University, Bratislava, Slovakia
| | - Miloslava Hučková
- Laboratory of Diabetes and Metabolic Disorders & DIABGENE, Institute of Experimental Endocrinology, Slovak Academy of Sciences, Bratislava, Slovakia
- Center for Molecular Medicine, Slovak Academy of Sciences, Bratislava, Slovakia
| | - Martina Sůrová
- Laboratory of Diabetes and Metabolic Disorders & DIABGENE, Institute of Experimental Endocrinology, Slovak Academy of Sciences, Bratislava, Slovakia
| | - Dana Šafka-Brožková
- DNA Laboratory, Department of Paediatric Neurology, Charles University 2nd Medical School and University Hospital Motol, Prague, Czech Republic
| | - Saima Anwar
- Department of Otorhinolaryngology Head & Neck Surgery, School of Medicine, University of Maryland, Baltimore, Maryland, United States of America
| | - Judit Bene
- Department of Medical Genetics, University of Pécs, Clinical Centre, Pécs, Hungary
- Szentagothai Research Centre, University of Pécs, Pécs, Hungary
| | - Slavomír Straka
- Department of Otorhinolaryngology—Head and Neck Surgery, Faculty Hospital of J. A. Reiman, Prešov, Slovakia
| | - Ingrid Janicsek
- Department of Medical Genetics, University of Pécs, Clinical Centre, Pécs, Hungary
| | - Zubair M. Ahmed
- Department of Otorhinolaryngology Head & Neck Surgery, School of Medicine, University of Maryland, Baltimore, Maryland, United States of America
| | - Pavel Seeman
- DNA Laboratory, Department of Paediatric Neurology, Charles University 2nd Medical School and University Hospital Motol, Prague, Czech Republic
| | - Béla Melegh
- Department of Medical Genetics, University of Pécs, Clinical Centre, Pécs, Hungary
- Szentagothai Research Centre, University of Pécs, Pécs, Hungary
| | - Milan Profant
- Department of Otorhinolaryngology—Head and Neck Surgery, Faculty of Medicine and University Hospital, Comenius University, Bratislava, Slovakia
| | - Iwar Klimeš
- Laboratory of Diabetes and Metabolic Disorders & DIABGENE, Institute of Experimental Endocrinology, Slovak Academy of Sciences, Bratislava, Slovakia
| | - Saima Riazuddin
- Department of Otorhinolaryngology Head & Neck Surgery, School of Medicine, University of Maryland, Baltimore, Maryland, United States of America
| | - Ľudevít Kádasi
- Department of Molecular Biology, Faculty of Natural Sciences, Comenius University, Bratislava, Slovakia
- Institute of Molecular Physiology and Genetics, Slovak Academy of Sciences, Bratislava, Slovakia
| | - Daniela Gašperíková
- Laboratory of Diabetes and Metabolic Disorders & DIABGENE, Institute of Experimental Endocrinology, Slovak Academy of Sciences, Bratislava, Slovakia
- Center for Molecular Medicine, Slovak Academy of Sciences, Bratislava, Slovakia
- * E-mail:
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Ondreičková K, Mihálik D, Ficek A, Hudcovicová M, Kraic J, Drahovská H. Impact of Genetically Modified Maize on the Genetic Diversity of Rhizosphere Bacteria: a Two-Year Study in Slovakia. Polish Journal of Ecology 2014. [DOI: 10.3161/104.062.0107] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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Polak E, Ficek A, Radvanszky J, Soltysova A, Urge O, Cmelova E, Kantarska D, Kadasi L. Phenylalanine hydroxylase deficiency in the Slovak population: genotype-phenotype correlations and genotype-based predictions of BH4-responsiveness. Gene 2013; 526:347-55. [PMID: 23764561 DOI: 10.1016/j.gene.2013.05.057] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2013] [Revised: 05/08/2013] [Accepted: 05/20/2013] [Indexed: 10/26/2022]
Abstract
We investigated the mutation spectrum of the phenylalanine hydroxylase gene (PAH) in a cohort of patients from 135 Slovak PKU families. Mutational screening of the known coding region, including conventional intron splice sites, was performed using high-resolution melting analysis, with subsequent sequencing analysis of the samples showing deviated melting profiles compared to control samples. The PAH gene was also screened for deletions and duplications using MLPA analysis. Forty-eight different disease causing mutations were identified in our patient group, including 30 missense, 8 splicing, 7 nonsense, 2 large deletions and 1 small deletion with frameshift; giving a detection rate of 97.6%. The most prevalent mutation was the p.R408W, occurring in 47% of all alleles, which concurs with results from neighboring and other Slavic countries. Other frequent mutations were: p.R158Q (5.3%), IVS12+1G>A (5.3%), p.R252W (5.1%), p.R261Q (3.9%) and p.A403V (3.6%). We also identified three novel missense mutations: p.F233I, p.R270I, p.F331S and one novel variant: c.-30A>T in the proximal part of the PAH gene promoter. A spectrum of 84 different genotypes was observed and a genotype based predictions of BH4-responsiveness were assessed. Among all genotypes, 36 were predicted to be BH4-responsive represented by 51 PKU families. In addition, genotype-phenotype correlations were performed.
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Affiliation(s)
- Emil Polak
- Comenius University, Faculty of Natural Sciences, Department of Molecular Biology, Mlynska Dolina, 842 15 Bratislava, Slovak Republic.
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Celec P, Tretinárová D, Minárik G, Ficek A, Szemes T, Lakatošová S, Schmidtová E, Turňa J, Kádaši Ľ, Ostatníková D. Genetic polymorphisms related to testosterone metabolism in intellectually gifted boys. PLoS One 2013; 8:e54751. [PMID: 23382957 PMCID: PMC3559825 DOI: 10.1371/journal.pone.0054751] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2012] [Accepted: 12/18/2012] [Indexed: 12/31/2022] Open
Abstract
Prepubertal testosterone levels are lower in intellectually gifted boys. The aim of this pilot study was to analyze potential genetic factors related to testosterone metabolism in control and gifted boys. Intellectually gifted (IQ>130; n = 95) and control (n = 67) boys were genotyped. Polymorphisms of interests were chosen in genes including androgen and estrogen receptors, 5-alpha reductase, aromatase and sex hormone binding globulin. Significant differences between control and gifted boys in genotype distributions were found for ESR2 (rs928554) and SHBG (rs1799941). A significantly lower number of CAG repeats in the AR gene were found in gifted boys. Our results support the role of genetic factors related to testosterone metabolism in intellectual giftedness. Increased androgen signaling might explain previous results of lower testosterone levels in intellectually gifted boys and add to the understanding of variability in cognitive abilities.
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Affiliation(s)
- Peter Celec
- Institute of Molecular Biomedicine, Comenius University, Bratislava, Slovak Republic.
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Radvansky J, Ficek A, Kadasi L. Upgrading molecular diagnostics of myotonic dystrophies: Multiplexing for simultaneous characterization of the DMPK and ZNF9 repeat motifs. Mol Cell Probes 2011; 25:182-5. [PMID: 21550396 DOI: 10.1016/j.mcp.2011.04.006] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2011] [Revised: 04/26/2011] [Accepted: 04/26/2011] [Indexed: 01/12/2023]
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18
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Abstract
Myotonic dystrophy type 1 (DM1) and type 2 (DM2) are the most common autosomal dominant neuromuscular disorders in adults. DM1 is caused by an unstable expansion of the (CTG)(n) repeat tract in the DMPK gene, whereas DM2 is caused by an unstable expansion of the (CCTG)(n) repeat tract in the ZNF9 gene. The (CCTG)(n) repeat is a part of a complex repetitive motif (TG)(n)(TCTG)(n)(CCTG)(n), in which each of the elements is highly polymorphic. Repeat-primed polymerase chain reaction (PCR) is a commonly used technique for the determination of the presence or absence of the expanded alleles in both DM1 and DM2. Besides the expansion detection, it can be used for the determination of the repeat structure (repeat number, presence of interruptions, and their localization) in healthy-range alleles. Because the (CCTG)(n) part of the motif in DM2 is generally interrupted with other sequences, "tetraplet" repeat-primed PCR (TP-PCR) results interpretation is more complicated than for DM1. Most of the studies, published so far, used TP-PCR in a direction such that they amplified through the (TG)(n)(TCTG)(n) part of the motif. We compared the features of TP-PCR performed in the commonly used direction with the results obtained by TP-PCR performed in the opposite direction. Our results suggest that the direction that does not include the (TG)(n)(TCTG)(n) tract leads to better quality and more informative results in comparison with the direction containing the (TG)(n)(TCTG)(n) tract.
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Affiliation(s)
- Jan Radvansky
- Department of Molecular Biology, Faculty of Natural Sciences, Comenius University, Bratislava, Slovakia.
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19
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Abstract
Autism is one of the most genetically influenced neuropsychiatric disorders. However, its detailed genetic basis is far from being clear. Genome-wide association studies have revealed a number of candidate genes, mostly related to synaptogenesis and various neuroendocrine pathways. In our study we have focused on oxytocin (OT), oxytocin receptor (OXTR), GABA receptor gamma 3 (GABRG3), neuroligin (NLGN4X), and reelin (RELN). After signed consent, 90 autistic boys and 85 healthy controls were enrolled in the study. Polymorphisms of OT (rs2740204), OXTR (rs2228485), GABRG3 (rs28431127), and NLGN4X (rs5916338) were analyzed using restriction fragment length polymorphism. (GGC)n STR polymorphism in the 5' UTR of the RELN gene was genotyped using fragment analysis. The only significant association in autistic boys in Slovakia was found with higher number of GGC repeats in the RELN gene (P=0.001) potentially explaining lower RELN levels in blood and brain of autistic patients.
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Affiliation(s)
- Silvia Kelemenova
- Institute of Physiology, Faculty of Medicine, Comenius University, Bratislava, Slovakia.
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20
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Soltysova A, Ficek A, Baldovic M, Kolesar P, Minarik G, Kadasi L, Polakova H, Kayserova H. Mutation analysis of CFTR gene in Slovak CF patients. J Cyst Fibros 2009. [DOI: 10.1016/s1569-1993(09)60037-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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21
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Celec P, Ostatníková D, Holešová Z, Minárik G, Ficek A, Kelemenová S, Putz Z, Kúdela M. Spatial Abilities in Prepubertal Intellectually Gifted Boys and Genetic Polymorphisms Related to Testosterone Metabolism. J PSYCHOPHYSIOL 2009. [DOI: 10.1027/0269-8803.23.1.1] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
Spatial abilities are known to be related to testosterone levels in men. Polymorphisms of genes related to androgen metabolism, however, have not been previously analyzed in association with spatial abilities. Our study analyzes genetic polymorphisms of androgen receptor (AR), aromatase (CYP19), and 5-alpha reductase (SRD5A2) in relation to mental rotation and spatial visualization in prepubertal intellectually gifted boys. DNA samples of 36 boys with an average age of 10.0 ± 0.7 years and an IQ higher than 130 were isolated from buccal cells in saliva. DNA was subsequently used for amplification by PCR. The CYP19 C1558-T polymorphism and SRD5A2 A49T polymorphism were determined by RFLP analysis, and the AR (CAG)n polymorphism was determined by fragment analysis. Salivary testosterone levels were measured with radioimmunoassay. Spatial abilities (mental rotation and spatial visualization) were assessed using standard psychometric tests. AR and CYP19 polymorphisms were not associated with spatial abilities. Heterozygotes in A49T polymorphisms (AT) of SRD5A2 had significantly better results in both mental rotation and spatial visualization tests compared to AA homozygotes. TT homozygotes were not found. The T allele of A49T polymorphism of the SRD5A2 was reported to have a 5-fold increased activity in comparison to the A allele. AT heterozygotes outscored AA homozygotes in tests of spatial performance. Since dihydrotestosterone – the product of 5-alpha reductase catalyzed reaction – has a higher affinity to AR, this might indicate a potential molecular mechanism for the influence of SRD5A2 polymorphism on spatial abilities in intellectually gifted prepubertal boys.
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Affiliation(s)
- Peter Celec
- Institute of Pathophysiology, Faculty of Medicine, Comenius University, Bratislava, Slovak Republic
- Department of Molecular Biology, Faculty of Natural Sciences, Comenius University, Bratislava, Slovak Republic
| | - Daniela Ostatníková
- Institute of Physiology, Faculty of Medicine, Comenius University, Bratislava, Slovak Republic
| | - Zuzana Holešová
- Department of Genetics, Faculty of Natural Sciences, Comenius University, Bratislava, Slovak Republic
| | - Gabriel Minárik
- Department of Molecular Biology, Faculty of Natural Sciences, Comenius University, Bratislava, Slovak Republic
- Institute of Molecular Physiology and Genetics, Slovak Academy of Sciences, Bratislava, Slovak Republic
| | - Andrej Ficek
- Department of Molecular Biology, Faculty of Natural Sciences, Comenius University, Bratislava, Slovak Republic
- Institute of Molecular Physiology and Genetics, Slovak Academy of Sciences, Bratislava, Slovak Republic
| | - Silvia Kelemenová
- Institute of Physiology, Faculty of Medicine, Comenius University, Bratislava, Slovak Republic
| | - Zdeněk Putz
- National Institute of Endocrinology and Diabetology, L’ubochňa, Slovak Republic
| | - Matúš Kúdela
- Department of Zoology, Faculty of Natural Sciences, Comenius University, Bratislava, Slovak Republic
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22
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Soltyszewski I, Plocienniczak A, Fabricius HA, Kornienko I, Vodolazhsky D, Parson W, Hradil R, Schmitter H, Ivanov P, Kuzniar P, Malyarchuk BA, Grzybowski T, Woźniak M, Henke J, Henke L, Olkhovets S, Voitenko V, Lagus V, Ficek A, Minárik G, de Knijff P, Rebała K, Wysocka J, Kapińska E, Cybulska L, Mikulich AI, Tsybovsky IS, Szczerkowska Z, Krajewski P, Ploski R. Analysis of forensically used autosomal short tandem repeat markers in Polish and neighboring populations. Forensic Sci Int Genet 2008; 2:205-11. [PMID: 19083822 DOI: 10.1016/j.fsigen.2008.02.003] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2007] [Revised: 02/02/2008] [Accepted: 02/13/2008] [Indexed: 11/28/2022]
Abstract
The purpose of this study was to evaluate the homogeneity of Polish populations with respect to STRs chosen as core markers of the Polish Forensic National DNA Intelligence Database, and to provide reference allele frequencies and to explore the genetic interrelationship between Poland and neighboring countries. The allele frequency distribution of 10 STRs included in the SGMplus kit was analyzed among 2176 unrelated individuals from 6 regional Polish populations and among 4321 individuals from Germany (three samples), Austria, The Netherlands, Sweden, Czech Republic, Slovakia, Belarus, Ukraine and the Russian Federation (six samples). The statistical approach consisted of AMOVA, calculation of pairwise Rst values and analysis by multidimensional scaling. We found homogeneity of present day Poland and consistent differences between Polish and German populations which contrasted with relative similarities between Russian and German populations. These discrepancies between genetic and geographic distances were confirmed by analysis of an independent data set on Y chromosome STRs. Migrations of Goths, Viking influences, German settlements in the region of Volga river and/or forced population resettlements and other events related to World War II are the historic events which might have caused these finding.
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Affiliation(s)
- Ireneusz Soltyszewski
- University of Varmia and Mazury, Department of Criminalistics and Forensic Medicine, Olsztyn, Poland
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23
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Kolesár P, Minárik G, Baldovic M, Ficek A, Kovács L, Kádasi L. Mutation analysis of the CFTR gene in Slovak cystic fibrosis patients by DHPLC and subsequent sequencing: identification of four novel mutations. Gen Physiol Biophys 2008; 27:299-305. [PMID: 19202204] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Abstract
Cystic fibrosis (CF) is the most common lethal autosomal recessive disorder in Caucasians. Its incidence is approximately 1:2500 newborns. CF is caused by mutations in the transmembrane conductance regulator (CFTR) gene, which encodes an important chloride ion channel. The disease affects the respiratory, digestive and reproductive systems. To date more than 1550 mutations and polymorphisms have been identified throughout the CFTR gene, making the DNA diagnosis more difficult. Rapid accurate identification of CFTR gene mutations is important for confirming the clinical diagnosis, for cascade screening in families at risk for CF, for understanding the correlation between genotype and phenotype, and moreover it is also the only means for prenatal diagnosis. Individuals suspect of CF are in Slovakia presently screened for the presence of 30 common mutations, giving mutation detection rate only approximately 48%. To increase the detection rate we applied a gene scanning approach using DHPLC system for analysing specifically all CFTR exons. The fragments showing abnormal elution profiles were subsequently sequenced to characterize the DNA change. We have identified a total of 28 different mutations up to present not found in Slovak CF patients, and 17 different polymorphisms. Four mutations (G437D, H954P, H1375N, and 3120+33G>T) are novel, not yet found in any other CF patient all over the word.
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Affiliation(s)
- Peter Kolesár
- Department of Molecular Biology, Faculty of Natural Science, Comenius University, Bratislava, Slovakia
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24
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Etzler J, Peyrl A, Zatkova A, Schildhaus HU, Ficek A, Merkelbach-Bruse S, Kratz C, Attarbaschi A, Hainfellner J, Yao S, Messiaen L, Slavc I, Wimmer K. RNA-based mutation analysis identifies an unusual MSH6 splicing defect and circumvents PMS2 pseudogene interference. Hum Mutat 2008; 29:299-305. [DOI: 10.1002/humu.20657] [Citation(s) in RCA: 59] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
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25
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Zmetáková I, Ferák V, Minárik G, Ficek A, Poláková H, Feráková E, Kádasi L. Identification of the deletions in the UGT1A1 gene of the patients with Crigler-Najjar syndrome type I from Slovakia. Gen Physiol Biophys 2007; 26:306-310. [PMID: 18281749] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/25/2023]
Abstract
Crigler-Najjar syndrome type I (CN I) is a rare autosomal recessive disorder due to hepatic dysfunction of uridine diphospho-glucuronosyltransferase (UGT) activity toward bilirubin. Complete inactivation of this enzyme causing CN I lead to accumulation of unconjugated bilirubin in serum and bile. Here we report the results of the molecular characterization of the uridine diphospho-glucuronosyltransferase 1A1 (UGT1A1) gene in a consanguineous family of Slovak Roms and an unrelated non-Romany family with CN I. Sequence analysis of UGT1A1 gene in all four Romany patients showed mutation in exon 4, a deletion of an A at codon 407 (1220delA), not yet described in homozygous status. All analysed patients were homozygous for 1220delA mutation and their 3 healthy sibs were heterozygous. The non-Romany patient was a compound heterozygote for two different deletions, 1220delA and 717-718delAG at codon 239. In the family of his cousin a son was born affected with CN I, who was homozygote for 717-718delAG mutation. His other niece affected with CN II was heterozygote for mutation 717-718delAG but homozygote for TA insertion and enhancer substitution T-3279G. Haplotype analysis suggests that the 1220delA mutation is identical by descent in both families, though they originate from two ethnically different populations (Slovaks vs. Roms).
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Affiliation(s)
- I Zmetáková
- Department of Molecular Biology, Faculty of Natural Sciences, Comenius University, Mlynská dolina B2-210, 842 15 Bratislava, Slovakia.
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26
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Poláková H, Katrincsáková B, Minárik G, Feráková E, Ficek A, Baldovic M, Kádasi L. Detection of His1069Gln mutation in Wilson disease by bidirectional PCR amplification of specific alleles (BI-PASA) test. Gen Physiol Biophys 2007; 26:91-6. [PMID: 17660582] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/16/2023]
Abstract
Wilson disease (WD) is an autosomal recessive disorder of hepatic copper metabolism caused by mutations in a gene encoding a copper-transporting P-type ATPase, ATP7B. The majority of known mutations affecting this gene are frequent in different populations, which may help to introduce rapid diagnostic procedures based on direct DNA analysis into routine clinical practise. The His1069Gln mutation in exon 14 is the most frequent one, accounting for 30-60% of all mutations in Caucasian patients. The aim of the present work was to introduce DNA-based direct analysis into routine molecular screening for the above mutation in Slovak WD patients and to assess its frequency in patients as well as in a control population. Twenty seven clinicaly diagnosed patients from twenty five families, twenty relatives of index patients and three hundred and six control DNA samples were tested using two different DNA-based methods: the earlier described amplification created restriction site (ACRS) for Alw21I in combination with nested PCR and the amplification refractory mutation system (ARMS). In 18 of 25 unrelated patients (72%), the mentioned genetic defect was present in at least one copy. In ten of them (40%), the above mutation was detected in homozygous and in eight individuals (32%) in heterozygous state. In seven WD patients (28%), this mutation was not detected. The allele frequency of His1069Gln in Slovak patients with WD was 56%, which was higher as reported in other populations. In a control group of 306 random DNA samples (612 alleles), the His1069Gln mutation was observed in 3 samples (carrier frequency 1%; allele frequency 0.49%). These frequencies correspond to figures observed in different population of European origin. Taken together, we have provided further evidence that the His1069Gln mutation is the prevalent ATP7B mutation in central-european WD patients. Although both methods used in this study worked in our hands reliably, there are in every-day use some drawbacks and limitations inherent to them (PCR reactions in two tubes, possibility of star activity or not complet digestion by restriction endonuclease, etc.). Therefore we developed a simpler, cost effective and rapid DNA diagnostic test based on bidirectional amplification of specific alleles (BI-PASA), which enables detection of homozygotes (wild and mutant) and heterozygotes, respectivelly, in one PCR reaction. The test was highly sensitive and specific, yielding no false-positive or false-negative results. Its reliability and discriminating power was tested on samples of 27 WD patients and 120 random control DNA's, previously genotyped by above mentioned methods. Comparing results of BI-PASA with ACRS and ARMS tests showed 100% concordance.
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Affiliation(s)
- H Poláková
- Institute of Molecular Physiology and Genetics, Slovak Academy of Sciences, Vlárska 5, 833 34 Bratislava 37, Slovakia.
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27
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Drahovská H, Mikasová E, Szemes T, Ficek A, Sásik M, Majtán V, Turna J. Variability in occurrence of multiple prophage genes in Salmonella Typhimurium strains isolated in Slovak Republic. FEMS Microbiol Lett 2007; 270:237-44. [PMID: 17355601 DOI: 10.1111/j.1574-6968.2007.00674.x] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022] Open
Abstract
Lysogenic bacteriophages are a significant source of variability in closely related Salmonella strains. In this study, screening for diversity of 152 Salmonella Typhimurium strains was performed using PCR detection of selected prophage regions derived from phages P22, Gifsy-1, Gifsy-2, Fels-1, ST104 and SopEPhi. A high degree of variability was observed in the presence of specific genes. Based on the presence of particular prophage genes, we divided strains into 37 different PCR-prophage profiles; 20 of them were represented by only a single strain. Using multilocus variable number tandem repeats analysis (MLVA), 152 Salmonella strains were separated into 82 MLVA strings. Similar grouping of Salmonella strains was observed in the case of PCR-prophage detection and MLVA and the results corresponded well with the phage type of strains. However, several Salmonella strains were detected, which were closely related according to MLVA; yet, they differed in PCR phage profiles. The observations support a view that integration/excision of bacteriophages in Salmonella strains are frequent events shaping the bacterial genome.
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Affiliation(s)
- Hana Drahovská
- Department of Molecular Biology, Faculty of Natural Sciences, Comenius University, Bratislava, Slovakia.
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28
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Minarik G, Ferakova E, Ficek A, Polakova H, Kadasi L. GJB2 gene mutations in Slovak hearing-impaired patients of Caucasian origin: spectrum, frequencies and SNP analysis. Clin Genet 2006; 68:554-7. [PMID: 16283888 DOI: 10.1111/j.1399-0004.2005.00529.x] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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29
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Minárik G, Ferák V, Feráková E, Ficek A, Poláková H, Kádasi L. High frequency of GJB2 mutation W24X among Slovak Romany (Gypsy) patients with non-syndromic hearing loss (NSHL). Gen Physiol Biophys 2003; 22:549-56. [PMID: 15113126] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/29/2023]
Abstract
Mutations in the GJB2 gene (connexin 26) represent a major cause of autosomal recessive non-syndromic hearing loss (NSHL) worldwide. In most Caucasian populations, the 35delG mutation in this gene was found to account for up to 50% of cases of the genetic non-syndromic childhood deafness. In populations of non-European ethnic background, other GJB2 gene mutations are occasionally common, e.g. 167delT in Ashkenazi Jews, R143W in Africaans and 235delC in Koreans. In this work, DNA samples from 54 unrelated NSHL patients from endogamous and inbred population of Slovak Roms (Gypsies) from Eastern Slovakia were screened for GJB2 mutations. The coding region of the GJB2 gene of patients was sequenced and mutations W24X, R127H, V153I, L90P and V37I were found. In Slovak Romany population, mutation W24X accounts for 23.2%, R127H for 19.4%, 35delG for 8.3%, V153I for 3.7%, L90P for 3.7% and V37I for 0.9% of screened chromosomes. As the W24X mutation was previously found in India and Pakistan, were from the European Romanies originate, it was brought by the European Romnanies from their Indian homeland. The carrier frequency of 35delG was estimated for Slovak non-Romany population to be 3.3%, and for Slovak Romany population to 0.88%. The carrier frequency of W24X varied in different Slovak Romany subpopulations from 0.0% up to 26.1%.
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Affiliation(s)
- G Minárik
- Department of Molecular Biology, Comenius University Faculty of Natural Sciences, Mlynská dolina B2-210, 842 15 Bratislava 4, Slovakia.
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30
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Dusinská M, Ficek A, Horská A, Raslová K, Petrovská H, Vallová B, Drlicková M, Wood SG, Stupáková A, Gasparovic J, Bobek P, Nagyová A, Kováciková Z, Blazícek P, Liegebel U, Collins AR. Glutathione S-transferase polymorphisms influence the level of oxidative DNA damage and antioxidant protection in humans. Mutat Res 2001; 482:47-55. [PMID: 11535248 DOI: 10.1016/s0027-5107(01)00209-3] [Citation(s) in RCA: 104] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Glutathione S-transferase genotypes GSTT1, GSTM1, GSTP1 were characterised in 155 middle-aged men and compared with parameters of oxidative stress at the level of DNA and lipids, with antioxidant enzymes, and with plasma antioxidants in smokers and non-smokers. Smokers had on average significantly lower levels of Vitamin C, beta-carotene and beta-cryptoxanthin and higher amounts of oxidised purines and pyrimidines in lymphocyte DNA. The GSTM1 null genotype was associated with elevated glutathione as well as with higher Vitamin C concentration in plasma. Vitamin C was higher in GSTT1+ compared with GSTT1 null--as was glucose-6-phosphate dehydrogenase activity. The homozygous GSTP1 a/a genotype was associated with significantly higher levels of GST activity measured in lymphocytes, in comparison with the b/b genotype. Using multifactorial statistical analysis we found significant associations between smoking, GSTP1 genotype, plasma Vitamin C, and purine base damage in lymphocyte DNA. The difference in Vitamin C plasma levels between smokers and non-smokers was seen only with the GSTP1 b/b genotype. This group accounted also for most of the increase in purine oxidation in smokers. In contrast, the link between smoking and oxidised pyrimidines in DNA was seen only in the GSTT1 null group. It seems that polymorphisms in the phase II metabolising enzyme glutathione S-transferase may be important determinants of commonly measured biomarkers.
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Affiliation(s)
- M Dusinská
- Department of Molecular and Genetic Toxicology, Institute of Preventive and Clinical Medicine, Limbova 14, 83301 Bratislava, Slovak Republic
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