Publications

@article{Kvapilova2024,

title = {Validated WGS and WES protocols proved saliva-derived gDNA as an equivalent to blood-derived gDNA for clinical and population genomic analyses},

author = {K. Kvapilova and P. Misenko and J. Radvanszky and O. Brzon and J. Budis and J. Gazdarica and O. Pos and M. Korabecna and M. Kasny and T. Szemes and P. Kvapil and J. Paces and Z. Kozmik},

url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-85185401063&doi=10.1186%2fs12864-024-10080-0&partnerID=40&md5=005d098ebc4c002ab39a2a6b70f9512d},

doi = {10.1186/s12864-024-10080-0},

issn = {14712164},

year  = {2024},

date = {2024-01-01},

urldate = {2024-01-01},

journal = {BMC Genomics},

volume = {25},

number = {1},

publisher = {BioMed Central Ltd},

abstract = {Background: Whole exome sequencing (WES) and whole genome sequencing (WGS) have become standard methods in human clinical diagnostics as well as in population genomics (POPGEN). Blood-derived genomic DNA (gDNA) is routinely used in the clinical environment. Conversely, many POPGEN studies and commercial tests benefit from easy saliva sampling. Here, we evaluated the quality of variant call sets and the level of genotype concordance of single nucleotide variants (SNVs) and small insertions and deletions (indels) for WES and WGS using paired blood- and saliva-derived gDNA isolates employing genomic reference-based validated protocols. Methods: The genomic reference standard Coriell NA12878 was repeatedly analyzed using optimized WES and WGS protocols, and data calls were compared with the truth dataset published by the Genome in a Bottle Consortium. gDNA was extracted from the paired blood and saliva samples of 10 participants and processed using the same protocols. A comparison of paired blood–saliva call sets was performed in the context of WGS and WES genomic reference-based technical validation results. Results: The quality pattern of called variants obtained from genomic-reference-based technical replicates correlates with data calls of paired blood–saliva-derived samples in all levels of tested examinations despite a higher rate of non-human contamination found in the saliva samples. The F1 score of 10 blood-to-saliva-derived comparisons ranged between 0.8030–0.9998 for SNVs and between 0.8883–0.9991 for small-indels in the case of the WGS protocol, and between 0.8643–0.999 for SNVs and between 0.7781–1.000 for small-indels in the case of the WES protocol. Conclusion: Saliva may be considered an equivalent material to blood for genetic analysis for both WGS and WES under strict protocol conditions. The accuracy of sequencing metrics and variant-detection accuracy is not affected by choosing saliva as the gDNA source instead of blood but much more significantly by the genomic context, variant types, and the sequencing technology used. © The Author(s) 2024.},

keywords = {Single nucleotide variants, Validation},

pubstate = {published},

tppubtype = {article}

}

@article{Cibulka2022,

title = {Alzheimer’s Disease-Associated SNP rs708727 in SLC41A1 May Increase Risk for Parkinson’s Disease: Report from Enlarged Slovak Study},

author = {M. Cibulka and M. Brodnanova and M. Grendar and J. Necpal and J. Benetin and V. Han and E. Kurca and V. Nosal and M. Skorvanek and B. Vesely and A. Stanclova and Z. Lasabova and Z. Pös and T. Szemes and S. Stuchlik and M. Grofik and M. Kolisek},

url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-85123515600&doi=10.3390%2fijms23031604&partnerID=40&md5=009dc372f51fed5ec11f299d743865bc},

doi = {10.3390/ijms23031604},

issn = {16616596},

year  = {2022},

date = {2022-01-01},

urldate = {2022-01-01},

journal = {International Journal of Molecular Sciences},

volume = {23},

number = {3},

publisher = {MDPI},

abstract = {SLC41A1 (A1) SNPs rs11240569 and rs823156 are associated with altered risk for Parkinson’s disease (PD), predominantly in Asian populations, and rs708727 has been linked to Alzheimer’s disease (AD). In this study, we have examined a potential association of the three aforementioned SNPs and of rs9438393, rs56152218, and rs61822602 (all three lying in the A1 promoter region) with PD in the Slovak population. Out of the six tested SNPs, we have identified only rs708727 as being associated with an increased risk for PD onset in Slovaks. The minor allele (A) in rs708727 is associated with PD in dominant and completely over-dominant genetic models (ORD = 1.36 (1.05–1.77)},

keywords = {Single nucleotide variants},

pubstate = {published},

tppubtype = {article}

}

@article{Pecimonova2021e26136,

title = {Admixed phenotype of NEDD4L associated periventricular nodular heterotopia: A case report},

author = {M Pecimonova and J Radvanszky and D Smolak and J Budis and M Lichvar and D Kristinova and I Rozova and J Turna and T Szemes},

url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-85107796467&doi=10.1097%2fMD.0000000000026136&partnerID=40&md5=6d8eac607b0de5b1897c2cee34a64ec9},

doi = {10.1097/MD.0000000000026136},

issn = {15365964},

year  = {2021},

date = {2021-01-01},

urldate = {2021-01-01},

journal = {Medicine},

volume = {100},

number = {22},

pages = {e26136},

publisher = {NLM (Medline)},

abstract = {RATIONALE: Periventricular nodular heterotopia-7 (PVNH7) is a neurodevelopmental disorder associated with improper neuronal migration during neurogenesis in cortex development caused by pathogenic variants in the NEDD4L gene. PATIENT CONCERNS: We report the case of a polystigmatized 2-year-old boy having significant symptomatologic overlap with PVNH7, such as delayed psychomotor and mental development, seizures and infantile spasms, periventricular nodular heterotopia, polymicrogyria, cleft palate, 2 to 3 toe syndactyly, hypotonia, microretrognathia, strabismus, and absent speech and walking. The patient showed also distinct symptoms falling outside PVNH7 symptomatology, also present in the proband's older brother, such as blue sclerae, hydronephrosis, transversal palmar crease (found also in their father), and bilateral talipes equinovarus. In addition, the patient suffered from many other symptoms. DIAGNOSES: The boy, his brother and their parents were subjected to whole-exome sequencing. Because of uncertainties in symptomatology and inheritance pattern, the top-down approach was hard to apply. Using the bottom-up approach, we identified a known pathogenic variant, NM_001144967.2(NEDD4L):c.2677G>A:p.Glu893Lys, in the proband's genome that absented in any other analyzed family member, suggesting its de novo origin. INTERVENTIONS AND OUTCOMES: The patient was treated with Convulex 300 mg/mL for the successful seizure control and Euthyrox 25mg for the treatment of thyroid malfunction. He also took various supplements for the metabolism support and digestion regulation. Moreover, the patient underwent the corrective surgeries of cleft palate and talipes equinovarus. LESSONS: We successfully identified the causative mutation NM_001144967.2(NEDD4L):c.2677G>A:p.Glu893Lys explaining symptoms overlapping those reported for PVNH7. Symptoms shared with the brother were not explained by this variant, since he was not a carrier of the pathogenic NEDD4L variant. These are most likely not extended phenotypes of PVNH7, rather an independent clinical entity caused by a yet unidentified genetic factor in the family, highlighting thus the importance of thorough evaluation of symptomatology and genomic findings in affected and unaffected family members, when such data are available. Copyright © 2021 the Author(s). Published by Wolters Kluwer Health, Inc.},

keywords = {Case study, Genetic testing, Single nucleotide variants, Variant interpretation},

pubstate = {published},

tppubtype = {article}

}

@article{Radvanszky2021,

title = {Characterisation of non-pathogenic premutation-range myotonic dystrophy type 2 alleles},

author = {J Radvanszky and M Hyblova and E Radvanska and P Spalek and A Valachova and G Magyarova and C Bognar and E Polak and T Szemes and L Kadasi},

url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-85114043590&doi=10.3390%2fjcm10173934&partnerID=40&md5=57bc1cfc4be446edf6fbfea3c9ad284a},

doi = {10.3390/jcm10173934},

issn = {20770383},

year  = {2021},

date = {2021-01-01},

urldate = {2021-01-01},

journal = {Journal of Clinical Medicine},

volume = {10},

number = {17},

publisher = {MDPI},

abstract = {Myotonic dystrophy type 2 (DM2) is caused by expansion of a (CCTG)n repeat in the cellular retroviral nucleic acid-binding protein (CNBP) gene. The sequence of the repeat is most commonly interrupted and is stably inherited in the general population. Although expanded alleles, premutation range and, in rare cases, also non-disease associated alleles containing uninterrupted CCTG tracts have been described, the threshold between these categories is poorly characterised. Here, we describe four families with members reporting neuromuscular complaints, in whom we identified altogether nine ambiguous CNBP alleles containing uninterrupted CCTG repeats in the range between 32 and 42 repeats. While these grey-zone alleles are most likely not pathogenic themselves, since other pathogenic mutations were identified and particular family structures did not support their pathogenic role, they were found to be unstable during intergenerational transmission. On the other hand, there was no observable general microsatellite instability in the genome of the carriers of these alleles. Our results further refine the division of CNBP CCTG repeat alleles into two major groups, i.e., interrupted and uninterrupted alleles. Both interrupted and uninterrupted alleles with up to approximately 30 CCTG repeats were shown to be generally stable during intergenerational transmission, while intergenerational as well as somatic instability seems to gradually increase in uninterrupted alleles with tract length growing above this threshold. © 2021 by the authors. Licensee MDPI, Basel, Switzerland.},

keywords = {Non-invasive prenatal testing, Oncology, Single nucleotide variants},

pubstate = {published},

tppubtype = {article}

}

@article{Budis201972,

title = {Non-invasive prenatal testing as a valuable source of population specific allelic frequencies},

author = {J Budis and J Gazdarica and J Radvanszky and M Harsanyova and I Gazdaricova and L Strieskova and R Frno and F Duris and G Minarik and M Sekelska and B Nagy and T Szemes},

url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-85064459936&doi=10.1016%2fj.jbiotec.2019.04.026&partnerID=40&md5=73c18a2081a2ec5ead08247b7543d15b},

doi = {10.1016/j.jbiotec.2019.04.026},

issn = {01681656},

year  = {2019},

date = {2019-01-01},

journal = {Journal of Biotechnology},

volume = {299},

pages = {72-78},

publisher = {Elsevier B.V.},

abstract = {Low-coverage massively parallel genome sequencing for non-invasive prenatal testing (NIPT)of common aneuploidies is one of the most rapidly adopted and relatively low-cost DNA tests. Since aggregation of reads from a large number of samples allows overcoming the problems of extremely low coverage of individual samples, we describe the possible re-use of the data generated during NIPT testing for genome scale population specific frequency determination of small DNA variants, requiring no additional costs except of those for the NIPT test itself. We applied our method to a data set comprising of 1501 original NIPT test results and evaluated the findings on different levels, from in silico population frequency comparisons up to wet lab validation analyses using a gold-standard method based on Sanger sequencing. The revealed high reliability of variant calling and allelic frequency determinations suggest that these NIPT data could serve as valuable alternatives to large scale population studies even for smaller countries around the world. © 2019 Elsevier B.V.},

keywords = {Non-invasive prenatal testing, Population study, Single nucleotide variants, Variant calling},

pubstate = {published},

tppubtype = {article}

}

@article{Kubiritova201964,

title = {On the critical evaluation and confirmation of germline sequence variants identified using massively parallel sequencing},

author = {Z Kubiritova and M Gyuraszova and E Nagyova and M Hyblova and M Harsanyova and J Budis and R Hekel and J Gazdarica and F Duris and L Kadasi and T Szemes and J Radvanszky},

url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-85064435175&doi=10.1016%2fj.jbiotec.2019.04.013&partnerID=40&md5=175358cc48df08933da3da830780ad66},

doi = {10.1016/j.jbiotec.2019.04.013},

issn = {01681656},

year  = {2019},

date = {2019-01-01},

journal = {Journal of Biotechnology},

volume = {298},

pages = {64-75},

publisher = {Elsevier B.V.},

abstract = {Although massively parallel sequencing (MPS) is becoming common practice in both research and routine clinical care, confirmation requirements of identified DNA variants using alternative methods are still topics of debate. When evaluating variants directly from MPS data, different read depth statistics, together with specialized genotype quality scores are, therefore, of high relevance. Here we report results of our validation study performed in two different ways: 1) confirmation of MPS identified variants using Sanger sequencing; and 2) simultaneous Sanger and MPS analysis of exons of selected genes. Detailed examination of false-positive and false-negative findings revealed typical error sources connected to low read depth/coverage, incomplete reference genome, indel realignment problems, as well as microsatellite associated amplification errors leading to base miss-calling. However, all these error types were identifiable with thorough manual revision of aligned reads according to specific patterns of distributions of variants and their corresponding reads. Moreover, our results point to dependence of both basic quantitative metrics (such as total read counts, alternative allele read counts and allelic balance) together with specific genotype quality scores on the used bioinformatics pipeline, stressing thus the need for establishing of specific thresholds for these metrics in each laboratory and for each involved pipeline independently. © 2019 Elsevier B.V.},

keywords = {Genetic testing, Single nucleotide variants, Validation, Variant calling},

pubstate = {published},

tppubtype = {article}

}

@article{Nagyova201946,

title = {Targeted next-generation sequencing in Slovak cardiomyopathy patients},

author = {E Nagyova and J Radvanszky and M Hyblova and V Simovicova and E Goncalvesova and F W Asselbergs and L Kadasi and T Szemes and G Minarik},

url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-85060659545&doi=10.4149%2fBLL_2019_007&partnerID=40&md5=4242fb0c864e6c82fe2565c6cc094102},

doi = {10.4149/BLL_2019_007},

issn = {00069248},

year  = {2019},

date = {2019-01-01},

journal = {Bratislava Medical Journal},

volume = {120},

number = {1},

pages = {46-51},

publisher = {Comenius University},

abstract = {OBJECTIVES: For the first time we used targeted next-generation sequencing to detect candidate pathogenic variants in Slovak cardiomyopathy patients. BACKGROUND: Targeted next-generation sequencing is considered to be the best practice in genetic diagnostics of cardiomyopathies. However, in Slovakia, with high cardiomyopathies prevalence of 1/440, the current diagnostic tests are still based on Sanger sequencing of a few genes. Consequently, little is known about the exact contribution of pathogenic variants in known cardiomyopathy genes in Slovak patients. METHODS: We used a panel of 46 known cardiomyopathy-associated genes to detect genetic variants in 16 Slovak cardiomyopathy patients (6 dilated, 8 hypertrophic, 2 non-compaction subtypes). RESULTS: We identified candidate pathogenic variants in 11 of 16 patients (69 %). Genes with higher count of candidate pathogenic variants were MYBPC3, MYH and TTN, each with 3 different variants. Seven variants ACTC1 (c.329C > T), ANKRD1 (c.683G > T), MYH7 (c.1025C > T), PKP2 (c.2003delA), TTN (c.51655C > T, c.84841G > T, c.101874_101881delAGAATTTG) have been detected for the first time and might represent Slovak- specific genetic cause. CONCLUSIONS: We have performed genetic testing of previously untested Slovak cardiomyopathy patients using next-generation sequencing cardiomyopathy gene panel. Given the high percentage of candidate pathogenic variants it should be recommended to implement this method into routine genetic diagnostic practice in Slovakia. © AEPress s.r.o.},

keywords = {Genetic testing, Single nucleotide variants, Variant calling},

pubstate = {published},

tppubtype = {article}

}

@article{Strieskova20198,

title = {Ultracentrifugation enrichment protocol followed by total RNA sequencing allows assembly of the complete mitochondrial genome},

author = {L Strieskova and I Gazdaricova and M Kajsik and K Soltys and J Budis and O Pos and M Lickova and B Klempa and T Szemes},

url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-85064954323&doi=10.1016%2fj.jbiotec.2019.04.019&partnerID=40&md5=90856f6a0fd40fd7eeaf877edfdbdeb3},

doi = {10.1016/j.jbiotec.2019.04.019},

issn = {01681656},

year  = {2019},

date = {2019-01-01},

journal = {Journal of Biotechnology},

volume = {299},

pages = {8-12},

publisher = {Elsevier B.V.},

abstract = {The mitochondrial genome is an independent genetic system in each eukaryotic cell outside the nuclear genome. Mitochondrial DNA (mtDNA) appears in high copy number within one cell, unlike nuclear DNA, which exists in two copies. But nevertheless, mtDNA represent only small part of total cellular DNA what causes problematic analysis and identification of relevant mutations. While most researchers tend to overlook it because of its small size, the mitochondrial genome contains genes that are essential for cellular energetics and survival. Because of the increased awareness on the importance of metabolism and bioenergetics in a wide variety of human diseases, more and more mtDNA studies were performed. Mitochondrial genome research has established the connection between mtDNA and a wide variety of diseases such as cancer or neurodegenerative disorders. At the present time, several methods are known, that allow sequencing of mtDNA. However, genomic analysis is often complicated due to the low content of mtDNA compared to nuclear DNA. For this reason, we have designed a new approach to obtaining the genomic mitochondrial sequence. We chose RNA based sequencing. Since human mtDNA does not contain introns, the reconstruction of whole mitochondrial genome through RNA sequencing seems to be effective. Our method is based on total RNA sequencing coupled with simple ultracentrifugation protocol and de novo assembly. Following our protocol, we were able to assemble a complete mammalian mitochondrial genome with a length of 16,505 bp and an average coverage of 156. The method is a relatively simple and inexpensive which could help in the further research or diagnostics of mtDNA-based diseases. © 2019 Elsevier B.V.},

keywords = {Assembly, Mitochondria, Single nucleotide variants, Transcriptomics},

pubstate = {published},

tppubtype = {article}

}

@article{Radvanszky2017339,

title = {Complex phenotypes blur conventional borders between Say–Barber–Biesecker–Young–Simpson syndrome and genitopatellar syndrome},

author = {J Radvanszky and M Hyblova and D Durovcikova and M Hikkelova and E Fiedler and L Kadasi and J Turna and G Minarik and T Szemes},

url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-84989325626&doi=10.1111%2fcge.12840&partnerID=40&md5=f3981a3dbb893dceec013f830ecf68f6},

doi = {10.1111/cge.12840},

issn = {00099163},

year  = {2017},

date = {2017-01-01},

journal = {Clinical Genetics},

volume = {91},

number = {2},

pages = {339-343},

publisher = {Blackwell Publishing Ltd},

abstract = {Say–Barber–Biesecker–Young–Simpson syndrome (SBBYSS) and genitopatellar syndrome (GTPTS) are clinically similar disorders with some overlapping features. Although they are currently considered to be distinct clinical entities, both were found to be caused by de novo truncating sequence variants in the KAT6B (lysine acetyltransferase 6B) gene, strongly suggesting that they are allelic disorders. Herein, we report the clinical and genetic findings in a girl presenting with a serious multiple congenital anomaly syndrome with phenotypic features overlapping both SBBYSS and GTPTS; pointing out that the clinical distinction between these disorders is not exact and there do exist patients, in whom conventional clinical classification is problematic. Genetic analyses revealed a truncating c.4592delA (p.Asn1531Thrfs*18) variant in the last KAT6B exon. Our findings support that phenotypes associated with typical KAT6B disease-causing variants should be referred to as ‘KAT6B spectrum disorders’ or ‘KAT6B related disorders’, rather than their current SBBYSS and GTPTS classification. © 2016 John Wiley & Sons A/S. Published by John Wiley & Sons Ltd},

keywords = {Case study, Genetic testing, Single nucleotide variants, Variant calling},

pubstate = {published},

tppubtype = {article}

}

@article{Radvánszky2015418,

title = {Interpretation of clinical significance of sequence variants in molecular genetics [Interpretácia klinického významu sekvenčných variantov v molekulovej genetike]},

author = {J Radvánszky and G Minárik and T Szemeš and M Konečný and L Kádaši},

url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-85020271195&partnerID=40&md5=bf647ff52f306470833ee835a42d012b},

issn = {04574214},

year  = {2015},

date = {2015-01-01},

journal = {Lekarsky Obzor},

volume = {64},

number = {11},

pages = {418-427},

publisher = {Slovenska zdravotnicka univerzita},

abstract = {By applications of genomic analyses we are able to get an enormous number of different sequence variants in each analysed individual. From these only a small, although constantly growing, number of variants are already known and well characterised, while the majority of them are yet not characterised unknown variants. Their correct classification and interpretation are key factors for the understanding and usage of their informational value in clinical practice. Consistent education of professional staff able to handle, interpret and transfer the generated data to clinical workflow represents therefore a very important factor of professional practice. This article summarizes different recommendations for the evaluation and interpretation of sequence variants, from their correct nomenclature up to assigning them certain clinically relevant significance.},

keywords = {Genetic testing, Review, Single nucleotide variants, Variant interpretation},

pubstate = {published},

tppubtype = {article}

}

@article{Minárik2013539,

title = {Spectrum of mutations in gastrointestinal stromal tumor patients - a population-based study from Slovakia},

author = {G Minárik and L Plank and Z Lasabová and T Szemes and T Burjanivová and P Szépe and V Buzalková and D Porubský and J Šufliarsky},

url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-84878263424&doi=10.1111%2fapm.12019&partnerID=40&md5=dbaf848510fcae4f4e67f5505c875199},

doi = {10.1111/apm.12019},

issn = {09034641},

year  = {2013},

date = {2013-01-01},

journal = {APMIS},

volume = {121},

number = {6},

pages = {539-548},

abstract = {Gastrointestinal stromal tumors (GISTs) are the most common mesenchymal neoplasms of gastrointestinal tract and are characterized by presence of mutations in tyrosine kinases cKIT (KIT) and PDGFRα (PDGFRA). Mutations identified are highly heterogeneous, but some mutations are associated with specific clinical features of the tumor. Samples from 278 GIST patients collected during the period 2004-2011 were screened for mutations in exons 9, 11, 13, and 17 of KIT and 12, 14 and 18 of PDGFRA. Results of mutation screening were summarized and tested for possible association with clinical parameters of tumors. Mutations were identified in 83.81% of patients. Most frequent mutations were found in KIT exon 11 reaching frequency of 62.95%. Other exons contributed to the mutation pool with frequencies 8.27%, 7.55%, 2.52%, 1.44%, 1.08%, and 0.00%, in decreasing order KIT exon 9, PDGRFA exons 18 and 12, KIT exon 13, PDGFRA exon 14, and KIT exon 17. General linear model analysis showed no effect of any individual analyzed mutation on the phenotypic variables, but we confirmed association between mutations KIT exon 9 p. 503-504_dup2, and PDGFRA exon 18 p. D842V and intestinal and gastric localization of tumors. © 2012 APMIS.},

keywords = {Oncology, Population study, Single nucleotide variants},

pubstate = {published},

tppubtype = {article}

}