LABORATORY OF GENOMICS AND PRENATAL DIAGNOSTICS

About the lab

The laboratory focuses on a wide range of genetic and epigenetic analyses. Besides the standard molecular-genetic methods, our portfolio includes also more elaborated microarray technology and massive parallel sequencing (NGS).

In addition to our scientific research activities, the laboratory also intensively participates in the implementation of personalized, predictive and preventive medicine into clinical practice.  In close cooperation with the University Hospital in Martin, we mainly focus on the determinants of oncological, cardiovascular and hematological diseases. We also offer modern and popular non-invasive fetal testing from maternal blood.

Staff

NGS

Our laboratory has been using the state-of-the-art sequencing platforms from Illumina company  (NextSeq, MiSeq and HiSeq) for more than five years. We mainly focus on the entire genome sequencing, targeted resequencing based on the PCR approach, as well as on hybrid capture of target fragments.

Equipment of the lab also allows to perform other techniques such as RNA sequencing – expression profile determination, sequencing of small non-coding RNAs and many others.

DNA / RNA analyses

Thanks to the cooperation with the Institute of Molecular Biology and Genomics JFMED CU, our laboratory is able to perform multiple DNA and RNA analyses using the methods of  ddPCR, Sanger sequencing, HRM, TagMan, RT-PCR and the others.

Epigenetics

In the field of epigenetics, our laboratory predominantly focuses on the detection of methylation of CpG islands by quantitative pyrosequencing.  The MS MLPA technique is used to detect DNA methylation changes, DNA copy number variability (CNV), as well as a methylation-specific PCR. The laboratory has extensive experience with miRCURY LNA miRNA method to perform the analysis of miRNA expression in several diagnoses. We have also introduced a microarray technology for tissue and plasma miRNA analyses.

DNA editing

Using CRISPR/Cas9 technology, we are able to create experimental cell lines with impaired expression of selected genes or modify these genes by introducing mutations. Moreover, we are able to label selected genes with sequences coding for fluorescent proteins, which allows us to gain new insights into the function of these genes. For this purpose, we have introduced methodologies for the preparation of plasmids and lentiviral vectors using advanced gene manipulation techniques, such as Gibson assembly, overlapping PCR, or site-directed mutagenesis, as well as cell culture techniques.

Non-invasive prenatal testing

Our laboratory offers also non-invasive prenatal testing of the fetus from the maternal blood. The trisomy of chromosomes 13, 18 and 21 and the sex of the fetus can be determined by the NGS method. In addition, the RT PCR method is used to specify the Rh factor of the fetal blood and the sex of the baby.

Video tour

Watch a video tour of the Laboratory of Genomics and Prenatal Diagnostics.

Laboratory infrastructure

The laboratory uses several devises of the Department of Molecular Biology and Genomics, JFMED CU. This collaboration has created a modern and excellent instrument portfolio that allows the selection of the most appropriate method according to the research and required analyses.

Main instruments: MiSeq (Illumina), NextSeq Dx (Illumina), SureScan Dx Microarray Scanner (Agilent), Droplet Digital PCR System (Bio-Rad), PyroMark Q96 ID (Qiagen), LightCycler 480 II (Roche), 3500 Genetic Analyzer (Applied Biosystems), Q-Tower3 G (Analytik Jena), TOne (Analytik Jena), Bioanalyser 2100 (Agilent), QSep 100 (BiOptic), Qubit 4 fluorometer (Thermo Fisher Scientific), NanoDropTM OneC Microvolume UV-Vis Spectrophotometers (Thermo Scientific) and other.

Virtual tour

Take a virtual tour of our modern Laboratory of Genomics and Prenatal Diagnostics.

Projects

a) Projects co-financed by EU resources:

ITMS 313011AUA4: New possibilities for laboratory diagnostics and massive screening of SARS-Cov-2 and identification of mechanisms of virus behavior in the human body. Operational Program Integrated Infrastructure. CovLab.

ITMS 310031AMR7: Management of emergency situations related to COVID-19 coordinated by the Ministry of Health of the Slovak Republic. Operational Program: Environmental Quality 2014 – 2020.

ITMS: 313011AFG5: Systemic public research infrastructure – biobank for cancer and rare diseases. Operational Program Integrated Infrastructure 2014-2020. Biobank
ITMS 313011V446: Integrative strategy in the development of personalized medicine of selected malignant tumors and its impact on quality of life. Operational Program Integrated Infrastructure 2014-2020. Lisper.

ITMS 313011V344: Long-term strategic research on prevention, intervention and mechanisms of obesity and its comorbidities. Operational Program Integrated Infrastructure 2014-2020. Obesity.

b) National projects – principal investigator:

APVV-16-0021: The role of microRNAs in breast cancer: biological significance, target molecules and signaling pathways.

VEGA 1/0199/17: Determination of the molecular basis of the methylator phenotype in selected types of cancer.

VEGA 1/0272/19: Using the circulating miRNAs as potential biomarkers of pregnancy complications

c) National projects – co-investigator:

APVV-17-0369: DNA methylation as a target for epigenetic editing and its utilization in personalizing the diagnosis and therapy of melanoma uvey.

APVV-16-0066: Genomic profile and transcriptional signature of colorectal cancer.

VEGA 1/0310/18: Relationship between early onset of microvascular complications and dysregulation of hemostasis in children with diabetes mellitus type 1.

VEGA 1/0380/18: Analysis of methylated DNA sequences in plasma as an universal marker for monitoring colorectal cancer relapse.

The most important publications

Snahnicanova Z, Kasubova I, Kalman M, Grendar M, Mikolajcik P, Gabonova E, Laca L, Caprnda M, Rodrigo L, Ciccocioppo R, Kruzliak P, Plank L, Lasabova Z. Genetic and epigenetic analysis of the beta-2-microglobulin gene in microsatellite instable colorectal cancer. Clin Exp Med. 2020; 20(1):87-95. doi: 10.1007/s10238-019-00601-7.

Kašubová I, Holubeková V, Janíková K, Váňová B, Sňahničanová Z, Kalman M, Plank L, Lasabová Z. Next Generation Sequencing in Molecular Diagnosis of Lynch Syndrome – a Pilot Study Using New Stratification Criteria.Acta Medica (Hradec Kralove). 2018; 61(3):98-102. doi: 10.14712/18059694.2018.125. 

Danková Z, Braný D, Dvorská D, Ňachajová M, Fiolka R, Grendár M, Hatok J, Kubatka P, Holubeková V, Halašová E, Bielik T, Žúbor P. Methylation status of KLF4 and HS3ST2 genes as predictors of endometrial cancer and hyperplastic endometrial lesions. Int J Mol Med. 2018; 42(6):3318-3328. doi: 10.3892/ijmm.2018.3872.

Grendár M, Loderer D, Laučeková Z, Švecová I, Hrtánková M, Hornáková A, Nagy B, Žúbor P, Lasabová Z, Danko J. Uncertainty of fetal fraction determination in Non-Invasive Prenatal Screening by highly polymorphic SNPs. J Biotechnol. 2019; 299:32-36. doi: 10.1016/j.jbiotec.2019.04.020.

Danková Z, Žúbor P, Grendár M, Zelinová K, Jagelková M, Stastny I, Kapinová A, Vargová D, Kasajová P, Dvorská D, Kalman M, Danko J, Lasabová Z. Predictive accuracy of the breast cancer genetic risk model based on eight common genetic variants: The BACkSIDE study. J Biotechnol. 2019; 299:1-7. doi: 10.1016/j.jbiotec.2019.04.014.

Soltysova A, Sedlackova T, Dvorska D, Jasek K, Chokhachi Baradaran P, Horvathova Kajabova V, Demkova L, Buocikova V, Kurucova T, Lyskova D, Furdova A, Minarik G, Babal P, Dankova Z, Smolkova B. Monosomy 3 Influences Epithelial-Mesenchymal Transition Gene Expression in Uveal Melanoma Patients; Consequences for Liquid Biopsy. Int J Mol Sci. 2020; 21(24):9651. doi: 10.3390/ijms21249651.

Holubekova V, Kolkova Z, Grendar M, Brany D, Dvorska D, Stastny I, Jagelkova M, Zelinova K, Samec M, Liskova A, Laucekova Z, Kudela E, Bobrovska M, Kalman M, Zubor P, Dankova Z. Pathway Analysis of Selected Circulating miRNAs in Plasma of Breast Cancer Patients: A Preliminary Study. Int J Mol Sci. 2020; 21(19):7288. doi: 10.3390/ijms21197288.

Deffieu MS, Cesonyte I, Delalande F, Boncompain G, Dorobantu C, Song E, Lucansky V, Hirschler A, Cianferani S, Perez F, Carapito C, Gaudin R. Rab7-harboring vesicles are carriers of the transferrin receptor through the biosynthetic secretory pathway. Sci Adv. 2021; 7(2):eaba7803. doi: 10.1126/sciadv.aba7803. 

Škereňová M, Sokol J, Biringer K, Ivanková J, Staško J, Kubisz P, Lasabová Z. GP6 Haplotype of Missense Variants is Associated with Sticky Platelet Syndrome Manifested by Fetal Loss. Clin Appl Thromb Hemost. 2018; 24(1):63-69. doi: 10.1177/1076029616685428. 

Dvorská D, Braný D, Nagy B, Grendár M, Poka R, Soltész B, Jagelková M, Zelinová K, Lasabová Z, Zubor P, Danková Z. Aberrant Methylation Status of Tumour Suppressor Genes in Ovarian Cancer Tissue and Paired Plasma Samples. Int J Mol Sci. 2019; 20(17):4119. doi: 10.3390/ijms20174119.

Simurda T, Vilar R, Zolkova J, Ceznerova E, Kolkova Z, Loderer D, Neerman-Arbez M, Casini A, Brunclikova M, Skornova I, Dobrotova M, Grendar M, Stasko J, Kubisz P. A Novel Nonsense Mutation in FGB (c.1421G>A; p.Trp474Ter) in the Beta Chain of Fibrinogen Causing Hypofibrinogenemia with Bleeding Phenotype. Biomedicines. 2020; 8(12):605. doi: 10.3390/biomedicines8120605.

Hallez C, Li X, Suspène R, Thiers V, Bouzidi MS, M Dorobantu C, Lucansky V, Wain-Hobson S, Gaudin R, Vartanian JP. Hypoxia-induced human deoxyribonuclease I is a cellular restriction factor of hepatitis B virus. Nat Microbiol. 2019; 4(7):1196-1207. doi: 10.1038/s41564-019-0405-x.

Holubekova V, Mersakova S, Grendar M, Snahnicanova Z, Kudela E, Kalman M, Lasabova Z, Danko J, Zubor P.The Role of CADM1 and MAL Promoter Methylation in Inflammation and Cervical Intraepithelial Neoplasia. Genet Test Mol Biomarkers. 2020; 24(5):256-263. doi: 10.1089/gtmb.2019.0188.

Kašubová I, Kalman M, Jašek K, Burjanivová T, Malicherová B, Vaňochová A, Meršaková S, Lasabová Z, Plank L.Stratification of patients with colorectal cancer without the recorded family history. Oncol Lett. 2019; 17(4):3649-3656. doi: 10.3892/ol.2019.10018. 

Simurda T, Snahnicanova Z, Loderer D, Sokol J, Stasko J, Lasabova Z, Kubisz P. Fibrinogen Martin: A Novel Mutation in FGB (Gln180Stop) Causing Congenital Afibrinogenemia. Semin Thromb Hemost. 2016; 42(4):455-8. doi: 10.1055/s-0036-1581104.

Škereňová M, Matakova T, Halasova E, Riskova L, Skorvanova M, Mistuna D, Halasa M, Dobrota D. Common gene haplotypes of gelatinases and their tissue inhibitors in abdominal aortic aneurysm. Gen Physiol Biophys. 2020; 39(1):37-47. doi: 10.4149/gpb_2019046. 

Simurda T, Zolkova J, Snahnicanova Z, Loderer D, Skornova I, Sokol J, Hudecek J, Stasko J, Lasabova Z, Kubisz P. Identification of Two Novel Fibrinogen Bβ Chain Mutations in Two Slovak Families with Quantitative Fibrinogen Disorders. Int J Mol Sci. 2017; 19(1):100. doi: 10.3390/ijms19010100.

Snahnicanova Z, Mendelova A, Grendar M, Holubekova V, Kostkova M, Pozorciakova K, Jancinová M, Kasubova I, Vojtkova J, Durdik P, Lasabova Z, Ciljakova M, Banovcin P. Association of Polymorphisms in CYBA, SOD1, and CAT Genes with Type 1 Diabetes and Diabetic Peripheral Neuropathy in Children and Adolescents. Genet Test Mol Biomarkers. 2018; 22(7):413-419. doi: 10.1089/gtmb.2018.0018.

Škereňová M, Halašová E, Matáková T, Jesenská Ľ, Jurečeková J, Šarlinová M, Čierny D, Dobrota DLow Variability and Stable Frequency of Common Haplotypes of the TP53 Gene Region in Colorectal Cancer Patients in a Slovak Population. Anticancer Res. 2017; 37(4):1901-1907. doi: 10.21873/anticanres.11528.