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About NCMG

National Center for Medical Genomics

Medical genomics is a dynamically evolving scientific discipline that gathers and uses the genomic information of patients, their genetic relatives and even the entire population to identify the genetic, genomic and molecular basis of human health and disease. NCMG is a distributed scientific infrastructure, which consists of following genomic laboratories: First and Second Faculty of Medicine and Faculty of Medicine in  Pilsen, Charles University in Prague, General University Hospital in Prague, Motol University Hospital; BIOCEV - Biotechnology and Biomedicine Center of the Academy of Sciences and Charles University in Vestec; Department of Internal Medicine, Hematology and Oncology (IHOK) and Centre of molecular biology and gene therapy (CMBGT) at University Hospital Brno; Central European Institute of Technology (CEITEC) at Masaryk University at Brno; Institute of Molecular and Translational Medicine at Faculty of Medicine and Dentistry at Palacký University Olomouc; University Hospital in Pilsen.

The objective of NCMG is to provide for an operation of next generation sequencing platforms and subsequent technologies for analysis of human genomes and to allow qualified usage of these technologies in biomedical research and translational medicine in Czech Republic. Different localization and partially different specialization of individual laboratories guarantee expansion of genomics in CR, corresponding with global trends. NCMG laboratories are equipped with modern instruments and provide fundamental instrumental, methodical and experimental expertise, which is necessary for genomic sequencing, whole genome genotyping, cytogenetic analysis and analysis of genome, transcriptome and epigenome. NCMG is also equipped with corresponding computational and data storage resources and offers bioinformatics and statistics support for projects with focus on study of both complex and rare diseases and also oncological diseases.


Services

Genome sequencing and bioinformatics analysis

       - NGS sequencing - genome, exome, targeted, RNA sequencing

       - Microarrays - SNP and CNV detection, expression

Teaching and consulting

       - We can help you with the design of your project, it's realization and with the data analysis

Access to the cohort of patients and controls

       - You can download our publicly available Czech database of genomic variants

If you need any other information or want to collaborate, please contact prof. Stanislav Kmoch: skmoch@lf1.cuni.cz


NCMG database

  • Description of our cohort and data processing

1055 samples (442 males and 613 females)

          - 572 samples, representing common czech poulation without severe diseases (neselektovana_populace)

          - 483 samples, representing czech poulation older than 70 years, without severe diseases (NCMG_controls)

variants: database contains all coding and splice variants with population frequency < 5 %

reference sequence: hg19

tools: novoalign, picard tools, GATK HaplotypeCaller, GEMINI

description of individual columns are part of the Excel file, tab "Legenda"

  • You can download the the database: Excel file -- updated on 23. 9. 2019
  • Users are obliged to acknowledge NCMG in any output (publications, patents, public presentations) that were created by using the NCMG instrumentation or expertise.

If you have any questions, please contact Viktor Stránecký (vstra@lf1.cuni.cz) or Anna Přistoupilová (anna.pristoupilova@lf1.cuni.cz)


News

NCMG and COVID-19 testing - 9. 10. 2020

Stanislav Kmoch on know-how that made testing for Covid safer

Professor Stanislav Kmoch has been researching rare diseases for thirty years. In the current coronavirus pandemic, knowledge from his laboratory, which is part of the NCMG, has significantly contributed to the development of a new procedure for the diagnosis of covid-19 and other viral diseases. "It's a secondary but nice result of our many years of research into rare diseases," Kmoch describes the creation of the university spin-off GeneSpector.

GeneSpector provides a unique solution for rapid Covid-19 detection.

  • viRNAtrap™ Collection Tube inactivates the infectious agents developed for save operations at ambient temperature
  • viRNAtrap™ Extraction Kit is a best-in-class solution for fast and high throughput extraction at any open automated platform or when using manual work-up
  • high-quality PCR kits for fast COVID-19 detection
  • triplex COVID-INFA-INFB (to be launched in October 2020)

New publications supported by NCMG added - 22. 10. 2020


Since 2020, NCMG has a new project number: LM2018132. Please, use in your publications this number. - 28. 5. 2020


New publications supported by NCMG added - 28. 5. 2020


NCMG and COVID-19 testing - 14. 4. 2020

- Researchers from the Department of Pediatrics and Adolescent Medicine and the National Center for Medical Genomics have developed a functional covid19 system in clinical material within 14 days.

A wide academic community has joined an initiative that aims to help with laboratory testing for COVID-19. Researchers from several departments of the 1st Medical Faculty of Charles University - from the Department of Pediatrics and Adolescent Medicine, Department of Biochemistry and Experimental Oncology, Department of Biology and Medical Genetics and Department of Immunology and Microbiology and the National Center of Medical Genomics developed in 14 days functional system for the determination of covid19 in clinical material. This system has been used by the VFN for two weeks to test employees and admitted patients. As stated by prof. Ing. Stanislav Kmoch, CSc., Currently about 100 samples are examined daily. The much higher capacity of the established procedure is so far limited by the logistics of sampling, administration and the demands on the processing of potentially infectious material. Employees of the 1st Faculty of Medicine of Charles University thus help to increase the capacity in testing for COVID-19 in the Czech Republic and together with VFN significantly contribute to managing epidemiological problems in this difficult time, adds another scientist, prof. RNDr. Libuše Kolářová, CSc.

- IMTM declares war against COVID-19

CEITEC Scientists Are Developing Faster Tests for COVID-19 Disease


New publications supported by NCMG added - 6. 1. 2020


New publications supported by NCMG added - 5. 11. 2019


We published a new version of Czech database of genomic variants - it contains 1055 samples (442 males a 613 females) - 23. 9. 2019


New publications supported by NCMG added - 23. 9. 2019


New publication supported by NCMG added - 19. 6. 2019


New publication supported by NCMG added - 11. 6. 2019


New publications supported by NCMG added - 4. 6. 2019


We upgraded our NGS sequencing workflow by installing a new high throughput sequencer - Illumina NovaSeq 6000 - 4. 3. 2019

NGS_workflow_EN


New publications supported by NCMG added - 5. 12. 2018


New publications supported by NCMG added - 20. 9. 2018


New publications supported by NCMG added - 12. 7. 2018


New version of our database of genomics variants - containing 468 samples from common population without severe diseases (252 males and 216 females) - 27. 4. 2018


New publications supported by NCMG added - 25. 4. 2018


We would like to invite you to attend and participate in the 2nd HVP Variant Effect Prediction Training Course that will be held from Monday 6 to Wednesday 8 November in the beautiful historic city of Prague, Czech Republic. More information and registration at http://vep.variome.org/. You can still register for a discounted price - Earlybird ends 11.59 PM CET 31st August 2017!

VEP

New publications supported by NCMG added - 28. 8. 2017


Two teams from NCMG have received Minister of Health of Czech Republic Awards for research and development in medicine for 2016. Team of doc. Ing. Stanislav Kmoch, CSc. was awarded for the project " Identification of the genetic and molecular basis of rare genetic disorders using novel genomic methods" and the team of prof. RNDr. Šárka Pospíšilová, Ph.D. for the project "Molecular characterization of B-cell receptors and its relation to the evolution of genetic changes in chronic lymphocytic leukemia." - 16. 12. 2016


We would like to introduce you our Scientific Advisory Board - 2. 12. 2016


Please visit our new social networks profiles on Facebook and Twitter. - 4. 10. 2016


Key people

Prof. Ing. Stanislav Kmoch, CSc.
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For First Faculty of Medicine, Charles University in Prague and General University Hospital in Prague; head of the research program Development of Diagnostic and Therapeutic Procedures at BIOCEV and head of Research Unit for Rare Diseases, First Faculty of Medicine and General University Hospital. His main focus lies in the study of genetic, molecular, cellular and pathologic causes of rare and complex diseases.

 
Prof. MUDr. Milan Macek, DrSc., MHA
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for Second Faculty of Medicine, Charles University in Prague and University Hospital Motol; chairman of the largest academic medical/molecular genetics institution in the Czech Republic - Department of Biology and Medical Genetics; ÚBLG. He is also the past President of the European Society of Human Genetics (ESHG.org; 2011), past-board member of the European Cystic Fibrosis Society (ECFS.eu; 2007-2015 and of the European Society for Human Reproduction and Embryology (ESHRE.eu; 2012-2014). He also serves at the Commission Expert Group on Rare Diseases (formerly EUCERD.eu). ÚBLG was designated by the Czech Ministry of Health as a National Coordination centre for rare diseases (Bulletin 4/2012) which serves as a "clearing centre" for the dissemination of knowledge in rare disease-related genomics gathered within various international / European projects such as CF Thematic Network, EuroGentest, EuroCareCF, Techgene.eu, RD-connect.eu, Norway Grants or EU ESF funds. His main research and clinical interest is genomics of rare diseases, and how to translate such knowledge to clinical diagnostics and/or bedside. Prof. Macek is also the Czech National coordinator of Orpha.net and member of the Diagnostic Committee of the International Rare Disease Consortium (IRDIRC.org).

Prof. RNDr. Šárka Pospíšilová, Ph.D.
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For Masaryk University and University Hospital Brno; research groupleader of Medical Genomics, coordinator of Molecular Medicine program at CEITEC, and head of Centre of molecular biology and gene therapy of University Hospital Brno. Research projects focus primarily on study of p53 signalling pathway and other molecular markers of hemato-oncological diseases, mutational and functional analyses of immunoglobulin genes and microRNAs in lymphoproliferative disorders. The laboratory is also intensively on application of genomic approaches in diagnostics of hematologic and oncologic diseases (leukemias, lymphomas, breast cancer and other malignancies) in postnatal but also in prenatal and pre-implantation diagnostics.

 
prim. MUDr. Ivan Šubrt, Ph.D.
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For the Faculty of Medicine in Pilsen, Charles University Prague and the University Hospital in Pilsen; head of the Department of Medical Genetics and of the research group Medical Genomics. Research projects are focused mainly on the study of molecular markers of disorders of human reproduction, susceptibility to infectious diseases, oncogenesis and on the utilization of genomic technologiesfor diagnosis of rare genetic diseases.

Assoc. Prof. Marian Hajduch, MD, Ph.D.
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Faculty of Medicine and Dentistry, Palacky University Olomouc and University Hospital Olomouc. Director of the Institute of Molecular and Translational Medicine, head of the research program Chemical biology and experimental therapeutics. Research projects are focused on research into the molecular biology of cancer in particular, on research and development of new drugs and diagnostic methods and translational medicine.

 

Institutions


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Research Unit for Rare Diseases, First Faculty of Medicine at Charles University in Prague, General University Hospital and BIOCEV

The laboratory is focused on studying the molecular basis of rare genetically determined disorders. In its work combines latest techniques and methods of medical genomics, bioinformatics, metabolomics, molecular biology and biochemistry with detailed clinic-pathologic evaluation of the studied diseases. In recent years this approach led to identification of causal genes and characterization of molecular basis of more than a dozen of severe genetic diseases. The laboratory offers it's expertise to clinical centers both in the Czech Republic and abroad.




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Department of Biology and Medical Genetics, Second Faculty of Medicine, Charles University and University Hospital Motol

Department of Biology and Medical Genetics is a clinical-diagnostic, academic and research institution. Main topics are diagnostics and further study of hereditary diseases in prenatal and postnatal phase of development by means of state of the art techniques of molecular genetics, molecular cytogenetics and next generation sequencing. By decision of Czech Ministry of Health a National coordination center for rare diseases was established at Department of Biology and Medical Genetics.




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Masaryk University - CEITEC

CEITEC MU was established as a part of scientific centre of excellence Central European Institute of Technology (CEITEC). Shared Core Facility Genomics and Laboratory of Medical Genomics are based in newly built premises University Campus that offers high-end equipment and optimal conditions to solve current issues of biomedical and clinical research (from genome analysis, mapping of key genetic defects, molecular genetic diagnostics to search for suitable targets for gene therapy). The portfolio of services of shared Genomics laboratory includes high throughput massively parallel sequencing, cell separation using FACS and MACS, real time PCR including microfluidic PCR, microarrays and other technologies. Scientists from the Czech and foreign universities and research institutes interested in using the services of Genomics Laboratory can apply for financial support from the Ministry of Education, Youth and Sports (MEYS).




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University Hospital Brno

Centre of molecular biology and gene therapy (CMBGT) forms a part of Department of Internal Medicine, Hematology and Oncology (IHOK) focused on research and development and is one of the key units of the University Hospital Brno. It deals with the molecular biological diagnostics in the field of haematooncology, solid tumors, inherited diseases and identification of pathogens in immunocompromised patients. It also applies cytometry and cytogenetic diagnostics in hematology and hematooncology an performs applied research in general field of human medicine.




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Department of Medical Genetics, Faculty of Medicine in Pilsen, Charles University Prague and the University Hospital in Pilsen

Research activities of the group focus on the study of molecular markers of disorders of human reproduction, susceptibility to infectious diseases, oncogenesis and on the clinical aspects of broad group of rare genetic diseases.




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Institute of Molecular and Translational Medicine,
Faculty of Medicine and Dentistry, Palacký University in Olomouc

The Institute of Molecular and Translational Medicine, Faculty of Medicine and Dentistry, Palacký University in Olomouc is cutting-edge biomedical research institute in the Czech Republic. The IMTM’s mission is basic and translational biomedical research with the goal to understand the underlying causes of cancer and infectious diseases and to develop future human medicines and diagnostics.



Research teams

Research Unit for Rare Diseases, First Faculty of Medicine at Charles University in Prague, General University Hospital and BIOCEV

Head of the group:
Prof. Ing. Stanislav Kmoch, CSc.
stanislav.kmoch@lf1.cuni.cz
+420 22496 7016, +420 22496 7691

Molecular biology, genetics and NGS sequencing:

Bioinformatics and biostatistics:

Lab technician:

Technical and administrative support:

Ethics:

Department of Biology and Medical Genetics, Second Faculty of Medicine, Charles University and University Hospital Motol

Head of the research team:

Prof. MUDr. Milan Macek, DrSc., MHA
milan.macek.jr@lfmotol.cuni.cz
+420  224 433 500

Deputy head of the research team:

Prof. Ing. Zdeněk Sedláček, DrSc.
zdenek.sedlacek@lfmotol.cuni.cz
+420 257 296 153

Molecular genetics, next generation sequencing:

Bioinformatics:

Molecular Medicine Program CEITEC MU – Genomics Core Facility and Research Group of Medical Genomics

Head of Molecular Medicine Program and Research Group of Medical Genomics:
prof. RNDr. Sarka Pospisilova, Ph.D.
sarka.pospisilova@ceitec.muni.cz
+420 532234622

Head of Genomics Core Facility:
MVDr. Boris Tichy, Ph.D.
boris.tichy@ceitec.muni.cz
+420 733141527

NGS, microarrays:

Biostatistics, bioinformatics:

Technical and administrative support:

Centre of Molecular Biology and Gene Therapy of University Hospital Brno (CMBGT)

Head of CMBGT:
prof. RNDr. Sarka Pospisilova, Ph.D.
sarka.pospisilova@fnbrno.cz
+420 532234622

Unit of congenital and genetic diseases:

Unit of Cancer Genomics:

Department of Medical Genetics, Faculty of Medicine in Pilsen, Charles University Prague and the University Hospital in Pilsen

Head of the research team:
MUDr. Ivan Šubrt, Ph.D.
subrti@fnplzen.cz
+420 377 402 800

Molecular biology, genetics and NGS sequencing:

Laboratory technician:

Institute of Molecular and Translational Medicine

Leader of the research team:
Assoc. Prof. Marian Hajduch, MD, PhD
marian.hajduch@upol.cz
+420 585632082, +420 585632083

Molecular biology, genetics, NGS sequencing:

Bioinformatics, biostatistics:


Our projects

Research Unit for Rare Diseases, First Faculty of Medicine at Charles University in Prague, General University Hospital and BIOCEV

779257 Solving the unsolved Rare Diseases — Solve-RD, Grant provider: Horizon 2020, H2020-SC1-2017-Single-Stage-RTD, Period of research project: 2018 – 2022

NV19-07-00136 Určení příčin vzácných geneticky podmíněných onemocnění v pediatrické populaci pomocí nových metod analýzy genomu, Grant provider: MZ0 - Ministry Of Health Of The Czech Republic, Main recipient: Charles University in Prague / First Faculty of Medicine, Recipient: Prof. Ing. Stanislav Kmoch, CSc., Period of research project: 2019 - 2022

NV19-08-00137 Využití nových metod analýzy genomu v případech vzácných geneticky podmíněných onemocnění s negativními výsledky genetických a genomických analýz, Grant provider: MZ0 - Ministry Of Health Of The Czech Republic, Main recipient: Charles University in Prague / First Faculty of Medicine, Recipient: Mgr. Viktor Stránecký, PhD, Period of research project: 2019 - 2022

17-29786A Identification and characterization of genetic factors contributing to inherited tubulointerstitial kidney disease, Grant provider: MZ0 - Ministry Of Health Of The Czech Republic. Main recipient: Charles University in Prague / First Faculty of Medicine, Period of research project: 2017-2020.

EF16_013/0001634 National Centrum of Medical Genomics - modernizace infrastruktury a výzkum genetické variability populace, Grant provider: The Ministry of Education, Youth and Sports (MEYS, MŠMT), Main recipient: Charles University in Prague / First Faculty of Medicine, Recipient: doc. Ing. Stanislav Kmoch, CSc. Period of research project: 2017 - 2019

NV15-27682A Využití metod sekvenování nové generace pro časnou diagnostiku a individualizovanou léčbu dilatační kardiomyopatie a příbuzných forem kardiomyopatií, Grant provider: MZ0 - Ministry Of Health Of The Czech Republic, Main recipient: Institute for Clinical and Experimental Medicine, Recipient: MUDr. Miloš Kubánek, Ph.D., Period of research project: 2015 - 2019

15-28208A  Characterization of the molecular basis of rare genetic diseases of pediatric onset using new methods of genome analysis, Grant provider: MZ0 - Ministry Of Health Of The Czech Republic. Main recipient: Charles University in Prague / First Faculty of Medicine, Period of research project: 2015-2018.

NT14025 Role of rare variants in genetic predisposition to statin myopathy, Grant provider: MZ0 - Ministry Of Health Of The Czech Republic, Main recipient: Institute for Clinical and Experimental Medicine, Period of research project: 2013-2015.

NT13116 Identification of the genetic and molecular basis of rare genetic disorders using novel genomic methods, Grant provider: MZ0 - Ministry Of Health Of The Czech Republic, Main recipient: Charles University in Prague / First Faculty of Medicine, Period of research project: 2012-2015.

LH12015 Identification and characterization of genetic factors contributing to chronic kidney disease, Grant provider: The Ministry of Education, Youth and Sports (MEYS, MŠMT), Main recipient: Charles University in Prague / First Faculty of Medicine, Period of research project: 2012-2015.

GB14-36804G Center of mitochondrial biology and pathology (MITOCENTRUM), Grant provider: GA0 - The Czech Science Foundation (GA CR), Main recipient: Institute of Physiology CAS, Period of research project: 2014-2018.

GA14-21903S Genetic architecture of impulsive violence, Grant provider: GA0 - The Czech Science Foundation (GA CR), Main recipient: Charles University in Prague / First Faculty of Medicine, Period of research project: 2014-2016.

 

Second Faculty of Medicine at Charles University, Motol University Hospital

305444 RD-CONNECT, An integrated platform connecting registries, biobanks and clinical bioinformatics for rare disease research, Grant provider: FP7. Period of research project: 2012-2018.

LD14073  Introduction of next generation sequencing into clinical diagnostics in the Czech Republic: ethical and clinical genetic indication criteria, Grant provider: COST. Period of research project: 2014-2017.

15-34904A  Next generation sequencing in early Diagnosis and individualised therapy of hypertrophic cardiomyopathies, Grant provider: AZV ČR. Period of research project: 2015-2018.

15-27682A Next generation sequencing for early diagnosis and individualized treatment of dilated cardiomyopathy and related forms of cardiomyopathy,Grant provider: MZ0 - Ministerstvo zdravotnictví (MZ). Hlavní příjemce: Institut klinické a experimentální medicíny. Period of research project: 2015-2018.

CZ.2.16/3.1.00/24022  Improvement of early Diagnosis, prevention and therapy of severe reproductive-, prenatal and postnatal developmental disorders in children and adults: sustainability period, Grant provider: Operační program Praha Konkurenceschopnost. Period of research project: 2013-2018.

NF-CZ11-PDP-3-003-2014 National Coordinating Centre for rare diseases at the Motol University Hospital, Grant provider: Norway Grants. Period of research project: 2014-2017.

 

Masaryk University – CEITEC

Projekt NGS-PTL (Next Generation Sequencing Platform for Targeted Personalized Therapy of Leukemia, FP7, číslo 306242) – the project goal is the application of the most modern approaches for genomics analysis for identification of novel diagnostics and prognostics biomarkers of leukemia and subsequent patient stratification and more effective application of therapeutical methodologies.

Projekt ALKATRAS (ALK activation as a target of translational science: break free from cancer, H2020, číslo 675712 ) – its main aim is to clarify yet unknown mechanisms of ALK-induced tumorigenesis and describe more specific role of oncogene ALK (anaplastic lymphoma kinase) in oncologic diseases like lymphomas, neuroblastomas and non-cell lung carcinoma (NSCLC).

 

University Hospital Brno

Project supported by Agency of biomedical research (AZV, number 15-30015A ) entitled as „Analysis of clonal heterogeneity of chronic lymphocytic leukemia using next-generation sequencing of B-cell receptor gene. National study.“ has an ambitious aim to establish technology for high throughput sequencing of immunoglobulin genes and perform national screening of newly diagnosed CLL patients.

New-generation sequencing is used as a tool within the project entitled „Generation and development of genetic defects in leukemia“ (AZV, number 15-10035S) for identification of genetic disorders contributing to clonal evolution of leukemia and for study of B-cell receptor mediated signalling that both play important role in cellular response to external stimuli and thus contribute to clonal evolution.

 

Institute of Molecular and Translational Medicine

ÚMTM addresses currently a number of international (EATRIS, FP7 INFLACARE, BBMRI etc.) and national grant projects (TACR, GACR, AZV etc.) focused on translational medicine, see more imtm.cz.


Available technologies

Institutes of First and Second Faculty of Medicine at Charles University in Prague

  • Focused-ultrasonicator Covaris E220
  • Robotic workstation Tecan Freedom EVO® 150
  • Massive parallel sequencers Illumina NovaSeq 6000, HiSeq 2500 a SOLiD4 + equipment for sample preparation and bioinformatics data analysis
  • Capillary sequencers ABI 3500xL, ABI3100 Avant a ABI PRISM 7000
  • System for DNA microarrays (Affymetrix, Agilent)
  • Quantitative PCR 7900HT Fast Real-Time PCR Applied Biosystem
  • LightCycler 480 Roche
  • Long read sequencer MinION Oxford Nanopore
  • Data storage and computer servers
  • Software specialists and bioinformaticians necessary for the operation of infrastructure

NGS_workflow_EN

CEITEC MU Brno

  • Massive paralel sequencers (Illumina MiSeq and Illumina NextSeq 500)
  • Systems for preparation of amplicon sequencing libraries (Wafergen SmartChip, Fluidigm AccessArray)
  • Capillary sequencer
  • System for DNA microarrays (Affymetrix, Agilent)
  • rReal-time qPCR and digital PCR (Life Technologies QuantStudio 12k, Life Technologies QuantStudio 3D, BioRad QX200, Wafergen SmartCycler)
  • System for RNA/DNA amplification from individual cells (Fluidigm C1)
  • Data storage 300TB and computational servers
  • Flow cytometer and sorter (BD FACS Aria Fusion and BD FACS Verse)
  • Fluorescent microscopes (Olympus ScanR, Incucyte ZOOM)
  • Magnetic cell separator (Milteniy AutoMACS)
  • Laser microdissection

University Hospital Brno

  • Capillary sequencer (LifeTechnologies)
  • System for DNA microarrays (Affymetrix)
  • Real-time qPCR (Life Technologies, Qiagen)
  • System for RNA/DNA amplification
  • Cell sorter (BD FACS Arial II)
  • Flow cytometer (BD FACS Canto II)

Department of Medical Genetics, Faculty of Medicine in Pilsen, Charles University Prague and the University Hospital in Pilsen

  • Massive parallel sequencers (Life Technologies IonTorrent, Illumina MiSeq)
  • Capillary sequencers (Life Technologies)
  • DNA microarray systems (Agilent, Innopsys)
  • Real-time qPCR (Corbett Research, Qiagen)
  • Fluorescent mikroscopes (Olympus)
  • Data storage and computational servers
  • DNA/RNA amplification systems

Institute of Molecular and Translational Medicine

  • Massively parallel sequencers (Illumina MiSeq and HiSeq Illumina, Qiagen PyroMark Q96, Roche GS Junior, Sequenom)
  • Systems for automated preparation of sequencing libraries (Illumina Neoprep)
  • Robotic system for nucleic acid isolation (Roche MagNA Pure 96 MagCore)
  • Microarray system (Affymetrix)
  • Real-Time qPCR (Roche LC 480, LC 1536, Cobas 4800, Eppendorf, BioRad CFX96)
  • Data storage and computer servers
  • The flow cytometer and sorter (BD FACS Aria Fusion II)
  • Fluorescence microscope (Olympus BX60)
  • Laser microdissection

NCMG Scientific Advisory Board

Dr. Robert Ivánek
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Robert Ivánek received his doctoral degree in Molecular Biology and Genetics from the Charles University, Prague, Czech Republic in 2009. During last two years of his PhD studies he was running the Genomics Core facility at the Institute of Molecular Genetics, Prague, Czech Republic. From 2009 till 2012 he trained as postdoctoral fellow at Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland. In 2012 he became Head of Bioinformatics Core Facility at Department of Biomedicine (DBM), University of Basel, Basel Switzerland. In his scientific career he contributed to identification of molecular basis for several human rare diseases by applying novel combination of genomic tools and bioinformatic approaches. He also investigate the effect of sequence variation on transcription factor binding, DNA methylation and chromatin structure. His team at DBM provides bioinformatic expertise and training for analysis of high-throughput genomic data in biomedical field.

Dr. Jacek Majewski
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Dr. Jacek Majewski obtained his Bachelor’s degree in physics and Master’s degree in electrical engineering from Stanford University, Palo Alto, USA in 1991. Following a short adventure in the real world, he returned to academics and in 1999 received a PhD. in Biological Sciences from Wesleyan University, USA. His post-doctoral training with Dr. Jurg Ott at the Rockefeller University in New York focused on statistical genetics and methodologies for identifying variants underlying human genetic disease. At the onset of the human genome era, his combined background in quantitative sciences, biology and statistics opened new venues into the field of genome sequence analysis. He is currently an Associate Professor at the Department of Human Genetics, McGill University, Montreal, Canada, Medical Scientist at the McGill University Health Centre, and Scientist at the Shriners Hospital. His research centers on the analysis of next generation sequencing data, with specific applications to human genetic disease and cancer research. He holds grants from major Canadian and US funding agencies and has co-authored over 220 publications.

Dr. Vladimír Beneš
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Vladimír Beneš, Head of GeneCore, studied in Prague, the Czech Republic. He has been at EMBL since 1994 when he came as a postdoc to Ansorge group in the Biochemical Instrumentation Unit. Vladimir worked on development of methodology supporting genome-wide high-throughput sequencing, mainly in the sample processing part. In 2001 he was appointed to build EMBL Genomics Core Facility, a technology orientated service laboratory founded to assist researchers with functional genomics projects. This facility is currently utilizing mainly massively parallel sequencing & microarray technologies as well as qPCR. Among Vladimir’s tasks belong also assessment of new technologies and functional genomics applications, in particular their suitability for implementation in the environment of core facilities. He is also strongly involved in teaching of methods applied in this field.

Dr. Jiří Zavadil
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Jiří Zavadil received his doctoral degree in Biomedicine/Molecular Genetics in 1998 from the Charles University, Prague, Czech Republic. From 1998 to 2003, he trained as postdoctoral fellow at Mount Sinai School of Medicine and at Albert Einstein College of Medicine, in New York. Between 2003 and 2012 he was Assistant/Associate Professor of Pathology, Director of the NYU Genome Technology Center and Faculty Member of the NYU Center for Health Informatics and Bioinformatics at the New York University Langone Medical Center, New York. In 2012, he became Head of the Molecular Mechanisms and Biomarkers Group at the WHO International Agency for Research on Cancer (IARC), Lyon, France. In his scientific career he has studied human pathologies including cancer, using innovative workflows and methodologies in genomics and bioinformatics. His work has been documented by dozens (of 110+ total) lead-authored or co-authored publications. His team at IARC focuses on deciphering molecular mechanisms of carcinogenesis, with a particular emphasis on understanding the effects of environmental causes of cancer, and on the impact of carcinogens on critical genome alterations leading to cancer cell phenotype outcomes.

 

Publications

Publications with the support of NCMG for the year 2020

  1. Skalicka P, Porter LF, Brejchova K, et al (2020) Brittle cornea syndrome: A systemic review of disease-causing mutations in ZNF469 and two novel variants identified in a patient followed for 26 years. Biomed Pap. Biomed Pap 164:183–188. doi: 10.5507/bp.2019.017
  2. Majer F, Kousal B, Dusek P, et al (2020) Alu-mediated Xq24 deletion encompassing CUL4B, LAMP2, ATP1B4, TMEM255A, and ZBTB33 genes causes Danon disease in a female patient. Am J Med Genet Part A 182:219–223. doi: 10.1002/ajmg.a.61416
  3. Kubánek M, Schimerová T, Piherová L, et al (2020) Desminopathy: Novel Desmin Variants, a New Cardiac Phenotype, and Further Evidence for Secondary Mitochondrial Dysfunction. J Clin Med 9:937. doi: 10.3390/jcm9040937
  4. Larose H, Prokoph N, Matthews JD, et al (2020) Whole Exome Sequencing reveals NOTCH1 mutations in anaplastic large cell lymphoma and points to Notch both as a key pathway and a potential therapeutic target. Haematologica 105:haematol.2019.238766. doi: 10.3324/haematol.2019.238766
  5. Jedličková I, Cadieux-Dion M, Přistoupilová A, et al (2020) Autosomal-dominant adult neuronal ceroid lipofuscinosis caused by duplication in DNAJC5 initially missed by Sanger and whole-exome sequencing. Eur J Hum Genet 87:579–84. doi: 10.1038/s41431-019-0567-2
  6. Kozlova V, Ledererova A, Ladungova A, et al (2020) CD20 is dispensable for B-cell receptor signaling but is required for proper actin polymerization, adhesion and migration of malignant B cells. PLoS One 15:1–20. doi: 10.1371/journal.pone.0229170
  7. Vrbovská V, Sedláček I, Zeman M, et al (2020) Characterization of staphylococcus intermedius group isolates associated with animals from antarctica and emended description of staphylococcus delphini. Microorganisms 8:1–18. doi: 10.3390/microorganisms8020204
  8. Bene Z, Fejes Z, Macek M, et al (2020) Laboratory biomarkers for lung disease severity and progression in cystic fibrosis. Clin Chim Acta. doi: 10.1016/j.cca.2020.05.015
  9. Cormican S, Kennedy C, Connaughton DM, et al (2020) Renal transplant outcomes in patients with autosomal dominant tubulointerstitial kidney disease. Clin Transplant 34:1–6. doi: 10.1111/ctr.13783
  10. Vozdova M, Kubickova S, Pal K, et al (2020) Recurrent gene mutations detected in canine mast cell tumours by next generation sequencing. Vet Comp Oncol 1–10. doi: 10.1111/vco.12572
  11. Sottas C, Reif J, Kreisinger J, et al (2020) Tracing the early steps of competition-driven eco-morphological divergence in two sister species of passerines. Evol. Ecol.
  12. Mazurova S, Tesarova M, Zeman J, et al (2020) Fatal neonatal nephrocutaneous syndrome in 18 Roma children with EGFR deficiency. J Dermatol 1–6. doi: 10.1111/1346-8138.15317
  13. Leeksma AC, Baliakas P, Moysiadis T, et al (2020) Genomic arrays identify high-risk chronic lymphocytic leukemia with genomic complexity: a multi-center study. Haematologica haematol.2019.239947. doi: 10.3324/haematol.2019.239947
  14. Olinger E, Hofmann P, Kidd K, et al (2020) Clinical and Genetic Spectra of Autosomal Dominant Tubulointerstitial Kidney Disease due to Mutations in UMOD and MUC1. Kidney Int. doi: 10.1016/j.kint.2020.04.038
  15. Lhotova K, Stolarova L, Zemankova P, et al (2020) Multigene panel germline testing of 1333 Czech patients with ovarian cancer. Cancers (Basel) 12:3–16. doi: 10.3390/cancers12040956
  16. Peska V, Mand T, Vitales D, et al (2020) Human-like telomeres in Zostera marina reveal a mode of transition from the plant to the human telomeric sequences. bioRxiv. doi: doi.org/10.1101/2020.03.11.987156
  17. Slavik H, Balik V, Vrbkova J, et al (2020) Identification of Meningioma Patients at High Risk ofTumor Recurrence Using MicroRNA Profiling. Neurosurgery 0:1–9. doi: 10.1093/neuros/nyaa009
  18. Sutton L-A, Ljungström V, et al (2020) Comparative analysis of targeted next-generation sequencing panels for the detection of gene mutations in chronic lymphocytic leukemia: an ERIC multi-center study. Haematologica 105:haematol.2019.234716. doi: 10.3324/haematol.2019.234716
  19. Tkáčiková Ľ, Mochnáčová E, Tyagi P, et al (2020) Comprehensive mapping of the cell response to E. coli infection in porcine intestinal epithelial cells pretreated with exopolysaccharide derived from Lactobacillus reuteri. Vet Res 51:1–13. doi: 10.1186/s13567-020-00773-1
  20. Snopková K, Čejková D, Dufková K, et al (2020) Genome sequences of two Antarctic strains of Pseudomonas prosekii: insights into adaptation to extreme conditions. Arch Microbiol 202:447–454. doi: 10.1007/s00203-019-01755-4Arch Microbiol. doi: 10.1007/s00203-019-01755-4
  21. Bleyer AJ, Kidd K, Robins V, et al (2020) Outcomes of patient self-referral for the diagnosis of several rare inherited kidney diseases. Genet Med 22:142–149. doi: 10.1038/s41436-019-0617-8Genet Med 0:1–8. doi: 10.1038/s41436-019-0617-8
  22. Lukes J, Danek P, Alejo-Valle O, et al (2020) Chromosome 21 gain is dispensable for transient myeloproliferative disorder driven by a novel GATA1 mutation. Leukemia. doi: 10.1038/s41375-020-0769-1
  23. Laidou S, Alanis-Lobato G, Pribyl J, et al (2020) Nuclear inclusions of pathogenic ataxin-1 induce oxidative stress and perturb the protein synthesis machinery. Redox Biol 32:101458. doi: 10.1016/j.redox.2020.101458
  24. Dudakova L, Skalicka P, Ulmanová O, et al (2020) Pseudodominant Nanophthalmos in a Roma Family Caused by a Novel PRSS56 Variant. J Ophthalmol 2020:1–9. doi: 10.1155/2020/6807809
  25. Jedličková I, Přistoupilová A, Nosková L, et al (2020) Spinal muscular atrophy caused by a novel Alu-mediated deletion of exons 2a-5 in SMN1 undetectable with routine genetic testing. Mol Genet genomic Med e1238. doi: 10.1002/mgg3.1238
  26. Geryk J, Krsička D, Vlčková M, et al (2020) The Key Role of Purine Metabolism in the Folate-Dependent Phenotype of Autism Spectrum Disorders: An In Silico Analysis. Metabolites 10:. doi: 10.3390/metabo10050184
  27. Schizophrenia Working Group of the Psychiatric Genomics Consortium., Ripke S, Walters JT, O’Donovan MC (2020) Mapping genomic loci prioritises genes and implicates synaptic biology in schizophrenia. medRxiv 2020.09.12.20192922
  28. Pěnčík O, Jiráčková K, Mašlaňová I, et al (2020) Spatial structure of permafrost and active layer from the James Ross Island , Antarctica : Geological and Microbiological Insights. CZECH POLAR REPORTS 10:127–128
  29. Jedlickova I, Pristoupilova A, Hulkova H, et al (2020) NOTCH2NLC CGG Repeats Are Not Expanded and Skin Biopsy Was Negative in an Infantile Patient With Neuronal Intranuclear Inclusion Disease. J Neuropathol Exp Neurol 79:1065–1071. https://doi.org/10.1093/jnen/nlaa070
  30. Stolarova L, Jelinkova S, Storchova R, et al (2020) Identification of Germline Mutations in Melanoma Patients with Early Onset, Double Primary Tumors, or Family Cancer History by NGS Analysis of 217 Genes. Biomedicines 8:404. https://doi.org/10.3390/biomedicines8100404
  31. Živná M, Kidd K, Zaidan M, et al (2020) An International Cohort Study of Autosomal Dominant Tubulointerstitial Kidney Disease due to REN Mutations Identifies Distinct Clinical Subtypes. Kidney Int. https://doi.org/10.1016/j.kint.2020.06.041
  32. Schneeberger PE, Kortüm F, Korenke GC, et al (2020) Biallelic MADD variants cause a phenotypic spectrum ranging from developmental delay to a multisystem disorder. Brain 143:2437–2453. https://doi.org/10.1093/brain/awaa204
  33. Franková V, Driscoll RO, Jansen ME, et al (2020) Regulatory landscape of providing information on newborn screening to parents across Europe. Eur J Hum Genet. https://doi.org/10.1038/s41431-020-00716-6
  34. Brinkmann J, Lissewski C, Pinna V, et al (2020) The clinical significance of A2ML1 variants in Noonan syndrome has to be reconsidered. Eur J Hum Genet 3–6. https://doi.org/10.1038/s41431-020-00743-3

Publications with the support of NCMG for the year 2019

  1. Hernández-Sánchez M, Kotaskova J, Rodríguez AE, et al (2019) CLL cells cumulate genetic aberrations prior to the first therapy even in outwardly inactive disease phase. Leukemia 33:518–558. doi: 10.1038/s41375-018-0255-1
  2. Cormican S, Connaughton DM, Kennedy C, et al (2019) Autosomal dominant tubulointerstitial kidney disease (ADTKD) in Ireland. Ren Fail 41:832–841. doi: 10.1080/0886022x.2019.1655452
  3. Bereshchenko O, Lo Re O, Nikulenkov F, et al (2019) Deficiency and haploinsufficiency of histone macroH2A1.1 in mice recapitulate hematopoietic defects of human myelodysplastic syndrome. Clin Epigenetics 11:1–14. doi: 10.1186/s13148-019-0724-z
  4. Balik V, Takizawa K (2019) Safe and bloodless exposure of the third segment of the vertebral artery: a step-by-step overview based on over 50 personal cases. Neurosurg Rev. doi: 10.1007/s10143-019-01158-5
  5. Fajkus P, Peška V, Závodník M, et al (2019) Telomerase RNAs in land plants. Nucleic Acids Res 1–15. doi: 10.1093/nar/gkz695
  6. Brejchova K, Dudakova L, Skalicka P, et al (2019) IPSC-Derived Corneal Endothelial-like Cells Act as an Appropriate Model System to Assess the Impact of SLC4A11 Variants on Pre-mRNA Splicing. Investig Opthalmology Vis Sci 60:3084. doi: 10.1167/iovs.19-26930
  7. Petrova G, Yaneva N, Hrbková J, et al (2019) Identification of 99% of CFTR gene mutations in Bulgarian‐, Bulgarian Turk‐, and Roma cystic fibrosis patients. Mol. Genet. Genomic Med. 7
  8. Souček P, Réblová K, Kramárek M, et al (2019) High-throughput analysis revealed mutations’ diverging effects on SMN1 exon 7 splicing. RNA Biol 16:1364–1376. doi: 10.1080/15476286.2019.1630796
  9. Kostovcikova K, Coufal S, Galanova N, et al (2019) Diet rich in animal protein promotes pro-inflammatory macrophage response and exacerbates colitis in mice. Front Immunol 10:1–14. doi: 10.3389/fimmu.2019.00919
  10. Oliver-De La Cruz J, Nardone G, Vrbsky J, et al (2019) Substrate mechanics controls adipogenesis through YAP phosphorylation by dictating cell spreading. Biomaterials 205:64–80. doi: 10.1016/j.biomaterials.2019.03.009
  11. Jelinkova S, Fojtik P, Kohutova A, et al (2019) Dystrophin Deficiency Leads to Genomic Instability in Human Pluripotent Stem Cells via NO Synthase-Induced Oxidative Stress. Cells 8:53. doi: 10.3390/cells8010053
  12. Mareckova A, Malcikova J, Tom N, et al (2018) ATM and TP53 mutations show mutual exclusivity but distinct clinical impact in mantle cell lymphoma patients. Leuk Lymphoma 60:1420–1428. doi: 10.1080/10428194.2018.1542144
  13. Králová S, Busse HJ, Švec P, et al (2019) Flavobacterium circumlabens sp. nov. and Flavobacterium cupreum sp. nov., two psychrotrophic species isolated from Antarctic environmental samples. Syst Appl Microbiol 42:291–301. doi: 10.1016/j.syapm.2018.12.005
  14. Kleiblová P, Stolařová L, Křížová K, et al (2019) Germline CHEK2 Gene Mutations in Hereditary Breast Cancer Predisposition – Mutation Types and their Biological and Clinical Relevance. Klin Onkol 32:36–50. doi: 10.14735/amko2019s36
  15. Bleyer AJ, Kmoch S, Greka A (2019) Diagnostic Utility of Exome Sequencing for Kidney Disease. N Engl J Med 380:2080. doi: 10.1056/NEJMc1903250
  16. Wayhelova M, Oppelt J, Smetana J, et al (2019) Novel de novo frameshift variant in the ASXL3 gene in a child with microcephaly and global developmental delay.Mol Med Rep 20:505–512. doi: 10.3892/mmr.2019.10303
  17. Doubková M, Staňo Kozubík K, Radová L, et al (2019) A novel germline mutation of the SFTPA1 gene in familial interstitial pneumonia. Hum Genome Var 6:12. doi: 10.1038/s41439-019-0044-z
  18. Zaliova M, Stuchly J, Winkowska L, et al (2019) Genomic landscape of pediatric B-other acute lymphoblastic leukemia in a consecutive European cohort. Haematologica 104:1396–1406. doi: 10.3324/haematol.2018.204974
  19. Nagy B, Bene Z, Fejes Z, et al (2019) Human epididymis protein 4 (HE4) levels inversely correlate with lung function improvement (delta FEV 1 ) in cystic fibrosis patients receiving ivacaftor treatment. J Cyst Fibros 18:271–277. doi: 10.1016/j.jcf.2018.08.013
  20. Zaliova M, Potuckova E, Hovorkova L, et al (2019) ERG deletions in childhood acute lymphoblastic leukemia with DUX4 rearrangements are mostly polyclonal, prognostically relevant and their detection rate strongly depends on method’s sensitivity. Haematologica 104:1407–1416. doi: 10.3324/haematol.2018.204487
  21. Wiatrek DM, Candela ME, Sedmík J, et al (2019) Activation of innate immunity by mitochondrial dsRNA in mouse cells lacking p53 protein. Rna 25:713–726. doi: 10.1261/rna.069625.118
  22. Kleiblova P, Stolarova L, Krizova K, et al (2019) Identification of deleterious germline CHEK2 mutations and their association with breast and ovarian cancer. Int J Cancer 145:1782–1797. doi: 10.1002/ijc.32385
  23. Holub D, Flodrova P, Pika T, et al (2019) Mass Spectrometry Amyloid Typing Is Reproducible across Multiple Organ Sites. Biomed Res Int 2019:1–9. doi: 10.1155/2019/3689091
  24. Dudakova L, Evans CJ, Pontikos N, et al (2019) The utility of massively parallel sequencing for posterior polymorphous corneal dystrophy type 3 molecular diagnosis. Exp Eye Res 182:160–166. doi: 10.1016/j.exer.2019.03.002
  25. Vevera J, Zarrei M, Hartmannová H, et al (2019) Rare copy number variation in extremely impulsively violent males.Genes, Brain Behav 18:e12536. doi: 10.1111/gbb.12536
  26. Pavlova S, Smardova J, Tom N, Trbusek M (2019) Detection and Functional Analysis of TP53 Mutations in CLL. In: Methods in molecular biology (Clifton, N.J.). pp 63–81
  27. Yu FP, Sajdak BS, Sikora J, et al (2019) Acid Ceramidase Deficiency in Mice Leads to Severe Ocular Pathology and Visual Impairment. Am J Pathol 189:320–338. doi: 10.1016/j.ajpath.2018.10.018
  28. Yu FPS, Molino S, Sikora J, et al (2019) Hepatic pathology and altered gene transcription in a murine model of acid ceramidase deficiency. Lab Investig 99:1572–1592. doi: 10.1038/s41374-019-0271-4
  29. Devuyst O, Olinger E, Weber S, et al (2019) Autosomal dominant tubulointerstitial kidney disease. Nat Rev Dis Prim 5:60. doi: 10.1038/s41572-019-0109-9
  30. Nunvar J, Hogan AM, Buroni S, et al (2019) The Effect of 2-Thiocyanatopyridine Derivative 11026103 on Burkholderia Cenocepacia: Resistance Mechanisms and Systemic Impact. Antibiotics 8:159. doi: 10.3390/antibiotics8040159
  31. Machálková M, Pavlatovská B, Michálek J, et al (2019) Drug Penetration Analysis in 3D Cell Cultures Using Fiducial-Based Semiautomatic Coregistration of MALDI MSI and Immunofluorescence Images. Anal Chem 91:13475–13484. doi: 10.1021/acs.analchem.9b02462
  32. Pelet A, Skopova V, Steuerwald U, et al (2019) PAICS deficiency, a new defect of de novo purine synthesis resulting in multiple congenital anomalies and fatal outcome. Hum Mol Genet 1–30. doi: 10.1093/hmg/ddz237
  33. Sedlar K, Kolek J, Gruber M, et al (2019) A transcriptional response of Clostridium beijerinckii NRRL B-598 to a butanol shock. Biotechnol Biofuels 12:243. doi: 10.1186/s13068-019-1584-7
  34. Káňová E, Tkáčová Z, Bhide K, et al (2019) Transcriptome analysis of human brain microvascular endothelial cells response to Neisseria meningitidis and its antigen MafA using RNA-seq. Sci Rep 9:18763. doi: 10.1038/s41598-019-55409-y
  35. Capkova Z, Capkova P, Srovnal J, et al (2019) Differences in the importance of microcephaly, dysmorphism, and epilepsy in the detection of pathogenic CNVs in ID and ASD patients.PeerJ 2019:e7979. doi: 10.7717/peerj.7979
  36. Stehlikova Z, Tlaskal V, Galanova N, et al (2019) Oral Microbiota Composition and Antimicrobial Antibody Response in Patients with Recurrent Aphthous Stomatitis. Microorganisms 7:636. doi: 10.3390/microorganisms7120636
  37. Vasylkivska M, Jureckova K, Branska B, et al (2019) Transcriptional analysis of amino acid, metal ion, vitamin and carbohydrate uptake in butanol-producing Clostridium beijerinckii NRRL B-598. PLoS One 14:e0224560. doi: 10.1371/journal.pone.0224560
  38. Bleyer AJ, Kidd K, Johnson E, et al (2019) Quality of life in patients with autosomal dominant tubulointerstitial kidney disease. Clin Nephrol 92:302–311. doi: 10.5414/CN109842

Publications with the support of NCMG for the year 2018

  1. Gstrein T, Edwards A, Přistoupilová A, et al (2018) Mutations in Vps15 perturb neuronal migration in mice and are associated with neurodevelopmental disease in humans. Nat Neurosci 1. doi: 10.1038/s41593-017-0053-5
  2. Dudakova L, Vercruyssen JHJ, Balikova I, et al (2018) Analysis of KERA in four families with cornea plana identifies two novel mutations. Acta Ophthalmol 96:e87–e91. doi: 10.1111/aos.13484
  3. Dudakova L, Cheong S-S, Merjava SR, et al (2018) Familial Limbal Stem Cell Deficiency: Clinical, Cytological and Genetic Characterization. Stem Cell Rev Reports 14:148–151. doi: 10.1007/s12015-017-9780-y
  4. Paderova J, Drabova J, Holubova A, et al (2018) Under the mask of Kabuki syndrome: Elucidation of genetic-and phenotypic heterogeneity in patients with Kabuki-like phenotype. Eur J Med Genet. doi: 10.1016/j.ejmg.2018.01.00
  5. van den Ameele J, Jedlickova I, Pristoupilova A, et al (2018) Teenage-onset progressive myoclonic epilepsy due to a familial C9orf72 repeat expansion. Neurology doi: 10.1212/WNL.0000000000004999
  6. Brazdilova K, Plevova K, Skuhrova Francova H, et al (2018) Multiple productive IGH rearrangements denote oligoclonality even in immunophenotypically monoclonal CLL. Leukemia 32:234–236. doi: 10.1038/leu.2017.274
  7. Kremlikova Pourova R, Paderova J, Copikova J, et al (2018) SD-OCT imaging as a valuable tool to support molecular genetic diagnostics of Usher syndrome type 1. J Am Assoc Pediatr Ophthalmol Strabismus 1–3. doi: 10.1016/j.jaapos.2017.12.009
  8. Liskova P, Dudakova L, Evans CJ, et al (2018) Ectopic GRHL2 Expression Due to Non-coding Mutations Promotes Cell State Transition and Causes Posterior Polymorphous Corneal Dystrophy 4. Am J Hum Genet 102:447–459. doi: 10.1016/j.ajhg.2018.02.002
  9. Zikánová M, Wahezi D, Hay A, et al (2018) Clinical manifestations and molecular aspects of phosphoribosylpyrophosphate synthetase superactivity in females. Rheumatology 1–6. doi: 10.1093/rheumatology/key041
  10. Slamova Z, Nazaryan-Petersen L, Mehrjouy MM, et al (2018) Very short DNA segments can be detected and handled by the repair machinery during germline chromothriptic chromosome reassembly. Hum Mutat. doi: 10.1002/humu.23408
  11. Springer D, Loucky J, Tesner P, et al (2018) Importance of the integrated test in the Down’s syndrome screening algorithm. J Med Screen 096914131775253. doi: 10.1177/0969141317752533
  12. Ivády G, Madar L, Dzsudzsák E, et al (2018) Analytical parameters and validation of homopolymer detection in a pyrosequencing-based next generation sequencing system. BMC Genomics 19:1–8. doi: 10.1186/s12864-018-4544-x
  13. Pafčo B, Čížková D, Kreisinger J, et al (2018) Metabarcoding analysis of strongylid nematode diversity in two sympatric primate species. Sci Rep 8:5933. doi: 10.1038/s41598-018-24126-3
  14. Malcikova J, Tausch E, Rossi D, et al (2018) ERIC recommendations for TP53 mutation analysis in chronic lymphocytic leukemia-update on methodological approaches and results interpretation. Leukemia 1–11. doi: 10.1038/s41375-017-0007-7
  15. Vlčková K, Kreisinger J, Pafčo B, et al (2018) Diversity of Entamoeba spp. in African great apes and humans: an insight from Illumina MiSeq high-throughput sequencing. Int J Parasitol. doi: 10.1016/j.ijpara.2017.11.008
  16. Sedlar K, Koscova P, Vasylkivska M, et al (2018) Transcription profiling of butanol producer Clostridium beijerinckii NRRL B-598 using RNA-Seq. BMC Genomics 19:415. doi: 10.1186/s12864-018-4805-8
  17. Kutilova I, Janecko N, Cejkova D, et al (2018) Characterization of blaKPC-3-positive plasmids from an Enterobacter aerogenes isolated from a corvid in Canada. J Antimicrob Chemother. doi: 10.1093/jac/dky199
  18. Čížková D, Baird SJE, Těšíková J, et al (2018) Host subspecific viral strains in European house mice: Murine cytomegalovirus in the Eastern ( Mus musculus musculus ) and Western house mouse ( Mus musculus domesticus ). Virology 521:92–98. doi: 10.1016/j.virol.2018.05.023
  19. Tom N, Tom O, Malcikova J, et al (2018) ToTem: a tool for variant calling pipeline optimization. BMC Bioinformatics 19:243. doi: 10.1186/s12859-018-2227-x
  20. Evans CJ, Dudakova L, Skalicka P, et al (2018) Schnyder corneal dystrophy and associated phenotypes caused by novel and recurrent mutations in the UBIAD1 gene. BMC Ophthalmol 18:250. doi: 10.1186/s12886-018-0918-8
  21. Majer F, Piherova L, Reboun M, et al (2018) LAMP2 exon-copy number variations in Danon disease heterozygote female probands: Infrequent or underdetected? Am J Med Genet Part A. doi: 10.1002/ajmg.a.40430
  22. Agrawal K, Das V, Táborská N, et al (2018) Differential Regulation of Methylation-Regulating Enzymes by Senescent Stromal Cells Drives Colorectal Cancer Cell Response to DNA-Demethylating Epi-Drugs. Stem Cells Int 2018:1–11. doi: 10.1155/2018/6013728
  23. Farrell P, Férec C, Macek M, et al (2018) Estimating the age of p.(Phe508del) with family studies of geographically distinct European populations and the early spread of cystic fibrosis. Eur J Hum Genet 1. doi: 10.1038/s41431-018-0234-z
  24. Hiatt SM, Neu MB, Ramaker RC, et al (2018) De novo mutations in the GTP/GDP-binding region of RALA, a RAS-like small GTPase, cause intellectual disability and developmental delay. PLOS Genet 14:e1007671. doi: 10.1371/journal.pgen.1007671
  25. Živná M, Kidd K, Přistoupilová A, et al (2018) Noninvasive Immunohistochemical Diagnosis and Novel MUC1 Mutations Causing Autosomal Dominant Tubulointerstitial Kidney Disease. J Am Soc Nephrol 29:2418–2431. doi: 10.1681/ASN.2018020180
  26. Trizuljak J, Kozubík KS, Radová L, et al (2018) A novel germline mutation in GP1BA gene N-terminal domain in monoallelic Bernard-Soulier syndrome. Platelets 1–7. doi: 10.1080/09537104.2018.1529300
  27. Gast C, Marinaki A, Arenas-Hernandez M, et al (2018) Autosomal dominant tubulointerstitial kidney disease-UMOD is the most frequent non polycystic genetic kidney disease. BMC Nephrol 19:301. doi: 10.1186/s12882-018-1107-y
  28. Čaplovičová M, Moslerová V, Dupej J, et al (2018) Modeling age-specific facial development in Williams-Beuren-, Noonan-, and 22q11.2 deletion syndromes in cohorts of Czech patients aged 3-18 years: A cross-sectional three-dimensional geometric morphometry analysis of their facial gestalt. Am J Med Genet Part A. doi: 10.1002/ajmg.a.40659
  29. Soukupova J, Zemankova P, Lhotova K, et al (2018) Validation of CZECANCA (CZEch CAncer paNel for Clinical Application) for targeted NGS-based analysis of hereditary cancer syndromes. PLoS One 13:e0195761. doi: 10.1371/journal.pone.0195761
  30. Puchmajerová A, Tornikidis J, Mrňa L, et al (2018) Hereditární formy karcinomu prsu : genetická etiologie a současné možnosti prevence a chirurgické léčby. Čas Lék čes 157:90–95
  31. Hlavac V, Kovacova M, Elsnerova K, et al (2018) Use of Germline Genetic Variability for Prediction of Chemoresistance and Prognosis of Breast Cancer Patients. Cancers (Basel) 10:511. doi: 10.3390/cancers10120511
  32. Kmoch S, Zeman J (2018) Moderní metody v diagnostice a výzkumu genetických příčin vzácných onemocnění. Cas Lek Cesk 157:133–136
  33. Harper JC, Aittomäki K, Borry P, et al (2018) Recent developments in genetics and medically-assisted reproduction: from research to clinical applications. Hum Reprod Open. doi: 10.1093/hropen/hox015
  34. Yu FP, Islam D, Sikora J, et al (2018) Chronic lung injury and impaired pulmonary function in a mouse model of acid ceramidase deficiency. Am J Physiol Cell Mol Physiol ajplung.00223.2. doi: 10.1152/ajplung.00223.2017

Publications with the support of NCMG for the year 2017

  1. Pal K, Bystry V, Reigl T, et al (2017) GLASS: assisted and standardized assessment of gene variations from Sanger sequence trace data. Bioinformatics 33:3802–3804. doi: 10.1093/bioinformatics/btx423
  2. Kim Y, Park S-J, Manson SR, et al (2017) Elevated urinary CRELD2 is associated with endoplasmic reticulum stress-mediated kidney disease. JCI insight. doi: 10.1172/jci.insight.92896
  3. Kristoffersson U, Macek M (2017) From Mendel to Medical Genetics. Eur J Hum Genet 25:S53–S58. doi: 10.1038/ejhg.2017.157
  4. Hojny J, Zemankova P, Lhota F, et al (2017) Multiplex PCR and NGS-based identification of mRNA splicing variants: Analysis of BRCA1 splicing pattern as a model. Gene 637:41–49. doi: 10.1016/j.gene.2017.09.025
  5. Bencurova P, Baloun J, Musilova K, et al (2017) MicroRNA and mesial temporal lobe epilepsy with hippocampal sclerosis: Whole miRNome profiling of human hippocampus. Epilepsia 58:1782–1793. doi: 10.1111/epi.13870
  6. Dudakova L, Stranecky V, Ulmanova O, et al (2017) Segregation of a novel p.(Ser270Tyr) MAF mutation and p.(Tyr56∗) CRYGD variant in a family with dominantly inherited congenital cataracts. Mol Biol Rep. doi: 10.1007/s11033-017-4121-4
  7. Růžička K, Zhang M, Campilho A, et al (2017) Identification of factors required for m(6) A mRNA methylation in Arabidopsis reveals a role for the conserved E3 ubiquitin ligase HAKAI. New Phytol 215:157–172. doi: 10.1111/nph.14586
  8. Krsička D, Geryk J, Vlčková M, et al (2017) Identification of likely associations between cerebral folate deficiency and complex genetic- and metabolic pathogenesis of autism spectrum disorders by utilization of a pilot interaction modeling approach. Autism Res. doi: 10.1002/aur.1780
  9. Liskova P, Dudakova L, Krepelova A, et al (2017) Replication of SNP associations with keratoconus in a Czech cohort. PLoS One 12:e0172365. doi: 10.1371/journal.pone.0172365
  10. Mazurova S, Magner M, Kucerova-Vidrova V, et al (2017) Thymidine kinase 2 and alanyl-tRNA synthetase 2 deficiencies cause lethal mitochondrial cardiomyopathy: case reports and review of the literature. Cardiol Young 27:936–944. doi: 10.1017/S1047951116001876

Publications with the support of NCMG for the year 2016

  1. Nagy B, Nagy B, Fila L, et al (2016) Human Epididymis Protein 4: A Novel Serum Inflammatory Biomarker in Cystic Fibrosis. Chest 150:661–72. doi: 10.1016/j.chest.2016.04.006
  2. Paděrová J, Holubová A, Simandlová M, et al (2016) Molecular genetic analysis in 14 Czech Kabuki syndrome patients is confirming the utility of phenotypic scoring. Clin Genet 90:230–7. doi: 10.1111/cge.12754
  3. Hubacek M, Kripnerova T, Nemcikova M, et al (2016) Odontogenic keratocysts in the Basal Cell Nevus (Gorlin-Goltz) Syndrome associated with paresthesia of the lower jaw: Case report, retrospective analysis of a representative Czech cohort and recommendations for the early diagnosis. Neuro Endocrinol Lett 37:269–276.
  4. Bolar NA, Golzio C, Živná M, et al (2016) Heterozygous Loss-of-Function SEC61A1 Mutations Cause Autosomal-Dominant Tubulo-Interstitial and Glomerulocystic Kidney Disease with Anemia. Am J Hum Genet 99:174–87. doi: 10.1016/j.ajhg.2016.05.028
  5. Hartmannová H, Piherová L, Tauchmannová K, et al (2016) Acadian variant of Fanconi syndrome is caused by mitochondrial respiratory chain complex I deficiency due to a non-coding mutation in complex I assembly factor NDUFAF6. Hum Mol Genet. doi: 10.1093/hmg/ddw245
  6. Kousal B, Dudakova L, Gaillyova R, et al (2016) Phenotypic features of CRB1-associated early-onset severe retinal dystrophy and the different molecular approaches to identifying the disease-causing variants. Graefe’s Arch Clin Exp Ophthalmol 1–7. doi: 10.1007/s00417-016-3358-2
  7. Mizzi C, Dalabira E, Kumuthini J, et al (2016) A European Spectrum of Pharmacogenomic Biomarkers: Implications for Clinical Pharmacogenomics. PLoS One 11:e0162866. doi: 10.1371/journal.pone.0162866
  8. Neřoldová M, Stránecký V, Hodaňová K, et al (2016) Rare variants in known and novel candidate genes predisposing to statin-associated myopathy. Pharmacogenomics 17:1405–14. doi: 10.2217/pgs-2016-0071
  9. Stránecký V, Neřoldová M, Hodaňová K, et al (2016) Large copy-number variations in patients with statin-associated myopathy affecting statin myopathy-related loci. Physiol Res 1–19.
  10. Weidler S, Stopsack KH, Hammermann J, et al (2016) A product of immunoreactive trypsinogen and pancreatitis-associated protein as second-tier strategy in cystic fibrosis newborn screening. J Cyst Fibros. doi: 10.1016/j.jcf.2016.07.0

NCMG users

Charles University provides support to users of a wide range of specializations, both domestic and foreign. The NCMG infrastructure is also used in teaching and specialization education for students of bachelor's, master's, and doctoral programs, as well as for medical staff - physicians in the fields of medical genetics, pediatrics, gynecology and obstetrics, and specialists in laboratory methods - clinical genetics.

Domestic universities:

  • 1.LF UK, Institute of Biochemistry and Experimental Oncology
  • 2. LF UK, Institute of Biology and Medical Genetics
  • 1.LF UK, KDDL, Laboratory of Eye Biology and Pathology
  • Department of Pediatric Neurology2. LF UK and University Hospital Motol
  • Department of Neurology, 2. LF UK and University Hospital Motol
  • Department of Cardiology, 2. LF UK and University Hospital Motol
  • Department of Urology, 2. LF UK and University Hospital Motol
  • Department of Stomatology of Children and Adults, 2. LF UK and University Hospital Motol
  • Department of Pediatrics, 2. LF UK and University Hospital Motol
  • Department of Gynaecology and Obstetrics, 2. LF UK and University Hospital Motol
  • Institute of Immunology, 2. LF UK and University Hospital Motol
  • Department of Pathology and Molecular Medicine, 2. LF UK and University Hospital Motol
  • Department of Surgery, 2. LF UK and University Hospital Motol
  • Department of Dermatovenerology, 2. LF UK and University Hospital Motol
  • Childhood Leukemia Investigation Prague, 2. LF UK
  • Institute of medical microbiology, 2. LF UK
  • Institute of Biology, Faculty of Medicine, Charles University in Pilsen
  • University of West Bohemia in Pilsen - Faculty of Health Studies

Domestic public research organizations:

  • Institute of Hematology and Blood Transfusion
  • Institute of Biotechnology of the Czech Academy of Sciences
  • Institute of Experimental Medicine of the Czech Academy of Sciences
  • Institute of Molecular Genetics of the Czech Academy of Sciences
  • IKEM, Prague, Department of Nephrology
  • IKEM, Prague, Department of Cardiology
  • IKEM, Prague, Department of Hepatogastroenterology
  • Society of Medical Genetics and Genomics, Czech Medical Society of J. E. Purkyně
  • Association of General Practitioners of the Czech Republic

Domestic health care providers:

  • University Hospital Motol, Prague, Children's Cardiocentre
  • University Hospital Motol, Prague, Laboratory of Molecular Genetics, Pediatric Clinic
  • University Hospital Vinohrady, Prague
  • University Hospital Motol, Department of Medical Molecular Genetics
  • II. Department of Internal Medicine - Department of Cardiology and Angiology
  • Psychiatric clinic of the General Teaching Hospital
  • III. Internal Clinic of General Teaching Hospital - Department of Endocrinology and Metabolism
  • Pediatric Nephrology, Department of Pediatric and Adolescent Medicine, General Teaching Hospital
  • Department of Nephrology, General Teaching Hospital
  • Department of Pediatric and Adolescent Medicine, General Teaching Hospital
  • Mitochondrial Laboratory of General Teaching Hospital
  • University Hospital Ostrava - Department of Medical Genetics
  • University Hospital Hradec Králové - Department of Medical Genetics

Industrial enterprises:

  • Pronatal.cz
  • Repromeda.cz
  • Gennet.cz
  • VZP
  • Biopharm
  • Biogen
  • GeneAge Technologies
  • Multiplicom
  • Vertex Pharmaceuticals
  • Luminex
  • Abbott Molecular
  • IVF Center prof Zech Ltd.
  • Bioptic laboratory s.r.o

Foreign universities, research institutions, and healthcare providers:

  • Laboratory of Molecular and Medical Genetics, Faculty of Pure and Applied Sciences, University of Cyprus, Cyprus; Constantinos Deltas
  • Clinical Genetics Department, National Research Center, Cairo, Egypt; Samia Temtamy
  • Clinica Pediatrica, Monza, Italy; Angelo Selicorni
  • Kinderklinik, Goettingen, Germany; Steinfeld
  • Broad Institute, USA; Lucien Ronco
  • Pediatric Nephrology Unit, University Hospital Reina Sofia, Cordoba, Spain; Montserrat Anton-Gamero
  • Section on Nephrology, Wake Forest University School of Medicine, Winston-Salem, USA; A. Bleyer
  • Nephrology Department, Hospital Fernando Fonseca, Portugal; Karin Soto
  • Nephrology Department, Portsmouth Hospitals, Portmouth, United Kingdom; Dr. Venkat-Raman, Dr. Christine Gast
  • Nephrology Unit, Guy's Hospital, London, United Kingdom; A. Marinaki
  • Center for Human Genetics, Leuven, Belgium; Gert Matthijs
  • Rare NCL Consortium, - a group of international laboratories
  • University of Zagreb, prof. Sertic
  • Children's Faculty Hospital in Košice - MUDr. Šaligová
  • Slovak Academy of Sciences - Institute of Experimental Endocrinology Skopkova
  • University of Uppsala
  • University of Vita-Salute of San Raffaele
  • Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry
  • University of Szeged
  • Center for Research and Technology Hellas - CERTH
  • University of Oslo

Foreign industrial enterprises:

  • Genzyme

Open Access

NCMG is a distributed multi-centered, nation-wide research infrastructure. The expertise and instrumentation available within NCMG can be used by the users from the Czech Republic and from abroad as well. It can be also used by the commercial sector. NCMG provides transparent information to their (potential) users on the access rules. NCMG through individual nodes (core facilities) support their users by providing an access to its instrumentation, analytical expertise, bioinformatic and statistical support, education and training and by providing an access to well defined cohorts of patients, control individuals and various clinical materials. Users have to adapt to the concrete access rules of the core facility they visit.

Users are obliged to acknowledge NCMG in any output (publications, patents, public presentations) that were created by using the NCMG instrumentation or expertise:

Since 2020:

"The project "Modernization and instrumental upgrade of the National Center for Medical Genomics" (reg. No. CZ.02.1.01/0.0/0.0/18_046/0015515) is supported by the Operational Programme Research, Development and Education."

and

„We acknowledge the CF [name of the Core Facility] supported by the NCMG research infrastructure (LM2018132 funded by MEYS CR) for their support with obtaining scientific data presented in this paper.“

Before 2020:

"The authors would like to thank to The National Center for Medical Genomics (LM2015091) for providing allelic frequencies in ethnically matched population for comparison (project CZ.02.1.01/0.0/0.0/16_013/0001634)"

or

"We acknowledge the CF [name of the Core Facility] supported by the NCMG research infrastructure (LM2015091 funded by MEYS CR) for their support with obtaining scientific data presented in this paper."

 


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