Application of genomic approaches in cancer research and diagnostics
The transformation of normal to malignant cells may be caused by many different mechanisms that share a single common feature – the alteration of genetic information and subsequent disruption of cellular regulatory mechanisms, which thus lead to uncontrolled proliferation. Some of these genetic alterations have already been described and are routinely analysed in oncological diagnostics, e.g. TP53, ATM or BRCA gene mutations or specific translocations occurring in leukemias, lymphomas and other tumours. The importance of many other genomic aberrations found in tumours and their influence on the malignant potential of transformed cells should be analysed as well as the impact of individual genetic variants on tumour behaviour. Novel technologies including high-resolution SNP microarrays and high-throughput genome sequencing (massive parallel sequencing) provide fast and complex analysis of the human genome. These methods will be used to characterise genetic information of the patient‘s malignant and non-malignant cells to reveal the mechanisms of cellular transformation.
The expected outputs of this work package are:
1) the identification of recurrent genomic alterations in hematological and other malignancies, which could be used in cancer diagnostics and as a potential therapeutic target,
2) the analysis of the influence of the host genome on disease progression,
3) the characterisation of the regulatory pathways disrupted in tumour cells. The outcome of these studies is expected to be used as an initial point for focused research as well as for direct use in diagnostics of haematological and oncological malignancies.
Technologies used: massive parallel DNA sequencing (next-generation high-throughput sequencing), SNP mapping (high resolution SNP microarrays), gene expression profiling (microarrays, QRT-PCR), FACS, bioinformatic processing.
Brochure about the FP7 project "Next Generation Sequencing platform for targeted Personalized Therapy of Leukemia" to download can be found HERE.
list / cards
Name and position |
Phone |
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Prof. Jiří Mayer Senior Researcher |
+420 54949 1301, +420 532 233 643, +420 532 233 603 | |
Vasileios Bikos Researcher |
+420 54949 8196 | |
Kateřina Černá Researcher |
+420 54949 8144, +420 532 234 177 | |
Daniela Komrsková, Ph.D. Technician |
+420 54949 7922, +420 532 234 623 | |
Jana Kotašková, Ph.D. Researcher |
+420 54949 5442, +420 532 234 396 | |
Kateřina Staňo Kozubík, Ph.D. Researcher |
+420 54949 8293, +420 54949 7947, +420 532 234 623 | |
Radana Studená, Ph.D. Researcher |
+420 54949 8194 | |
Jan Verner, Ph.D. Researcher |
+420 54949 5437, +420 532 234 206 | |
Barbara Kantorová, Ph.D. PhD student |
+420 54949 7918 | |
Nikola Tom PhD student |
+420 54949 6926, +420 54949 5786 | |
Tereza Cermanová Specialist |
+420 54949 7934 | |
Alexey Nikolayevich Nikolayevich Davydov Specialist |
+420 54949 5892 | |
Jana Jedličková laborantka |
+420 54949 6997 | |
Tomáš Loja, Ph.D. Researcher |
+420 54949 7455 | |
Lenka Fajkusová associate professor |
+420 532 234 625 | |
Gabriela Pavlasová odborná pracovnice, odborná pracovnice - PhD student |
+420 54949 8144, +420 532 234 177 | |
Václav Šeda odborný pracovník, odborný pracovník - PhD student |
+420 54949 8144 | |
Tomáš Reigl odborný pracovník |
+420 54949 7428 | |
Lenka Radová, Ph.D. senior researcher |
+420 54949 5841 | |
Jana Pavloušková PhD student |
+420 54949 7584, +420 532 234 624 | |
Petr Kulhánek Researcher |
+420 54949 5459 | |
Marianna Romžová, Ph.D. senior researcher |
+420 54949 7918 | |
Cosimo Lobello odborný pracovník - PhD student |
+420 54949 8196 | |
Prof. Zdeněk Ráčil, Ph.D. Senior Researcher |
+420 532 232 144, +420 532 233 603 | |
Vojtěch Bystrý PhD student |
+420 54949 8964, +420 54949 6926 | |
Karla Plevová, Ph.D. PhD student |
+420 54949 5314, +420 532 234 396 | |
Petra Sedláková laborantka |
+420 54949 6997 | |
Ivona Blaháková Specialist |
+420 54949 6997, +420 532 234 623 | |
Veronika Mančíková, Ph.D. odborná pracovnice ve výzkumu - postdoc |
+420 54949 5875 | |
Ondrej Šedo, Ph.D. Senior researcher |
+420 54949 7304, +420 54949 8427 | |
Přemysl Souček, Ph.D. senior researcher |
+420 54949 7567 | |
Tomáš Freiberger, Ph.D. Research Group Leader |
+420 543 182 548 | |
Kamila Réblová, Ph.D. Researcher |
+420 54949 7586, +420 532 234 625 | |
Karol Pál PhD student |
+420 54949 6926 | |
Lenka Humpolíková Adámková, Ph.D. odborná pracovnice |
+420 54949 3878 | |
Lucie Kopálková laborantka |
+420 54949 7567 | |
Michal Růžička odborný pracovník - PhD student |
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Michael Doubek profesor |
+420 532 232 144, +420 532 233 603 | |
Sonali Sharma |
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Marek Svoboda, Ph.D. Researcher |
+420 54949 6899 | |
Marie Jarošová odborná pracovnice ve výzkumu |
+420 532 234 232 | |
Adam Krejčí |
+420 54949 8293 | |
Andrea Grioni odborný pracovník |
+420 54949 6926 | |
Jaromír Gumulec PhD student |
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Renata Hurníková |
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Jitka Kabáthová Researcher |
+420 532 234 188 | |
Viera Vakulová PhD student |
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Jiří Baloun Researcher |
+420 54949 3595 | |
Jitka Malčíková Researcher |
+420 54949 7948, +420 532 234 396 | |
Jiří Štika odborný pracovník ve výzkumu |
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Jakub Trizuljak |
+420 532 233 559, +420 532 233 603 | |
Helena Peschelová |
+420 54949 5875 | |
Anastasiya Volakhava |
+420 54949 7803 | |
Šárka Pospíšilová Research Group Leader |
+420 54949 7917, +420 532 234 622 | |
Helena Olbertová PhD student |
+420 54949 7584, +420 532 234 188 | |
Šárka Pospíšilová Research Group Leader |
+420 54949 7917, +420 532 234 622 | |
Blanka Kubešová PhD student |
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Martina Lengerová Researcher |
+420 532 234 629 | |
Šárka Pavlová Researcher |
+420 532 234 207 | |
Martin Čulen Specialist |
+420 532 234 641 |
Molecular – biological diagnostic and research laboratory equipped with instrumentation for routine diagnostic tasks such as PCR, qPCR, DNA electrophoresis and DNA sequencing as well as equipment serving mainly for research needs such as microarray scanners (short and long oligonucleotide platforms) or nucleofector for high-efficient transfections.
Supervisor: Mgr. Karla Plevová, Ph.D.
Consultants: Mgr. Kamila Réblová, Ph.D., Mgr. Karol Pál
With the advent of massively parallel sequencing (MPS), many challenges in molecular biology and medicine have emerged including the discovery of novel molecular mechanisms and biological networks. Due to the accelerated development in genomics and computational technologies it is possible to study molecular processes at various levels ranging from primary DNA structure, through genome organization, to its expression in a comprehensive manner. Among other biological contexts this is especially important in human diseases, such as cancer. In the proposed PhD project, a PhD candidate will perform advanced bioinformatics analyses of genomic data obtained using MPS in cases with chronic lymphocytic leukemia (CLL). The student will focus on discovery of genetic and expression patterns related to specific disease conditions, namely CLL early development, and accumulation of adverse genomic defects leading to refractory disease. In particular, tumor signatures will be extracted from DNA and RNA sequencing data in an attempt to provide a detailed picture of molecular processes underlying CLL clonal evolution. It is expected that the student will acquire good knowledge of existing solutions, design his/her own bioinformatics tools and employ computing approaches based on machine learning, if necessary. Obtained data will be validated using available independent datasets and will serve as a basis for consequent wet-lab experiments aiming to define novel clinically relevant biomarkers for better disease stratification and management.
Keywords: chronic lymphocytic leukemia, cancer genome, clonal evolution, biomarkers, mutation signature, expression pattern, tumor interactions, bioinformatics tools, computing technologies
Supervisor: prof. RNDr. Šárka Pospíšilová, Ph.D.
Consultants: RNDr. Jitka Malčíková, Ph.D., MVDr. Boris Tichý, Ph.D.
The development of human leukemias is closely associated with the genomic changes in relevant blood and bone marrow cells. The amount and type of these changes significantly influences the disease development, patient prognosis and therapy response. The aim of the PhD study will be focused on detailed genomic analysis of B-lymphocytes derived from patients with lymphoproliferative disorders, e.g. with chronic lymphocytic leukemia (CLL), acute lymphoblastic leukemia (ALL) or lymphomas. The novel genomic approaches including high-throughput next-generation sequencing, SNP microarrays or quantitative / digital PCR will be used to characterize genetic information of the patient‘s malignant and non-malignant cells to reveal the mechanisms of cellular transformation and detect the evolution of B- or T-cell clones during the disease development. The novel technologies could also enable to discover novel diagnostic and prognostic markers, which would facilitate the administration of the patient treatment.
Supervisor: Mgr. Vojtěch Bystrý, Ph.D.
Consultants: prof. RNDr. Šárka Pospíšilová, Ph.D.
Human lymphoproliferative disorders such as leukemias are known to be associated with a characteristic genomic alterations, such as chromosomal translocations typically affecting a limited number of recurrent genes with several variable partner genes. The presence of such fusion genes might be instrumental for the development of the disease and its recognition and identification an important prognostic marker. Even more importantly fusion genes can be targeted by chemotherapy and/or new drugs, therefore genomic profiling has the potential to identify new potentially druggable targets. The aim of the PhD study will be to work with NGS systems and to analyse the resulting data with the focus on detection and characterisation of genetic abnormalities associated with leukemia. Student should also design and implement an automated system for identification, storing and classification of the genomic aberrations.
Supervisor: Mgr. Vojtěch Bystrý, Ph.D.
Consultants: prof. RNDr. Šárka Pospíšilová, Ph.D.
The immunoglobulin superfamily of proteins is a group of recognition and signalling proteins expressed on cell surfaces. Analysis of immunoglobulin (IG) and T cell receptor (TR) repertoires – or immunoprofiling, has been instrumental in understanding a wide range of diseases with an underlying immune basis, such as lymphomas, infections, and allergies. With the introduction of next generation sequencing (NGS) methods, much more detailed insights are now available. However, this also poses unique challenges for sequence analysis due to the enormous inherent complexity, huge diversity and temporal variation of immune responses combined with imprecise and bias-prone nature of current NGS technologies. The aim of the PhD study will be to design, implement and apply in silico analytical methods for processing of NGS data from leukemia patient samples. The focus will be the recognition and quantification of repertoire abnormalities in general and the clonality assessment and MRD monitoring in particular.
29. ledna 2018 9:46
LECTURE: Dr. Ondrej Hovorka: Models of magnetic nanoparticles for biomedical applications
25. ledna 2018 18:21
WHEN: 30. 01. 2018 WHERE: CEITEC BUT, Purkynova 123, large meeting room SPEAKER: Dr Andriy Marko TALK: Advances in PELDOR…