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Advanced Nano and Microtechnologies Advanced Materials Structural Biology Gen. and Prot. of Plant Systems Molecular Medicine Brain and Mind Research Molecular Vet. Medicine

Medical Genomics

Research Group Leader
Researcher ID
Phone: +420 54949 7917, +420 532 234 622
E-mail:
Office:

Research areas

  • Introduction of high-throughput analyses into medical research and diagnostics, development of new diagnostic techniques
  • Identification and analysis of novel diagnostic and prognostic markers and therapeutical targets

Main objectives

  • Introduction of high-throughput analyses of human genomes (whole genome/exom sequencing, transcriptome profiling, microRNA detection, SNP analysis, etc.). Utilization of these technologies in medicine and development of diagnostic tests based on high-throughput methods
  • Mutational analyses of human cells in relation to cancer, neuromuscular, neurodegenerative, metabolic and skin disorders; the detection of novel prognostic markers

Content of research

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

E-mail

Phone

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
Daniela Komrsková, Ph.D.
Technician
+420 54949 7922
Jana Kotašková, Ph.D.
Researcher
+420 54949 5442
Kateřina Staňo Kozubík, Ph.D.
Researcher
+420 54949 8293, +420 54949 7947, +420 532 234 207
Radana Studená, Ph.D.
Researcher
+420 54949 8194
Jan Verner, Ph.D.
Researcher
+420 54949 5437, +420 532 234 206
Kristína Zápražná, Ph.D.
Researcher
+420 54949 7938
Jana Chovancová
PhD student
Barbara Kantorová, Ph.D.
PhD student
+420 54949 7918
Helena Kočková
PhD student
+420 54949 7584
Nikola Tom
PhD student
+420 54949 6926, +420 54949 5786
Tereza Cermanová
Specialist
+420 54949 7934
Alexey Nikolayevich Nikolayevich Davydov
Specialist
+420 54949 5892
Kateřina Kolesová
Project Financial Manager
+420 54949 4064
Jana Jedličková
Laborant
+420 54949 6997
Tomáš Loja, Ph.D.
Researcher
+420 54949 7455
Lenka Fajkusová
associate professor
+420 532 234 625
Gabriela Pavlasová
+420 54949 8144
Václav Šeda
+420 54949 8144
Adam Krejčí
+420 54949 8293
Tomáš Reigl
+420 54949 7428
Lenka Radová, Ph.D.
+420 54949 5841
Maria Elena Candela, Ph.D.
+420 54949 5651
Tatiana Kováčová
PhD student
Katarína Vondrášková
Jana Pavloušková
PhD student
+420 54949 7584, +420 532 234 624
Tereza Kršjaková
PhD student
Pavla Hujová
Student
Petr Kulhánek
Researcher
+420 54949 5459
Michal Kramárek
Hana Plešingerová
PhD student
+420 532 234 109
Kristýna Hrnčířová, Ph.D.
Researcher
Marianna Romžová, Ph.D.
+420 54949 7918
Iva Kotásková
Cosimo Lobello
+420 54949 8196
Prof. Zdeněk Ráčil, Ph.D.
Senior Researcher
+420 532 232 214
Vojtěch Bystrý
PhD student
+420 54949 6926
Jakub Carda
Project financial manager
Prof. Šárka Pospíšilová, Ph.D.
Research Group Leader
+420 54949 7917, +420 532 234 622
Kristýna Fiedorová
Karla Plevová, Ph.D.
PhD student
+420 54949 5314, +420 532 234 396
Petra Sedláková
+420 54949 6997
Veronika Kozlová
Jakub Hynšt
+420 54949 6926
Ivona Blaháková
Specialist
+420 54949 6997
Michal Šmída, Ph.D.
Researcher
+420 54949 6695
Viera Vakulová
PhD student
Jiří Baloun, Ph.D.
Researcher
+420 54949 3595
Lucie Poppová
PhD student
Veronika Mančíková, Ph.D.
Ondrej Šedo, Ph.D.
Researcher
+420 54949 7304, +420 54949 8427
Přemysl Souček, Ph.D.
+420 54949 7567
Tomáš Freiberger, Ph.D.
Research Group Leader
+420 543 182 548
Kamila Réblová, Ph.D.
Researcher
+420 54949 7586
Karol Pál
PhD student
+420 54949 6926
Lenka Humpolíková Adámková, Ph.D.
+420 54949 3878
Lucie Kopálková
+420 54949 7567
Michal Růžička
Michael Doubek
+420 532 233 514
Andrea Grioni
Jaromír Gumulec
PhD student
Martina Burešová
Sonali Sharma
Helena Peschelová
Aneta Ledererová
Michaela Pešová
Marek Svoboda, Ph.D.
Researcher
+420 54949 6899
Kamila Brázdilová
PhD student
Jana Mokrá
+420 54949 6997
Jitka Malčíková
Researcher
+420 54949 7948, +420 532 234 396
Marie Jarošová

SELECTED PUBLICATIONS

2017

  • BYSTRY, V.; REIGL, T; KREJCI, A; DEMKO, M; HANAKOVA, B; GRIONI, A; KNECHT, H; SCHLITT, M.; DREGER, P; SELLNER, L;HERRMANN, D; PINGEON, M; BOUDJOGHRA, M; RIJNTJES, J; POTT, C; LANGERAK, A W; GROENEN P. J; DAVI, F; BRÜGGEMANN, M; DARZENTAS, N, 2017:ARResT/Interrogate: an interactive immunoprofiler for IG/TR NGS data. 33 (3), p. 435 - 437.
  • DELGADO, J; DOUBEK, M; BAUMANN, T; KOTASKOVA, J; MOLICA, S; MOZAS, P; RIVAS-DELGADO, A.; MORABITO, F; POSPISILOVA, S; MONTSERRAT, E, 2017:Chronic lymphocytic leukemia: A prognostic model comprising only two biomarkers (IGHV mutational status and FISH cytogenetics) separates patients with different outcome and simplifies the CLL-IPI. AMERICAN JOURNAL OF HEMATOLOGY

2016

  • BOUSIOS, A; DIEZ, CM; TAKUNO, S; BYSTRY, V; DARZENTAS, N; GAUT, BS, 2016:A role for palindromic structures in the cis-region of maize Sirevirus LTRs in transposable element evolution and host epigenetic response. GENOME RESEARCH 26 (2), p. 226 - 237.
  • BRONSON, PG; CHANG, D; BHANGALE, T; SELDIN, MF; ORTMANNL, W; FERREIRA, RC; URCELAY, E; PEREIRA, LF; MARTIN, J; PLEBANI, A; LOUGARIS, V; FRIMAN, V; FREIBERGER, T; LITZMAN, J; THON, V; PAN-HAMMARSTROM, Q; HAMMARSTROM, L; GRAHAM, RR; BEHRENS, TW, 2016:Common variants at PVT1, ATG13-AMBRA1, AHI1 and CLEC16A are associated with selective IgA deficiency. NATURE GENETICS 48 (11), p. 1425 - 1429.
  • BUCKOVA, H; NOSKOVA, H; BORSKA, R; REBLOVA, K; PINKOVA, B; ZAPLETALOVA, E; KOPECKOVA, L; HORKY, O; NEMECKOVA, J; GAILLYOVA, R; NAGY, Z; VESELY, K; HERMANOVA, M; STEHLIKOVA, K; FAJKUSOVA, L, 2016:Autosomal recessive congenital ichthyoses in the Czech Republic. BRITISH JOURNAL OF DERMATOLOGY 174 (2), p. 405 - 407.
  • JANOVSKA, P; POPPOVA, L; PLEVOVA, K; PLESINGEROVA, H; BEHAL, M; KAUCKA, M; OVESNA, P; HLOZKOVA, M; BORSKY, M; STEHLIKOVA, O; BRYCHTOVA, Y; DOUBEK, M; MACHALOVA, M; BASKAR, S; KOZUBIK, A; POSPISILOVA, S; PAVLOVA, S; BRYJA, V, 2016:Autocrine Signaling by Wnt-5a Deregulates Chemotaxis of Leukemic Cells and Predicts Clinical Outcome in Chronic Lymphocytic Leukemia. CLINICAL CANCER RESEARCH 22 (2), p. 459 - 469.
  • MELAZZINI, F; PALOMBO, F; BALDUINI, A; DE ROCCO, D; MARCONI, C; NORIS, P; GNAN, C; PIPPUCCI, T; BOZZI, V; FALESCHINI, M; BAROZZI, S; DOUBEK, M; DI BUDUO, CA; KOZUBIK, KS; RADOVA, L; LOFFREDO, G; POSPISILOVA, S; ALFANO, C; SERI, M; BALDUINI, CL; PECCI, A; SAVOIA, A, 2016:Clinical and pathogenic features of ETV6-related thrombocytopenia with predisposition to acute lymphoblastic leukemia. HAEMATOLOGICA 101 (11), p. 1333 - 1342.
  • POPPOVA, L; JANOVSKA, P; PLEVOVA, K; RADOVA, L; PLESINGEROVA, H; BORSKY, M; KOTASKOVA, J; KANTOROVA, B; HLOZKOVA, M; FIGULOVA, J; BRYCHTOVA, Y; MACHALOVA, M; URIK, M; DOUBEK, M; KOZUBIK, A; POSPISILOVA, S; PAVLOVA, S; BRYJA, V, 2016:Decreased WNT3 expression in chronic lymphocytic leukaemia is a hallmark of disease progression and identifies patients with worse prognosis in the subgroup with mutated IGHV. BRITISH JOURNAL OF HAEMATOLOGY 175 (5), p. 851 - 859.
  • SEDO, O; KORAN, M; JAKESOVA, M; MIKULIKOVA, R; BOHAC, M; ZDRAHAL, Z, 2016:Rapid assignment of malting barley varieties by matrix-assisted laser desorption-ionisation - Time-of-flight mass spectrometry. FOOD CHEMISTRY 206 , p. 124 - 130.
  • SLANINOVA, V; KRAFCIKOVA, M; PEREZ-GOMEZ, R; STEFFAL, P; TRANTIREK, L; BRAY, SJ; KREJCI, A, 2016:Notch stimulates growth by direct regulation of genes involved in the control of glycolysis and the tricarboxylic acid cycle. OPEN BIOLOGY 6 (2)
  • SMIDA, M; DE LA CRUZ, FF; KERZENDORFER, C; URAS, IZ; MAIR, B; MAZOUZI, A; SUCHANKOVA, T; KONOPKA, T; KATZ, AM; PAZ, K; NAGY-BOJARSZKY, K; MUELLNER, MK; BAGO-HORVATH, Z; HAURA, EB; LOIZOU, JI; NIJMAN, SMB, 2016:MEK inhibitors block growth of lung tumours with mutations in ataxia-telangiectasia mutated. Nature Communications 7

2015

  • AGATHANGELIDIS, A; BYSTRY, V; HADZIDIMITRIOU, A; SUTTON, LA; MINGA, E; KIENLE, D; DAVIS, Z; YAN, XJ; SHANAFELT, T; BOUDJOGRA, M; PLEVOVA, K; GOUNARI, M; XOCHELLI, A; NAVARRO, A; CHATZOULI, M; PEDERSEN, LB; BALIAKAS, P; SCARFO, L; ROSSI, D; VERONESE, S; FACCO, M; BIKOS, V; KARAN-DJURASEVIC, T; PAVLOVIC, S; MANSOURI, L; POIRON, C; CHU, CC; STALIKA, E; GIUDICELLI, V; PANAGIOTIDIS, P; SUDARIKOV, A; ANAGNOSTOPOULOS, A; TRENTIN, L; CATHERWOOD, M; MONTILLO, M; GAIDANO, G; CAMPO, E; GEISLER, CH; LANGERAK, AW; POSPISILOVA, S; LEFRANC, MP; CHIORAZZI, N; OSCIER, D; JELINEK, DF; STILGENBAUER, S; BELESSI, C; DAVI, F; ROSENQUIST, R; GHIA, P; DARZENTAS, N; STAMATOPOULOS, K, 2015:HIGHER-ORDER IMMUNOGLOBULIN SEQUENCE RELATIONS FOR MAJOR SUBSETS OF CHRONIC LYMPHOCYTIC LEUKEMIA: UNIQUENESS VERSUS EQUIVALENCE. HAEMATOLOGICA 100 , p. 47 - 48.
  • BALIAKAS, P; AGATHANGELIDIS, A; HADZIDIMITRIOU, A; SUTTON, LA; MINGA, E; TSANOUSA, A; SCARFO, L; DAVIS, Z; YAN, XJ; SHANAFELT, T; PLEVOVA, K; SANDBERG, Y; VOJDEMAN, FJ; BOUDJOGRA, M; TZENOU, T; CHATZOULI, M; CHU, CC; VERONESE, S; GARDINER, A; MANSOURI, L; SMEDBY, KE; PEDERSEN, LB; MORENO, D; VAN LOM, K; GIUDICELLI, V; FRANCOVA, HS; NGUYEN-KHAC, F; PANAGIOTIDIS, P; JULIUSSON, G; ANGELIS, L; ANAGNOSTOPOULOS, A; LEFRANC, MP; FACCO, M; TRENTIN, L; CATHERWOOD, M; MONTILLO, M; GEISLER, CH; LANGERAK, AW; POSPISILOVA, S; CHIORAZZI, N; OSCIER, D; JELINEK, DF; DARZENTAS, N; BELESSI, C; DAVI, F; GHIA, P; ROSENQUIST, R; STAMATOPOULOS, K, 2015:Not all IGHV3-21 chronic lymphocytic leukemias are equal: prognostic considerations. BLOOD 125 (5), p. 856 - 859.
  • BALIAKAS, P; HADZIDIMITRIOU, A; AGATHANGELIDIS, A; ROSSI, D; SUTTON, LA; KMINKOVA, J; SCARFO, L; POSPISILOVA, S; GAIDANO, G; STAMATOPOULOS, K; GHIA, P; ROSENQUIST, R, 2015:Prognostic relevance of MYD88 mutations in CLL: the jury is still out. BLOOD 126 (8), p. 1043 - 1044.
  • BALIAKAS, P; HADZIDIMITRIOU, A; MATTSSON, M; XOCHELLI, A; SUTTON, LA; MINGA, E; SCARFO, L; ROSSI, D; DAVIS, Z; AGATHANGELIDIS, A; VILLAMOR, N; PARKER, H; KOTASKOVA, J; STALIKA, E; PLEVOVA, K; MANSOURI, L; CORTESE, D; LOPEZ, AN; DELGADO, J; LARRAYOZ, M; ANAGNOSTOPOULOS, A; BELESSI, C; SMEDBY, KE; JULIUSSON, G; STREFFORD, JC; POSPISILOVA, S; OSCIER, D; GAIDANO, G; CAMPO, E; GHIA, P; ROSENQUIST, R; STAMATOPOULOS, K, 2015:REFINING PROGNOSIS OF CHRONIC LYMPHOCYTIC LEUKEMIA WITH SOMATICALLY HYPERMUTATED B-CELL RECEPTORS: A NOVEL PROGNOSTIC INDEX ON BEHALF OF THE EUROPEAN RESEARCH INITIATIVE ON CLL (ERIC). HAEMATOLOGICA 100 , p. 52 - 52.
  • BALIAKAS, P; HADZIDIMITRIOU, A; SUTTON, LA; ROSSI, D; MINGA, E; VILLAMOR, N; LARRAYOZ, M; KMINKOVA, J; AGATHANGELIDIS, A; DAVIS, Z; TAUSCH, E; STALIKA, E; KANTOROVA, B; MANSOURI, L; SCARFO, L; CORTESE, D; NAVRKALOVA, V; ROSE-ZERILLI, MJJ; SMEDBY, KE; JULIUSSON, G; ANAGNOSTOPOULOS, A; MAKRIS, AM; NAVARRO, A; DELGADO, J; OSCIER, D; BELESSI, C; STILGENBAUER, S; GHIA, P; POSPISILOVA, S; GAIDANO, G; CAMPO, E; STREFFORD, JC; STAMATOPOULOS, K; ROSENQUIST, R, 2015:Recurrent mutations refine prognosis in chronic lymphocytic leukemia. LEUKEMIA 29 (2), p. 329 - 336.
  • BALIAKAS, P; PUIGGROS, A; XOCHELLI, A; SUTTON, LA; NGUYEN-KHAC, F; GARDINER, A; PLEVOVA, K; ORTEGA, M; COLLADO, R; GONZALEZ, T; GRANADA, I; LUNO, E; KOTASKOVA, J; DAVIS, Z; ANAGNOSTOPOULOS, A; STREFFORD, J; POSPISILOVA, S; DAVI, F; ATHANASIADOU, A; ROSENQUIST, R; OSCIER, D; SOLA, BE; STAMATOPOULOS, K, 2015:ADDITIONAL TRISOMIES AMONGST PATIENTS WITH CHRONIC LYMPHOCYTIC LEUKEMIA CARRYING TRISOMY 12: THE PARTNER CHROMOSOME MAKES A DIFFERENCE. HAEMATOLOGICA 100 , p. 224 - 224.
  • BESSE, L; SEDLARIKOVA, L; KRYUKOV, F; NEKVINDOVA, J; RADOVA, L; SLABY, O; KUGLIK, P; ALMASI, M; PENKA, M; KREJCI, M; ADAM, Z; POUR, L; SEVCIKOVA, S; HAJEK, R, 2015:Circulating Serum MicroRNA-130a as a Novel Putative Marker of Extramedullary Myeloma. PLOS ONE 10 (9)
  • BRAZDILOVA, K; PLEVOVA, K; FRANCOVA, HS; KOCKOVA, H; CHMELIKOVA, M; BORSKY, M; BURCKOVA, K; KANTOROVA, B; TICHY, B; SKABRAHOVA, H; BRYCHTOVA, Y; MAYER, J; DOUBEK, M; POSPISILOVA, S, 2015:Single Cell Analysis of IG Genes in CLL: Cases with Multiple IGH Rearrangements Are Constituted of Several Independent Clones Even When Indistinguishable By Flow Cytometry. BLOOD 126 (23)
  • BRUGGERMANN, M; KNECHT, H; BARTRAM, J; BYSTRY, V; CAZZANIGA, G; FAZIO, G; FERRERO, S; FRONKOVA, E; GARCIA-SANZ, R; GRIONI, A; HANCOCK, J; JIMINEZ, C; KOTROVA, M; LADETTO, M; MOPPETT, J; SONGIA, S; TRKA, J; LANGERAK, AW; DARZENTAS, N; HERRMANN, D; POTT, C, 2015:INTERNATIONAL MULTI-LABORATORY NEXT-GENERATION SEQUENCING FOR MRD ANALYSIS IN ALL. A PILOT STUDY BY THE EUROCLONALITY-NGS CONSORTIUM. HAEMATOLOGICA 100 , p. 31 - 31.
  • BYSTRY, V; AGATHANGELIDIS, A; BIKOS, V; SUTTON, LA; BALIAKAS, P; HADZIDIMITRIOU, A; STAMATOPOULOS, K; DARZENTAS, N, 2015:ARResT/AssignSubsets: a novel application for robust subclassification of chronic lymphocytic leukemia based on B cell receptor IG stereotypy. BIOINFORMATICS 31 (23), p. 3844 - 3846.
  • DUSKOVA, M; KAMENIK, J; SEDO, O; ZDRAHAL, Z; SALAKOVA, A; KARPISKOVA, R; LACANIN, I, 2015:Survival and growth of lactic acid bacteria in hot smoked dry sausages (non-fermented salami) with and without sensory deviations. FOOD CONTROL 50 , p. 804 - 808.
  • CHATZILARI, E; BALIAKAS, P; XOCHELLI, A; MARONIDIS, A; VARDI, A; MATTSSON, M; LARSSON, K; DOUKA, V; ISKAS, M; KARAVALAKIS, G; PAPALEXANDRI, A; NIEMANN, C; MONTILLO, M; ANAGNOSTOPOULOS, A; OSCIER, D; POSPISILOVA, S; DAVI, F; STAVROYIANNI, N; GHIA, P; HADZIDIMITRIOU, A; ROSENQUIST, R; NIKOLOPOULOS, S; STAMATOPOULOS, K; KOMPATSIARIS, Y, 2015:Personalized Modeling of Disease Evolution in CLL: Does Statistical Significance Translate into Predictive Accuracy?. BLOOD 126 (23)
  • CHU, VH; PARK, LP; ATHAN, E; DELAHAYE, F; FREIBERGER, T; LAMAS, C; MIRO, JM; MUDRICK, DW; STRAHILEVITZ, J; TRIBOUILLOY, C; DURANTE-MANGONI, E; PERICAS, JM; FERNANDEZ-HIDALGO, N; NACINOVICH, F; RIZK, H; KRAJINOVIC, V; GIANNITSIOTI, E; HURLEY, JP; HANNAN, MM; WANG, A, 2015:Association Between Surgical Indications, Operative Risk, and Clinical Outcome in Infective Endocarditis A Prospective Study From the International Collaboration on Endocarditis. CIRCULATION 131 (2), p. 131 - U46.
  • CHU, VH; PARK, LP; ATHAN, E; DELAHAYE, F; FREIBERGER, T; LAMAS, C; MIRO, JM; MUDRICK, DW; STRAHILEVITZ, J; TRIBOUILLOY, C; DURANTE-MANGONI, E; PERICAS, JM; FERNANDEZ-HIDALGO, N; NACINOVICH, F; RIZK, H; KRAJINOVIC, V; GIANNITSIOTI, E; HURLEY, JP; HANNAN, MM; WANG, A, 2015:Response to Letter Regarding Article, "Association Between Surgical Indications, Operative Risk, and Clinical Outcome in Infective Endocarditis: A Prospective Study From the International Collaboration on Endocarditis". CIRCULATION 132 (14), p. E184 - E185.
  • JANOUSKOVA, E; NECASOVA, I; PAVLOUSKOVA, J; ZIMMERMANN, M; HLUCHY, M; MARINI, V; NOVAKOVA, M; HOFR, C, 2015:Human Rap1 modulates TRF2 attraction to telomeric DNA. NUCLEIC ACIDS RESEARCH 43 (5), p. 2691 - 2700.
  • JASKOVA, Z; MALCIKOVA, J; SMARDOVA, J; BRYCHTOVA, Y; MAYER, J; TRBUSEK, M, 2015:ELIMINATION OF MUTATED P53 PROTEIN AND INDUCTION OF P53 DOWNSTREAM GENES IN CHRONIC LYMPHOCYTIC LEUKEMIA CELLS USING PRIMA-1MET. HAEMATOLOGICA 100 , p. 414 - 414.
  • KANTOROVA, B; MALCIKOVA, J; BRAZDILOVA, K; BORSKY, M; PLEVOVA, K; SMARDOVA, J; TRBUSEK, M; BRYCHTOVA, Y; DOUBEK, M; MAYER, J; POSPISILOVA, S, 2015:Single Cell Analysis Proves the Coexistence of NOTCH1 and TP53 Mutations within the Same Cancer Cells in Patients with Chronic Lymphocytic Leukemia. BLOOD 126 (23)
  • KOTASKOVA, J; MALCIKOVA, J; DIVISKOVA, E; PAVLOVA, S; MEJSTRIKOVA, S; VRANOVA, V; PLEVOVA, K; PLESINGEROVA, H; DOUBEK, M; MAYER, J; POSPISILOVA, S, 2015:13Q DELETION IS PREDOMINANT CYTOGENETIC ABERRATION NEWLY AQUIRED DURING CHRONIC LYMPHOCYTIC LEUKEMIA COURSE IRRESPECTIVE OF DISEASE ACTIVITY AND TREATMENT STATUS. HAEMATOLOGICA 100 , p. 417 - 418.
  • KOTROVA, M; KNECHT, H; BARTRAM, J; BYSTRY, V; CAZZANIGA, G; FAZIO, G; FERRERO, S; GENUARDI, E; GARCIA-SANZ, R; GRIONI, A; HANCOCK, J; JIMINEZ, C; LADETTO, M; MOPPETT, J; SONGIA, S; HERRMANN, D; POTT, C; LANGERAK, AW; DARZENTAS, N; TRKA, J; FRONKOVA, E; BRUGGEMANN, M, 2015:Library Preparation Is the Major Factor Affecting Differences in Results of Immunoglobulin Gene Rearrangements Detection on Two Major Next-Generation Sequencing Platforms. BLOOD 126 (23)
  • KRYUKOV, F; NEMEC, P; RADOVA, L; KRYUKOVA, E; KUFOVA, Z; SEDLARIKOVA, L; SEVCIKOVA, S; HAJEK, R, 2015:CENTROSOME ASSOCIATED GENES PATTERN FOR RISK SUBSTRATIFICATION IN MULTIPLE MYELOMA. HAEMATOLOGICA 100 , p. 247 - 247.
  • LJUNGSTROM, V; CORTESE, D; YOUNG, E; PANDZIC, T; MANSOURI, L; PLEVOVA, K; SUTTON, LA; STAVROYIANNI, N; AGATHANGELIDIS, A; ROSSI, D; HOGLUND, M; OSCIER, D; GAIDANO, G; DAVI, F; POTT, C; TRENTIN, L; POSPISILOVA, S; GHIA, P; STAMATOPOULOS, K; SJOBLOM, T; ROSENQUIST, R, 2015:DISSECTING RESISTANCE MECHANISMS IN CHRONIC LYMPHOCYTIC LEUKEMIA USING WHOLE-EXOME SEQUENCING: IMPACT OF RECURRENT RPS15 MUTATIONS ON P53 DYSREGULATION. HAEMATOLOGICA 100 , p. 10 - 11.
  • MALCIKOVA, J; STANO-KOZUBIK, K; TICHY, B; KANTOROVA, B; PAVLOVA, S; TOM, N; RADOVA, L; SMARDOVA, J; PARDY, F; DOUBEK, M; BRYCHTOVA, Y; MRAZ, M; PLEVOVA, K; DIVISKOVA, E; OLTOVA, A; MAYER, J; POSPISILOVA, S; TRBUSEK, M, 2015:Detailed analysis of therapy-driven clonal evolution of TP53 mutations in chronic lymphocytic leukemia. LEUKEMIA 29 (4), p. 877 - 885.
  • MANSOURI, L; SUTTON, LA; LJUNGSTROM, V; BONDZA, S; ARNGARDEN, L; BHOI, S; LARSSON, J; CORTESE, D; KALUSHKOVA, A; PLEVOVA, K; YOUNG, E; GUNNARSSON, R; FALK-SORQVIST, E; LONN, P; MUGGEN, AF; YAN, XJ; SANDER, B; ENBLAD, G; SMEDBY, KE; JULIUSSON, G; BELESSI, C; RUNG, J; CHIORAZZI, N; STREFFORD, JC; LANGERAK, AW; POSPISILOVA, S; DAVI, F; HELLSTROM, M; JERNBERG-WIKLUND, H; GHIA, P; SODERBERG, O; STAMATOPOULOS, K; NILSSON, M; ROSENQUIST, R, 2015:Functional loss of I kappa B epsilon leads to NF-kappa B deregulation in aggressive chronic lymphocytic leukemia. JOURNAL OF EXPERIMENTAL MEDICINE 212 (6), p. 833 - 843.
  • MLCOCHOVA, J; FALTEJSKOVA-VYCHYTILOVA, P; FERRACIN, M; ZAGATTI, B; RADOVA, L; SVOBODA, M; NEMECEK, R; JOHN, S; KISS, I; VYZULA, R; NEGRINI, M; SLABY, O, 2015:MicroRNA expression profiling identifies miR-31-5p/3p as associated with time to progression in wild-type RAS metastatic colorectal cancer treated with cetuximab. ONCOTARGET 6 (36), p. 38695 - 38704.
  • MUSILOVA, K; MRAZ, M, 2015:MicroRNAs in B-cell lymphomas: how a complex biology gets more complex. LEUKEMIA 29 (5), p. 1004 - 1017.
  • NAVRKALOVA, V; KAFKOVA, LR; DIVOKY, V; POSPISILOVA, S, 2015:Oxidative stress as a therapeutic perspective for ATM-deficient chronic lymphocytic leukemia patients. HAEMATOLOGICA 100 (8), p. 994 - 996.
  • NAVRKALOVA, V; YOUNG, E; BALIAKAS, P; RADOVA, L; PLEVOVA, K; SUTTON, LA; MANSOURI, L; LJUNGSTROM, V; NTOUFA, S; DAVIS, Z; JULIUSSON, G; SMEDBY, KE; BELESSI, C; PANAGIOTIDIS, P; DAVI, F; LANGERAK, AW; GHIA, P; STREFFORD, JC; OSCIER, DG; STAMATOPOULOS, K; POSPISILOVA, S; ROSENQUIST, R; TRBUSEK, M, 2015:ATM Mutations in Major Stereotyped CLL Subsets: Enrichment in Subset #2 is Associated with Unfavourable Outcome. BLOOD 126 (23)
  • NOERENBERG, D; YOUNG, E; LJUNGSTROM, V; MANSOURI, L; PLEVOVA, K; BALIAKAS, P; BLAKEMORE, S; ROSSI, D; CLIFFORD, R; NAVRKALOVA, V; SUTTON, LA; SMEDBY, KE; JULIUSSON, G; BELESSI, C; PANAGIOTIDIS, P; CHIORAZZI, N; DAVI, F; LANGERAK, AW; SCHUH, A; GAIDANO, G; STREFFORD, JC; GHIA, P; STAMATOPOULOS, K; POSPISILOVA, S; ZENZ, T; ROSENQUIST, R; DAMM, F, 2015:EGR2 Mutations in Chronic Lymphocytic Leukemia: A New Bad Player. BLOOD 126 (23)
  • PAVLASOVA, G; SEDA, V; BORSKY, M; CERNA, K; OSICKOVA, J; MAYER, J; POSPISILOVA, S; DAVIDS, MS; BROWN, JR; MRAZ, M, 2015:Microenvironmental Interactions up-Regulate CD20 Expression in CLL B Cells through the CXCR4/SDF-1 Axis: Implications for CD20-Targeting Antibodies and the Use of BCR-Inhibitors in Combination. BLOOD 126 (23)
  • PLESINGEROVA, H; JANOVSKA, P; POPPOVA, L; SHAIK, A; JURCICKOVA, Z; LIBRA, A; PLEVOVA, K; MACHAC, J; SLAPAK, I; PAVLOVA, S; OVESNA, P; KOTASKOVA, J; DOUBEK, M; POSPISILOVA, S; BRYJA, V, 2015:UPREGULATED COBLL1 IN CHRONIC LYMPHOCYTIC LEUKAEMIA (CLL) PATIENTS WITH UNMUTATED IGHV IDENTIFIES A COHORT WITH INFERIOR PROGNOSIS. HAEMATOLOGICA 100 , p. 50 - 50.
  • PUDJA, A; MILOSEVIC, JD; KLAMPFL, T; HARUTYUNYAN, A; BERG, T; BAGIENSKI, K; CHEN, D; GISSLINGER, B; RUMI, E; MALCOVATI, L; PIETRA, D; ELENA, C; DELLA PORTA, MG; PIERI, L; GUGLIELMELLI, P; DOUBEK, M; DVORAKOVA, D; SUVAJDZIC, N; TOMIN, D; TOSIC, N; RACIL, Z; STEURER, M; PAVLOVIC, S; VANNUCCHI, AM; CAZZOLA, M; GISSLINGER, H; KRALOVICS, R, 2015:HIGH RESOLUTION CYTOGENETIC MAPPING AND WHOLE EXOME SEQUENCING REVEAL A COMPLEX PATTERN OF CHROMOSOME 6P ABERRATIONS IN PATIENTS WITH MYELOID MALIGNANCIES. HAEMATOLOGICA 100 , p. 97 - 97.
  • REBLOVA, M; JAKLITSCH, WM; REBLOVA, K; STEPANEK, V, 2015:Phylogenetic Reconstruction of the Calosphaeriales and Togniniales Using Five Genes and Predicted RNA Secondary Structures of ITS, and Flabellascus tenuirostris gen. et sp nov.. PLOS ONE 10 (12)
  • SEDA, V; MRAZ, M, 2015:B-cell receptor signalling and its crosstalk with other pathways in normal and malignant cells. EUROPEAN JOURNAL OF HAEMATOLOGY 94 (3), p. 193 - 205.
  • SELLNER, L; DREGER, P; SCHLITT, M; KNECHT, H; HERRMANN, D; REIGL, T; KREJCI, A; BYSTRY, V; DARZENTAS, N; RIEGER, M; DIETRICH, S; ZENZ, T; HO, AD; KNEBA, M; BRUEGGEMANN, M, 2015:T-Prolymphocytic Leukemia Is Sensitive to Polyclonal T Cell-Derived Graft-Versus-Leukemia Effects: Evidence from Minimal Residual Disease Kinetics and TCR Repertoire Diversity Analyses. BLOOD 126 (23)
  • SUTTON, LA; LJUNGSTROM, V; MANSOURI, L; YOUNG, E; CORTESE, D; NAVRKALOVA, V; MALCIKOVA, J; MUGGEN, AF; TRBUSEK, M; PANAGIOTIDIS, P; DAVI, F; BELESSI, C; LANGERAK, AW; GHIA, P; POSPISILOVA, S; STAMATOPOULOS, K; ROSENQUIST, R, 2015:Targeted next-generation sequencing in chronic lymphocytic leukemia: a high-throughput yet tailored approach will facilitate implementation in a clinical setting. HAEMATOLOGICA 100 (3), p. 370 - 376.
  • TE RAA, GD; DERKS, IAM; NAVRKALOVA, V; SKOWRONSKA, A; MOERLAND, PD; VAN LAAR, J; OLDREIVE, C; MONSUUR, H; TRBUSEK, M; MALCIKOVA, J; LODEN, M; GEISLER, CH; HULLEIN, J; JETHWA, A; ZENZ, T; POSPISILOVA, S; STANKOVIC, T; VAN OERS, MHJ; KATER, AP; ELDERING, E, 2015:The impact of SF3B1 mutations in CLL on the DNA-damage response. LEUKEMIA 29 (5), p. 1133 - 1142.
  • TOM, N; MALCIKOVA, J; RADOVA, L; KANTOROVA, B; PARDY, F; PAVLOVA, S; PAL, K; MRAZ, M; TICHY, B; DOUBEK, M; BRYCHTOVA, Y; PLEVOVA, K; MAYER, J; TRBUSEK, M; POSPISILOVA, S, 2015:MUTATIONS IN THE TP53 GENE SHOW FEATURES OF SOMATIC HYPERMUTATION PROCESS WITH PROMINENT DIFFERENCE BETWEEN IGHV MUTATED AND UNMUTATED CHRONIC LYMPHOCYTIC LEUKEMIA. HAEMATOLOGICA 100 , p. 224 - 225.
  • VARDI, A; KARIPIDOU, M; GEMENETZI, A; VLACHONIKOLA, E; BIKOS, V; STALIKA, E; KORAVOU, E; MARAMIS, C; SIORENTA, A; ANAGNOSTOPOULOS, A; POSPISILOVA, S; MAGLAVERAS, N; CHOUVARDA, I; STAMATOPOULOS, K; HADZIDIMITRIOU, A, 2015:Next Generation Sequence Immunoprofiling of the T-Cell Repertoire in Chronic Lymphocytic Leukemia Supports Selection By Shared Antigenic Elements. BLOOD 126 (23)
  • VARDI, A; STALIKA, E; GKOUFAS, A; KARIPIDOU, M; MARAMIS, C; BIKOS, V; POSPISILOVA, S; ANAGNOSTOPOULOS, A; MAGLAVERAS, N; CHOUVARDA, I; STAMATOPOULOS, K; HADZIDIMITRIOU, A, 2015:HIGH-THROUGHPUT T-CELL RECEPTOR GENE REPERTOIRE PROFILING IN CHRONIC LYMPHOCYTIC LEUKEMIA SUBSET #4: FURTHER EVIDENCE OF ANTIGENIC STIMULATION. HAEMATOLOGICA 100 , p. 11 - 12.
  • XOCHELLI, A; BIKOS, V; POLYCHRONIDOU, E; AGATHANGELIDIS, A; CHARLOTTE, F; MOSCHONAS, P; DAVIS, Z; COLOMBO, M; ROUMELIOTI, M; SUTTON, LA; GROENEN, P; BOUDJOGHRA, M; ALGARA, P; TRAVERSE-GLEHEN, A; FERRER, A; STALIKA, E; KARYPIDOU, M; KANELLIS, G; KALPADAKIS, C; MOLLEJO, M; PANGALIS, G; VLAMOS, P; AMINI, RM; POSPISILOVA, S; GONZALEZ, D; PONZONI, M; ANAGNOSTOPOULOS, A; GIUDICELLI, V; LEFRANC, MP; ESPINET, B; PANAGIOTIDIS, P; PIRIS, MA; DU, M; ROSENQUIST, R; PAPADAKI, T; BELESSI, C; FERRARINI, M; OSCIER, D; TZOVARAS, D; GHIA, P; DAVI, F; HADZIDIMITRIOU, A; STAMATOPOULOS, K, 2015:Unique Versus Common: Disease-Biased Immunoglobulin Gene Repertoires Along with Public Antigen Receptor Stereotypes in Marginal Zone B-Cell Lymphoproliferations. BLOOD 126 (23)
  • ZEMANOVA, J; PARUCH, K; KREJCI, L; SOUCEK, K; HYLSE, O; BOUDNY, M; BORSKY, M; OSICKOVA, J; KHIRSARIYA, P; SEBEJOVA, L; NAVRKALOVA, V; MALCIKOVA, J; DIVISKOVA, E; BRYCHTOVA, Y; MAYER, J; TRBUSEK, M, 2015:CHRONIC LYMPHOCYTIC LEUKEMIA CELLS ARE HIGHLY SUSCEPTIBLE TO DIRECT INHIBITION OF CHECKPOINT KINASE 1. HAEMATOLOGICA 100 , p. 417 - 417.

2014

  • BALIAKAS, P; HADZIDIMITRIOU, A; SUTTON, LA; MINGA, E; AGATHANGELIDIS, A; TSANOUSA, A; SCARFO, L; DAVIS, Z; YAN, J; SHANAFELT, TD; PLEVOVA, K; SANDBERG, Y; VOJDEMAN, FJ; BOUDJOGHRA, M; TZENOU, T; CHATZOULI, M; CHU, CC; VERONESE, S; GARDINER, AC; MANSOURI, L; SMEDBY, KE; PEDERSEN, L; MORENO, D; VAN LOM, K; GIUDICELLI, V; FRANCOVA, H; NGUYEN-KHAC, F; PANAGIOTIDIS, P; JULIUSSON, G; ANGELIS, L; ANAGNOSTOPOULOS, A; LEFRANC, MP; FACCO, M; TRENTIN, L; CATHERWOOD, M; MONTILLO, M; GEISLER, CH; LANGERAK, AW; POSPISILOVA, S; CHIORAZZI, N; OSCIER, D; JELINEK, DF; DARZENTAS, N; BELESSI, C; DAVI, F; ROSENQUIST, R; GHIA, P; STAMATOPOULOS, K, 2014:Clinical Impact of Stereotyped Antigen Receptors in Chronic Lymphocytic Leukemia. BLOOD 124 (21)
  • BALIAKAS, P; HADZIDIMITRIOU, A; SUTTON, LA; MINGA, E; AGATHANGELIDIS, A; TSANOUSA, A; SCARFO, L; DAVIS, Z; YAN, XJ; SHANAFELT, T; PLEVOVA, K; SANDBERG, Y; VOJDEMAN, FJ; BOUDJOGRA, M; TZENOU, T; CHATZOULI, M; CHU, CC; VERONESE, S; GARDINER, A; MANSOURI, L;, 2014:NOT ALL IGHV3-21 CLL ARE EQUAL: SUBSET #2 DISPLAYS A DISTINCTIVE CLINICOBIOLOGICAL PROFILE WITH REMARKABLE SIMILARITIES TO SUBSET #169, ITS CLOSE IMMUNOGENETIC RELATIVE. HAEMATOLOGICA 99 , p. 48 - 49.
  • DOUBEK, M; SROVNAL, J; PLEVOVA, K; TRIZULJAK, J; BRYCHTOVA, Y; SEMERAD, L; LETALOVA, E; BENEDIKOVA, A; MAYER, J; HAJDUCH, M; POSPISILOVA, S, 2014:ANALYSIS OF MERKEL CELL POLYOMAVIRUS PROGNOSTIC SIGNIFICANCE IN CHRONIC LYMPHOCYTIC LEUKEMIA. HAEMATOLOGICA 99 , p. 325 - 325.
  • HOFFMANN, V; LINDOERFER, D; THALER, J; LABAR, B; MELANTHIOU, F; MAYER, J; EVERAUS, H; PORKKA, K; GUILLHOT, J; SCHUBERT-FRITSCHLE, G; CASTAGNETTI, F; LEJNIECE, S; GRISKEVICIUS, L; THIELEN, N; HELLMANN, A; TURKINA, A; ZARITSKEY, A; BOGDANOVIC, AD; INDRAK, K, 2014:THE EUTOS POPULATION BASED REGISTRY - INCIDENCES OF CML ACROSS EUROPE. HAEMATOLOGICA 99 , p. 72 - 72.
  • LENGEROVA, M; RACIL, Z; HRNCIROVA, K; KOCMANOVA, I; VOLFOVA, P; RICNA, D; BEJDAK, P; MOULIS, M; PAVLOVSKY, Z; WEINBERGEROVA, B; TOSKOVA, M; MAYER, J, 2014:Rapid Detection and Identification of Mucormycetes in Bronchoalveolar Lavage Samples from Immunocompromised Patients with Pulmonary Infiltrates by Use of High-Resolution Melt Analysis. JOURNAL OF CLINICAL MICROBIOLOGY 52 (8), p. 2824 - 2828.
  • LINDOERFER, D; HOFFMANN, VS; ROSTI, G; CASTAGNETTI, F; SAUSSELE, S; GUILHOT, J; SIMONSSON, B; STEEGMANN, JL; MAYER, J; INDRAK, K; TURKINA, AG; ZARITSKEY, A; LABAR, B; ZUPAN, IP; THIELEN, N; CLARK, RE; THALER, J; MELANTHIOU, F; EVERAUS, H; PORKKA, K; BOGDA, 2014:THE EUTOS POPULATION-BASED REGISTRY: EVALUATION OF BASELINE CHARACTERISTICS AND FIRST TREATMENT CHOICES OF 2983 NEWLY DIAGNOSED CHRONIC MYELOID LEUKEMIA (CML) PATIENTS FROM 20 EUROPEAN COUNTRIES. HAEMATOLOGICA 99 , p. 238 - 239.
  • NAVRKALOVA, V; MARECKOVA, A; JANIKOVA, A; DOUBEK, M; MAYER, J; POSPISILOVA, S; TRBUSEK, M, 2014:INCORPORATION OF NEXT-GENERATION SEQUENCING INTO ATM GENE ANALYSIS IN PATIENTS WITH CLL AND MCL. HAEMATOLOGICA 99 , p. 312 - 312.
  • POLANSKA, E; POSPISILOVA, S; STROS, M, 2014:Binding of Histone H1 to DNA Is Differentially Modulated by Redox State of HMGB1. PLOS ONE 9 (2)
  • ROBESOVA, B; BAJEROVA, M; LISKOVA, K; SKRICKOVA, J; TOMISKOVA, M; POSPISILOVA, S; MAYER, J; DVORAKOVA, D, 2014:TaqMan based real time PCR assay targeting EML4-ALK fusion transcripts in NSCLC. LUNG CANCER 85 (1), p. 25 - 30.
  • SHUGAY, M; BRITANOVA, OV; MERZLYAK, EM; TURCHANINOVA, MA; MAMEDOV, IZ; TUGANBAEV, TR; BOLOTIN, DA; STAROVEROV, DB; PUTINTSEVA, EV; PLEVOVA, K; LINNEMANN, C; SHAGIN, D; POSPISILOVA, S; LUKYANOV, S; SCHUMACHER, TN; CHUDAKOV, DM, 2014:Towards error-free profiling of immune repertoires. NATURE METHODS 11 (6), p. 653 - +.
  • SUTTON, LA; LJUNGSTROM, V; MANSOURI, L; YOUNG, E; CORTESE, D; NAVRKALOVA, V; MALCIKOVA, J; MUGGEN, AF; TRBUSEK, M; DAVI, F; BELESSI, C; LANGERAK, AW; GHIA, P; POSPISILOVA, S; STAMATOPOULOS, K; ROSENQUIST, R, 2014:TARGETED NEXT-GENERATION SEQUENCING FOR MUTATIONAL SCREENING IN CHRONIC LYMPHOCYTIC LEUKEMIA: A HIGH-THROUGHPUT YET TAILORED APPROACH WILL FACILITATE IMPLEMENTATION WITHIN A CLINICAL SETTING. HAEMATOLOGICA 99 , p. 313 - 314.
  • SUTTON, LA; MOSCHONAS, P; VARDI, A; BIKOS, V; YAN, XJ; CHATZOULI, M; ANAGNOSTOPOULOS, A; BELESSI, C; CHIORAZZI, N; ROSENQUIST, R; TZOVARAS, D; STAMATOPOULOS, K; HADZIDIMITRIOU, A, 2014:MATCHED PATTERN DISCOVERY ACROSS PAIRED IMMUNOGLOBULIN HEAVY AND LIGHT CHAINS IN CLL REVEALS UNIQUE SUBSET-DEFINING AMINO ACID ASSOCIATIONS. HAEMATOLOGICA 99 , p. 50 - 50.
  • VARDI, A; AGATHANGELIDIS, A; SUTTON, LA; CHATZOULI, M; SCARFO, L; MANSOURI, L; DOUKA, V; ANAGNOSTOPOULOS, A; DARZENTAS, N; ROSENQUIST, R; GHIA, P; BELESSI, C; STAMATOPOULOS, K, 2014:IgG-Switched CLL Has a Distinct Immunogenetic Signature from the Common MD Variant: Ontogenetic Implications. CLINICAL CANCER RESEARCH 20 (2), p. 323 - 330.
  • VERNER, J; TRBUSEK, M; CHOVANCOVA, J; SKABRAHOVA, H; JASKOVA, Z; MOULIS, M; FOLBER, F; HALOUZKA, R; MAYER, J; POSPISILOVA, S; DOUBEK, M, 2014:NOD/SCID GAMMA XENOGRAFT MODEL OF B-CELL MALIGNANCIES USING TP53-AND/OR ATM-DEFICIENT CELL LINES. HAEMATOLOGICA 99 , p. 312 - 313.
  • XOCHELLI, A; AGATHANGELIDIS, A; KAVAKIOTIS, I; MINGA, E; SUTTON, LA; BALIAKAS, P; CHOUVARDA, I; GIUDICELLI, V; VLAHAVAS, I; MAGLAVERAS, N; BONELLO, L; TRENTIN, L; MONTILLO, M; PANAGIOTIDIS, P; GEISLER, C; LANGERAK, AW; POSPISILOVA, S; JELINEK, DF; OSCIER,, 2014:IMMUNOGLOBULIN HEAVY VARIABLE GENES AND ALLELES: NEW ENTITIES, NEW NAMES AND IMPLICATIONS FOR RESEARCH AND PROGNOSTICATION IN CLL. HAEMATOLOGICA 99 , p. 49 - 49.
  • XOCHELLI, A; KAVAKIOTIS, I; AGATHANGELIDIS, A; KIENLE, D; DAVIS, Z; YAN, XJ; SHANAFELT, T; BOUDJOGRA, M; PLEVOVA, K; CHATZOULI, M; PEDERSEN, LB; VERONESE, S; FACCO, M; MORENO, D; CHU, CC; GIUDICELLI, V; PANAGIOTIDIS, P; VLAHAVAS, I; ANAGNOSTOPOULOS, A; MAGLAVERAS, N; TRENTIN, L; CATHERWOOD, M; MONTILLO, M; GEISLER, CH; LANGERAK, AW; POSPISILOVA, S; LEFRANC, MP; CHIORAZZI, N; OSCIER, D; JELINEK, DF; STILGENBAUER, S; BELESSI, C; GHIA, P; DAVI, F; ROSENQUIST, R; DARZENTAS, N; CHOUVARDA, I; SUTTON, LA; HADZIDIMITRIOU, A; STAMATOPOULOS, K, 2014:Charting Unique Signatures of Somatic Hypermutation Amongst Chronic Lymphocytic Leukemia Patients Expressing IGHV4-34 Clonotypic B Cell Receptors. BLOOD 124 (21)

2013

  • BACCARANI, M; DEININGER, MW; ROSTI, G; HOCHHAUS, A; SOVERINI, S; APPERLEY, JF; CERVANTES, F; CLARK, RE; CORTES, JE; GUILHOT, F; HJORTH-HANSEN, H; HUGHES, TP; KANTARJIAN, HM; KIM, DW; LARSON, RA; LIPTON, JH; MAHON, FX; MARTINELLI, G; MAYER, J; MULLER, MC; , 2013:European LeukemiaNet recommendations for the management of chronic myeloid leukemia: 2013. BLOOD 122 (6), p. 872 - 884.
  • FINK, AM; BOTTCHER, S; RITGEN, M; FISCHER, K; PFLUG, N; EICHHORST, B; WENDTNER, CM; WINKLER, D; BUHLER, A; ZENZ, T; STAIB, P; MAYER, J; HENSEL, M; HOPFINGER, G; WENGER, M; FINGERLE-ROWSON, G; DOHNER, H; KNEBA, M; STILGENBAUER, S; BUSCH, R; HALLEK, M, 2013:Prediction of poor outcome in CLL patients following first-line treatment with fludarabine, cyclophosphamide and rituximab. LEUKEMIA 27 (9), p. 1949 - 1952.
  • HOFFMANN, VS; BACCARANI, M; LINDOERFER, D; CASTAGNETTI, F; TURKINA, A; ZARITSKY, A; HELLMANN, A; PREJZNER, W; STEEGMANN, JL; MAYER, J; INDRAK, K; COLITA, A; ROSTI, G; PFIRRMANN, M, 2013:The EUTOS prognostic score: review and validation in 1288 patients with CML treated frontline with imatinib. LEUKEMIA 27 (10), p. 2016 - 2022.
  • KAUCKA, M; PLEVOVA, K; PAVLOVA, S; JANOVSKA, P; MISHRA, A; VERNER, J; PROCHAZKOVA, J; KREJCI, P; KOTASKOVA, J; OVESNA, P; TICHY, B; BRYCHTOVA, Y; DOUBEK, M; KOZUBIK, A; MAYER, J; POSPISILOVA, S; BRYJA, V, 2013:The Planar Cell Polarity Pathway Drives Pathogenesis of Chronic Lymphocytic Leukemia by the Regulation of B-Lymphocyte Migration. CANCER RESEARCH 73 (5), p. 1491 - 1501.
  • KHARE, V; LYAKHOVICH, A; DAMMANN, K; LANG, M; BORGMANN, M; TICHY, B; POSPISILOVA, S; LUCIANI, G; CAMPREGHER, C; EVSTATIEV, R; PFLUEGER, M; HUNDSBERGER, H; GASCHE, C, 2013:Mesalamine modulates intercellular adhesion through inhibition of p-21 activated kinase-1. BIOCHEMICAL PHARMACOLOGY 85 (2), p. 234 - 244.
  • KLAMPFL, T; MILOSEVIC, JD; PUDA, A; SCHONEGGER, A; BAGIENSKI, K; BERG, T; HARUTYUNYAN, AS; GISSLINGER, B; RUMI, E; MALCOVATI, L; PIETRA, D; ELENA, C; DELLA PORTA, MG; PIERI, L; GUGLIELMELLI, P; BOCK, C; DOUBEK, M; DVORAKOVA, D; SUVAJDZIC, N; TOMIN, D; TOS, 2013:Complex Patterns of Chromosome 11 Aberrations in Myeloid Malignancies Target CBL, MLL, DDB1 and LMO2. PLOS ONE 8 (10)
  • KREJCI, M; DOUBEK, M; BRYCHTOVA, Y; STEHLIKOVA, O; CHOVANCOVA, J; TICHY, B; FRANCOVA, HS; NAVRATIL, M; TOMISKA, M; HORKY, O; POSPISILOVA, S; MAYER, J, 2013:Fludarabine with cytarabine followed by reduced-intensity conditioning and allogeneic hematopoietic stem cell transplantation in patients with poor-risk chronic lymphocytic leukemia. ANNALS OF HEMATOLOGY 92 (2), p. 249 - 254.
  • PAGANO, L; CORNELY, OA; BUSCA, A; CAIRA, M; CESARO, S; GASBARRINO, C; GIRMENIA, C; HEINZ, WJ; HERBRECHT, R; LASS-FLORL, C; NOSARI, A; POTENZA, L; RACIL, Z; RICKERTS, V; SHEPPARD, DC; SIMON, A; ULLMANN, AJ; VALENTINI, CG; VEHRESCHILD, JJ; CANDONI, A; VEHRE, 2013:Combined antifungal approach for the treatment of invasive mucormycosis in patients with hematologic diseases: a report from the SEIFEM and FUNGISCOPE registries. HAEMATOLOGICA 98 (10)
  • POTLUKOVA, E; FREIBERGER, T; LIMANOVA, Z; JISKRA, J; TELICKA, Z; BARTAKOVA, J; SPRINGER, D; VITKOVA, H; TRENDELENBURG, M, 2013:Association between Low Levels of Mannan-Binding Lectin and Markers of Autoimmune Thyroid Disease in Pregnancy. PLOS ONE 8 (12)
  • RACIL, Z; RAZGA, F; DRAPALOVA, J; BURESOVA, L; ZACKOVA, D; PALACKOVA, M; SEMERAD, L; MALASKOVA, L; HALUZIK, M; MAYER, J, 2013:Mechanism of impaired glucose metabolism during nilotinib therapy in patients with chronic myelogenous leukemia. HAEMATOLOGICA 98 (10)
  • REBLOVA, M; UNTEREINER, WA; REBLOVA, K, 2013:Novel Evolutionary Lineages Revealed in the Chaetothyriales (Fungi) Based on Multigene Phylogenetic Analyses and Comparison of ITS Secondary Structure. PLOS ONE 8 (5)
  • SEDO, O; NEMEC, A; KRIZOVA, L; KACALOVA, M; ZDRAHAL, Z, 2013:Improvement of MALDI-TOF MS profiling for the differentiation of species within the Acinetobacter calcoaceticus-Acinetobacter baumannii complex. SYSTEMATIC AND APPLIED MICROBIOLOGY 36 (8), p. 572 - 578.
  • SKALOVA, D; ZIDKOVA, J; VOHANKA, S; MAZANEC, R; MUSOVA, Z; VONDRACEK, P; MRAZOVA, L; KRAUS, J; REBLOVA, K; FAJKUSOVA, L, 2013:CLCN1 Mutations in Czech Patients with Myotonia Congenita, In Silico Analysis of Novel and Known Mutations in the Human Dimeric Skeletal Muscle Chloride Channel. PLOS ONE 8 (12)
  • STANDARA, S; KULHANEK, P; MAREK, R; STRAKA, M, 2013:Xe-129 NMR chemical shift in Xe@C-60 calculated at experimental conditions: Essential role of the relativity, dynamics, and explicit solvent. JOURNAL OF COMPUTATIONAL CHEMISTRY 34 (22), p. 1890 - 1898.
  • SUTTON, LA; AGATHANGELIDIS, A; BELESSI, C; DARZENTAS, N; DAVI, F; GHIA, P; ROSENQUIST, R; STAMATOPOULOS, K, 2013:Antigen selection in B-cell lymphomas-Tracing the evidence. SEMINARS IN CANCER BIOLOGY 23 (6), p. 399 - 409.
  • SUTTON, LA; KOSTARELI, E; STALIKA, E; TSAFTARIS, A; ANAGNOSTOPOULOS, A; DARZENTAS, N; ROSENQUIST, R; STAMATOPOULOS, K, 2013:Temporal Dynamics of Clonal Evolution in Chronic Lymphocytic Leukemia with Stereotyped IGHV4-34/IGKV2-30 Antigen Receptors: Longitudinal Immunogenetic Evidence. MOLECULAR MEDICINE 19 , p. 230 - 236.
  • VYCHODILOVA, L; MATIASOVIC, J; BOBROVA, O; FUTAS, J; KLUMPLEROVA, M; STEJSKALOVA, K; CVANOVA, M; JANOVA, E; OSICKOVA, J; VYSKOCIL, M; SEDLINSKA, M; DUSEK, L; MARTI, E; HORIN, P, 2013:Immunogenomic analysis of insect bite hypersensitivity in a model horse population. VETERINARY IMMUNOLOGY AND IMMUNOPATHOLOGY 152 (42097), p. 260 - 268.
  • ZD'ARSKA, M; ZATLOUKALOVA, P; BENITEZ, M; SEDO, O; POTESIL, D; NOVAK, O; SVACINOVA, J; PESEK, B; MALBECK, J; VASICKOVA, J; ZDRAHAL, Z; HEJATKO, J, 2013:Proteome Analysis in Arabidopsis Reveals Shoot- and Root-Specific Targets of Cytokinin Action and Differential Regulation of Hormonal Homeostasis. PLANT PHYSIOLOGY 161 (2), p. 918 - 930.

2012

  • AGATHANGELIDIS, A; DARZENTAS, N; HADZIDIMITRIOU, A; BROCHET, X; MURRAY, F; YAN, XJ; DAVIS, Z; VAN GASTEL-MOL, EJ; TRESOLDI, C; CHU, CC; CAHILL, N; GIUDICELLI, V; TICHY, B; PEDERSEN, LB; FORONI, L; BONELLO, L; JANUS, A; SMEDBY, K; ANAGNOSTOPOULOS, A; MERLE, 2012:Stereotyped B-cell receptors in one-third of chronic lymphocytic leukemia: a molecular classification with implications for targeted therapies. BLOOD 119 (19), p. 4467 - 4475.
  • BIKOS, V; STALIKA, E; BALIAKAS, P; DARZENTAS, N; DAVIS, Z; TRAVERSE-GLEHEN, A; DAGKLIS, A; KANELLIS, G; ANAGNOSTOPOULOS, A; TSAFTARIS, A; PONZONI, M; BERGER, F; FELMAN, P; GHIA, P; PAPADAKI, T; OSCIER, D; BELESSI, C; STAMATOPOULOS, K, 2012:Selection of antigen receptors in splenic marginal-zone lymphoma: further support from the analysis of the immunoglobulin light-chain gene repertoire. LEUKEMIA 26 (12), p. 2567 - 2569.
  • BIKOS, V; STALIKA, E; KARYPIDOU, M; BALIAKAS, P; DAVIS, Z; ALGARA, P; KANELLIS, G; DAGKLIS, A; TRAVERSE-GLEHEN, A; HOCKLEY, S; MOLLEJO, M; TSAFTARIS, A; ANAGNOSTOPOULOS, A; PONZONI, M; BERGER, F; FELMAN, P; GONZALEZ, D; MATUTES, E; PIRIS, MA; PAPADAKI, T; GHIA, P; OSCIER, D; BELESSI, C; DARZENTAS, N; STAMATOPOULOS, K, 2012:Clonal Selection in the Ontogeny and Evolution of Splenic Marginal Zone Lymphoma Confirming the Existence of Distinct Molecular Subtypes. BLOOD 120 (21)
  • BOUSIOS, A; MINGA, E; KALITSOU, N; PANTERMALI, M; TSABALLA, A; DARZENTAS, N, 2012:MASiVEdb: the Sirevirus Plant Retrotransposon Database. BMC GENOMICS 13
  • CINCAROVA, L; LOCHMANOVA, G; NOVAKOVA, K; SULTESOVA, P; KONECNA, H; FAJKUSOVA, L; FAJKUS, J; ZDRAHAL, Z, 2012:A combined approach for the study of histone deacetylase inhibitors. MOLECULAR BIOSYSTEMS 8 (11), p. 2937 - 2945.
  • CORNELISSEN, JJ; GRATWOHL, A; SCHLENK, RF; SIERRA, J; BORNHAUSER, M; JULIUSSON, G; RACIL, Z; ROWE, JM; RUSSELL, N; MOHTY, M; LOWENBERG, B; SOCIE, G; NIEDERWIESER, D; OSSENKOPPELE, GJ, 2012:The European LeukemiaNet AML Working Party consensus statement on allogeneic HSCT for patients with AML in remission: an integrated-risk adapted approach. NATURE REVIEWS CLINICAL ONCOLOGY 9 (10), p. 579 - 590.
  • DOLEZALOVA, D; MRAZ, M; BARTA, T; PLEVOVA, K; VINARSKY, V; HOLUBCOVA, Z; JAROS, J; DVORAK, P; POSPISILOVA, S; HAMPL, A, 2012:MicroRNAs Regulate p21(Waf1/Cip1) Protein Expression and the DNA Damage Response in Human Embryonic Stem Cells. STEM CELLS 30 (7), p. 1362 - 1372.
  • GANOPOULOS, I; MADESIS, P; DARZENTAS, N; ARGIRIOU, A; TSAFTARIS, A, 2012:Barcode High Resolution Melting (Bar-HRM) analysis for detection and quantification of PDO "Fava Santorinis" (Lathyrus clymenum) adulterants. FOOD CHEMISTRY 133 (2), p. 505 - 512.
  • JANIKOVA, A; MARECKOVA, A; DVORAKOVA, D; BORTLICEK, Z; TICHY, B; NAVRATIL, M; KRAL, Z; POSPISILOVA, S; MAYER, J, 2012:A real-time (PCR) for a real life ...? Quantitative evaluation of BCL2/IGH in follicular lymphoma and its implications for clinical practice. EXPERIMENTAL HEMATOLOGY 40 (7), p. 528 - 539.
  • KOSTARELI, E; GOUNARI, M; JANUS, A; MURRAY, F; BROCHET, X; GIUDICELLI, V; POSPISILOVA, S; OSCIER, D; FORONI, L; DI CELLE, PF; TICHY, B; PEDERSEN, LB; JURLANDER, J; PONZONI, M; KOUVATSI, A; ANAGNOSTOPOULOS, A; THOMPSON, K; DARZENTAS, N; LEFRANC, MP; BELESS, 2012:Antigen receptor stereotypy across B-cell lymphoproliferations: the case of IGHV4-59/IGKV3-20 receptors with rheumatoid factor activity. LEUKEMIA 26 (5), p. 1127 - 1131.
  • KOZUBIK, KS; MALCIKOVA, J; TRBUSEK, M; TOM, N; DOUBEK, M; BRYCHTOVA, Y; SMARDOVA, J; MAYER, J; POSPISILOVA, S; TICHY, B, 2012:Clonal Selection of TP53 Mutations in Chronic Lymphocytic Leukaemia Detected by Ultra-deep Pyrosequencing. EUROPEAN JOURNAL OF CANCER 48 , p. S146 - S146.
  • LENGEROVA, M; KOCMANOVA, I; RACIL, Z; HRNCIROVA, K; POSPISILOVA, S; MAYER, J; NAJVAR, LK; WIEDERHOLD, NP; KIRKPATRICK, WR; PATTERSON, TF, 2012:Detection and Measurement of Fungal Burden in a Guinea Pig Model of Invasive Pulmonary Aspergillosis by Novel Quantitative Nested Real-Time PCR Compared with Galactomannan and (1,3)-beta-D-Glucan Detection. JOURNAL OF CLINICAL MICROBIOLOGY 50 (3), p. 602 - 608.
  • MRAZ, M; DOLEZALOVA, D; PLEVOVA, K; KOZUBIK, KS; MAYEROVA, V; CERNA, K; MUSILOVA, K; TICHY, B; PAVLOVA, S; BORSKY, M; VERNER, J; DOUBEK, M; BRYCHTOVA, Y; TRBUSEK, M; HAMPL, A; MAYER, J; POSPISILOVA, S, 2012:MicroRNA-650 expression is influenced by immunoglobulin gene rearrangement and affects the biology of chronic lymphocytic leukemia. BLOOD 119 (9), p. 2110 - 2113.
  • MRAZ, M; POSPISILOVA, S, 2012:MicroRNAs in chronic lymphocytic leukemia: from causality to associations and back. EXPERT REVIEW OF HEMATOLOGY 5 (6), p. 579 - 581.

2011

  • JANIKOVA, A; TICHY, B; SUPIKOVA, J; STANO-KOZUBIK, K; POSPISILOVA, S; KREN, L; VASOVA, I; SALEK, D; MAYER, J, 2011:Gene expression profiling in follicular lymphoma and its implication for clinical practice. LEUKEMIA & LYMPHOMA 52 (1), p. 59 - 68.
  • MRAZ, M; ZENT, CS; CHURCH, AK; JELINEK, DF; WU, XS; POSPISILOVA, S; ANSELL, SM; NOVAK, AJ; KAY, NE; WITZIG, TE; NOWAKOWSKI, GS, 2011:Bone marrow stromal cells protect lymphoma B-cells from rituximab-induced apoptosis and targeting integrin alpha-4-beta-1 (VLA-4) with natalizumab can overcome this resistance. BRITISH JOURNAL OF HAEMATOLOGY 155 (1), p. 53 - 64.
  • TRBUSEK, M; SMARDOVA, J; MALCIKOVA, J; SEBEJOVA, L; DOBES, P; SVITAKOVA, M; VRANOVA, V; MRAZ, M; FRANCOVA, HS; DOUBEK, M; BRYCHTOVA, Y; KUGLIK, P; POSPISILOVA, S; MAYER, J, 2011:Missense Mutations Located in Structural p53 DNA-Binding Motifs Are Associated With Extremely Poor Survival in Chronic Lymphocytic Leukemia. JOURNAL OF CLINICAL ONCOLOGY 29 (19), p. 2703 - 2708.
  • VAN DER FITS, L; SANDBERG, Y; DARZENTAS, N; ZOUTMAN, WH; TIELEMANS, D; WOLVERS-TETTERO, ILM; VERMEER, MH; LANGERAK, AW, 2011:A restricted clonal T-cell receptor alpha beta repertoire in Sezary syndrome is indicative of superantigenic stimulation. BRITISH JOURNAL OF DERMATOLOGY 165 (1), p. 78 - 84.
  • VARGOVA, K; CURIK, N; BURDA, P; BASOVA, P; KULVAIT, V; POSPISIL, V; SAVVULIDI, F; KOKAVEC, J; NECAS, E; BERKOVA, A; OBRTLIKOVA, P; KARBAN, J; MRAZ, M; POSPISILOVA, S; MAYER, J; TRNENY, M; ZAVADIL, J; STOPKA, T, 2011:MYB transcriptionally regulates the miR-155 host gene in chronic lymphocytic leukemia. BLOOD 117 (14), p. 3816 - 3825.
  • WALEWSKI, J; PASZKIEWICZ-KOZIK, E; WARSZEWSKA, A; BORSARU, G; MOICEAN, A; HELLMANN, A; MAYER, J; HAUNS, B; MAIS, A; HENNING, SW; HENTSCH, B, 2011:Final Results of the Phase II SAPHIRE Trial of Resminostat (4SC-201) in Patients with Relapsed/Refractory Hodgkin Lymphoma. BLOOD 118 (21), p. 1149 - 1149.

2010

  • DARZENTAS, N; HADZIDIMITRIOU, A; MURRAY, F; HATZI, K; JOSEFSSON, P; LAOUTARIS, N; MORENO, C; ANAGNOSTOPOULOS, A; JURLANDER, J; TSAFTARIS, A; CHIORAZZI, N; BELESSI, C; GHIA, P; ROSENQUIST, R; DAVI, F; STAMATOPOULOS, K, 2010:A different ontogenesis for chronic lymphocytic leukemia cases carrying stereotyped antigen receptors: molecular and computational evidence. LEUKEMIA 24 (1), p. 125 - 132.
  • KOTASKOVA, JANA; TICHY, BORIS; TRBUSEK, MARTIN; FRANCOVA, HANA SKUHROVA; KABATHOVA, JITKA; MALCIKOVA, JITKA; DOUBEK, MICHAEL; BRYCHTOVA, YVONA; MAYER, JIRI; POSPISILOVA, SARKA, 2010:High Expression of Lymphocyte-Activation Gene 3 (LAG3) in Chronic Lymphocytic Leukemia Cells Is Associated with Unmutated lmmunoglobulin Variable Heavy Chain Region (IGHV) Gene and Reduced Treatment-Free Survival. JOURNAL OF MOLECULAR DIAGNOSTICS 12 (3), p. 328 - 334.
  • MALCIKOVA, J; TICHY, B; DAMBORSKY, J; KABATHOVA, J; TRBUSEK, M; MAYER, J; POSPISILOVA, S, 2010:Analysis of the DNA-binding activity of p53 mutants using functional protein microarrays and its relationship to transcriptional activation. BIOLOGICAL CHEMISTRY 391 (2 III), p. 197 - 205.

2009

  • MRAZ, M., MALINOVA, K., KOTASKOVA, J., PAVLOVA, S., TICHY, B., MALCIKOVA, J., STANO-KOZUBIK, K., SMARDOVA, J., BRYCHTOVA, Y., DOUBEK, M., TRBUSEK, M., MAYER, J., POSPISILOVA, S., 2009:miR-34a, miR-29c and miR-17-5p are downregulated in CLL patients with TP53 abnormalities. Leukemia 23 (6), p. 1159 - 1163.

GRANTY

  • Expression and function of activation-induced cytidine deaminase splice variants in normal B cell physiology and chronic lymphocytic leukemia (3SGA5792), South Moravian Region - SoMoPro, 2013 - 2016
  • Analysis of changes in genome and its expression in chronic lymphocytic leukemia patients during the disease development (NS10439), Ministry of Health - Departmental Programme of Research and Development (2008-2011), 2009 - 2011
  • Functional and structural changes of microRNAs in lymphoproliferative malignancies and their impact on prognosis and prediction of therapy response (NT11218), Ministry of Health - Ministry of Health's Departmental Research and Development Programme III (2010-2015), 2010 - 2015
  • Functional and molecular characteristics of cancer and normal stem cells – identification of targets for novel therapeutics and therapeutic strategies (MSM0021622430), MEYS - Institutional Research Plan, 2007 - 2013
  • Real-time PCR kits for detection in oncology (FR-TI2/254), Ministry of Industry and Trade - TIP, 2010 - 2013
  • Support of professional growth and international integration of research in the field of molecular medicine (CZ.1.07/2.3.00/20.0045), MEYS - OP Education for Competiteveness, 2011 - 2014
  • Involvement of nuclear HMGB proteins in sensitizing of human cells to anticancer drugs inhibiting DNA topoizomerases (GAP301/10/0590), Czech Science Foundation - Standard Grants, 2010 - 2012

CURRENT RESEARCH INFRASTRUCTURE

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. 

1. Genomic analysis of leukemic cells using next generation sequencing approaches

Supervisor: prof. RNDr. Šárka Pospíšilová, Ph.D.
Consultants: RNDr. Jitka Malčíková, Ph.D., MVDr. Boris Tichý, Ph.D.

Annotation:

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.

2. Identification of genomic lesions in NGS data of leukemic cells for clinical applications

Supervisor: Mgr. Vojtěch Bystrý, Ph.D.
Consultants: prof. RNDr. Šárka Pospíšilová, Ph.D.

Annotation:

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.

3. High throughput sequencing data analysis of IG/TR rearranged genes in leukemia clinical research

Supervisor: Mgr. Vojtěch Bystrý, Ph.D.
Consultants: prof. RNDr. Šárka Pospíšilová, Ph.D.

Annotation:

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.

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