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Core Facility - Genomics

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Head of Core Facility
Researcher ID
Phone: +420 54949 8317, +420 733 141 527, +420 532 234 206
E-mail: ,
Office:

Main Activity

The Core Facility offers services and access to the instrument for genomic analyses. Equipment for massively parallel (Next Generation) sequencing, DNA microarrays as well as capillary sequencing and real-time qPCR (including high-throughput and digital PCR) is available or will be available soon. Services: Nextera and TruSeq compatible NGS library preparation including precise small samples, capillary sequencing, gene expression microarrays, CGH and cytogenetics microarrays.

Unique Features

Combination of high-end equipment and expertise for the complete experimental workflow from advanced sample preparation to complex genome analysis. Precise sample preparation techniques (cell sorting, microdissection) followed by combination of various complementary approaches in the analysis of the genome (massive parallel sequencing, microarrays, quantitative PCR) will make it possible to perform even very complex experimental designs including single cell genomics or diseased vs. healthy cells genome and transcriptome analyses.

Key Equipment (Core Facility fully operational from 2014)

  • High-throughput massive parallel sequencers
    • Illumina MiSeq
    • Roche GS Junior
    • whole-genome NG sequencer (end 2014)
  • Cell analysis system
    • Olympus Scan^R
  • Microarray system
    • Agilent SureScan
  • qPCR
    • Roche LC480
    • HT and digital PCR system (end 2014)

All CEITEC core facilities are available to external users (academia and companies). Czech and international researchers from universities and research institutes interested in accessing core facilities can benefit from support of research infrastructure NCLG, funded by the Ministry of Education, Youth and Sports of the Czech Republic.

msmt

list / cards

Name and position

E-mail

Phone

Tereza Cermanová
Specialist
+420 54949 7934
Jana Jedličková
Laborant
+420 54949 6997
Andrea Ondrůjová
Karol Pál
PhD student
+420 54949 6926
Lukáš Tichý, Ph.D.
PhD student
+420 532 234 626
Nina Dvořáčková
Zuzana Vrzalová
PhD student
Boris Tichý, Ph.D.
Research Group Leader
+420 54949 8317, +420 733 141 527, +420 532 234 206
Filip Pardy
Specialist
+420 54949 8630
Kamila Réblová, Ph.D.
Researcher
+420 54949 7586

SELECTED PUBLICATIONS

2016

  • MARECKOV, A; MALCIKOVA, J; TOM, N; PAL, K; SALEK, D; POSPISILOVA, S; TRBUSEK, M, 2016:ATM GENE MUTATIONS REPRESENT A HALLMARK OF MANTLE CELL LYMPHOMA BUT DO NOT IMPACT PATIENTS' SURVIVAL. HAEMATOLOGICA 101 , p. 271 - 271.

2015

  • 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)
  • 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.
  • 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.

2013

  • 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.
  • 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.

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.
  • 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.
  • 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.

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.

2010

  • 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.

PROJECTS

  • NCLG - Natioonal Center for Medical Genomic (LM2015091), MEYS, 2016 - 2019
  • NCLG - Národní centrum lékařské genomiky - modernizace infrastruktury a výzkum genetické variability populace (CZ.02.1.01/0.0/0.0/16_013/0001634), MEYS, 2017 - 2019
  • RIAT-CZ (ATCZ40), Interreg CZ-AT, 2016 - 2018
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Equipment Research group / CF Profile card
Amplicon Sequencer Amplicon Sequencer
CF: Core Facility - Genomics
Capillary sequencer Capillary sequencer
CF: Core Facility - Genomics
Cell analysis system Cell analysis system
CF: Core Facility - Genomics
Droplet digital PCR CF: Core Facility - Genomics
FACS cell sorter CF: Core Facility - Genomics
Flow cytometer CF: Core Facility - Genomics
Fluidigm AccessArray CF: Core Facility - Genomics
Fluidigm C1 CF: Core Facility - Genomics
High-density DNA microarray system High-density DNA microarray system
CF: Core Facility - Genomics
High-throughput massive parallel genomic analyzer for sequencing by synthesis method High-throughput massive parallel genomic analyzer for sequencing by synthesis method
CF: Core Facility - Genomics
Laser capture microdissection CF: Core Facility - Genomics
Liquid handling robot Liquid handling robot
CF: Core Facility - Genomics
Massively parallel table sequenator Massively parallel table sequenator
CF: Core Facility - Genomics
Microfluidic electrophoresis Microfluidic electrophoresis
CF: Core Facility - Genomics
Personal sequencer CF: Core Facility - Genomics
qPCR CF: Core Facility - Genomics
qPCR CF: Core Facility - Genomics
Real-time PCR Real-time PCR
CF: Core Facility - Genomics
Real-time PCR Real-time PCR
CF: Core Facility - Genomics
Wafergen SmartChip CF: Core Facility - Genomics
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Diagnostics

Genomics Core Facility offers its services and access to instruments for genomic analysis mainly for scientific projects. Some capacity also provides for specialized diagnostic testing for the general public.

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