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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
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
laborantka
+420 54949 6997
Andrea Ondrůjová
odborná pracovnice
Karol Pál
PhD student
+420 54949 6926
Lukáš Tichý, Ph.D.
PhD student
+420 532 234 626
Nina Dvořáčková
odborná asistentka
Zuzana Vrzalová
PhD student
Boris Tichý, Ph.D.
Research Group Leader
+420 54949 8317, +420 733 141 527
Filip Pardy
Specialist
+420 54949 8630
Kamila Réblová, Ph.D.
Researcher
+420 54949 7586, +420 532 234 625
Jiří Štika
odborný pracovník ve výzkumu
Larissa Wartha

SELECTED PUBLICATIONS

2017

  • BENCUROVA, P; BALOUN, J; MUSILOVA, K; RADOVA, L; TICHY, B; PAIL, M; ZEMAN, M; BRICHTOVA, E; HERMANOVA, M; POSPISILOVA, S; MRAZ, M; BRAZDIL, M, 2017:MicroRNA and mesial temporal lobe epilepsy with hippocampal sclerosis: Whole miRNome profiling of human hippocampus. EPILEPSIA 58 (10), p. 1782 - 1793.
  • PAL, K; BYSTRY, V; REIGL, T; DEMKO, M; KREJCI, A; TOULOUMENIDOU, T; STALIKA, E; TICHY, B; GHIA, P; STAMATOPOULOS, K; POSPISILOVA, S; MALCIKOVA, J; DARZENTAS, N, 2017:GLASS: assisted and standardized assessment of gene variations from Sanger sequence trace data. BIOINFORMATICS 33 (23), p. 3802 - 3804.

2016

  • KUBESOVA, B; PAVLOVA, S; MALCIKOVA, J; KABATHOVA, J; RADOVA, L; TOM, N; TICHY, B; PLEVOVA, K; KANTOROVA, B; FIEDOROVA, K; KISSOVA, J; GISSLINGER, B; GISSLINGER, H; MAYER, J; KRALOVICS, R; POSPISILOVA, S; DOUBEK, M, 2016:Low-Burden TP53 Mutations Occur in Chronic Phase of Myeloproliferative Neoplasms Regardless of Hydroxyurea Administration, Disease Type, and JAK2 Status. BLOOD 128 (22)

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
Agilent Tapestation Agilent Tapestation
CF: Core Facility Genomics
Capillary sequencer ABI3500 Capillary sequencer ABI3500
CF: Core Facility Genomics
DNA microarray scanner DNA microarray scanner
CF: Core Facility Genomics
Droplet digital PCR BioRad QX200 CF: Core Facility Genomics
FACS cell sorter BD Aria Fusion CF: Core Facility Genomics
Flow cytometer FACS Verse CF: Core Facility Genomics
Fluidigm C1 single-cell system CF: Core Facility Genomics
Illumina MiSeq Illumina MiSeq
CF: Core Facility Genomics
Illumina MiSeq CF: Core Facility Genomics
Illumina NextSeq 500 Illumina NextSeq 500
CF: Core Facility Genomics
Illumina NextSeq 500 CF: Core Facility Genomics
Liquid handling robot Tecan Liquid handling robot Tecan
CF: Core Facility Genomics
Olympus ScanR inverted fluorescent microscope Olympus ScanR inverted fluorescent microscope
CF: Core Facility Genomics
qPCR QuantStudio 12k CF: Core Facility Genomics
qPCR QuantStudio 12k CF: Core Facility Genomics
Real-time PCR LightCycler 480 Real-time PCR LightCycler 480
CF: Core Facility Genomics
Real-time PCR LightCycler 480 Real-time PCR LightCycler 480
CF: Core Facility Genomics

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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