7. Facts about the University of
Debrecen
33000
students
Teaching
More
in Hungarian and English
than 1500 faculty members
15
branches
21
Doctoral Schools
15%
of Hungarian RnD is located here
8. Brief overview of the region:
Underdeveloped region with large Regional Developmental Funds
University City with long history
Medical Centre that serves 2 mil people
Pharmapolis Cluster:
TEVA (Biogal)
Richter Gedeon new Pharma Plant for Biological drugs (recombinant proteins and
antibodies)
Cell Therapy Unit (already performing clinical studies)
Stem Cell Research Unit (starts 2010)
RCMM twinning with EMBL
Several EMBO members locally
Personalized Health Care Unit (from 2011)
Well organized Medical Centre open to patients from foreign countries
SAP and ISO implementation at the Medical Centre level
9. Our vision is to channel the advances in
genomics towards medical research for the
benefit of the patients in the form of
Personalized Medicine
10. Goals:
Leader
in the Personalized Medicine in the region
Implementation
of novel research tools for the benefit
of the patients through clinical research
Take
the opportunity of the regional grants and use
them to develop tools that can be used on a global
scale
Taking
care of every spent pence in a very
conservative way
11. Activities to implement our Goals:
Activities
in two directions:
Clinical Research
Common projects with clinicians
Infrastructure for clinical research
Regional training
From PCR oligo design through Study design till Data analysis
Global gene expression and functional genomics, Epigenetics
01/22/14
11
12. Activities in the field of Clinical Research:
Genomics
National
Genomics Technological Platform
Biomarker
discovery and Biobanking
Partners: Pfizer, Astra Zeneca, Richter Gedeon, Biosystems International,
Roche Hungary
Biobanking: COPD, Schizophrenia, Lung cancer, Leukemias
Tools for Biomarker discovery: UPL based miRNA measurement
(Roche Hungary and Astrid Research)
Epigenetics
Partners: Diagenode Belgium and Millipore USA
Areas: developing of standards for epigenetic studies and protocols for
HTS and clinical research in the field of epigenetics
01/22/14
12
13. Coordinated from the University of Debrecen:
1. Genomic Research for Human Health Consortium
(GRHH) 2002-2008- FP6 (www.humangenom.hu)
2. National Genomic Technological Platform (NGTP) 2009-2011National Grant
www.genomika.net
14. Core facility:
Implementation
of novel technologies require expensive infrastructure
Expensive
infrastructure can be best used if shared by several
research groups and operated by dedicated staff
Without
streets
knowledge dissemination core facilities are like dead end
16. Relevant output
Lifecycles of technologies
Additional
developments
Original
innovation
Distinctive technology / development phase/
time
Both instrument and reagent costs are high
Peak technology / penetretion phase/
Instrument price is high, reagent price is decreasing
Basic technology / spreading phase/
Both instrument and reagent costs are rapidly decreasing
Based on: „Pataki Béla: Technológia menedzsment”
17. Relevant output
Lifecycles of technologies
Distinctive technology / development phase/
time
Both instrument and reagent costs are high
Peak technology / penetretion phase/
Instrument price is high, reagent price is decreasing
Basic technology / spreading phase/
Both instrument and reagent costs are rapidly decreasing
Based on: „Pataki Béla: Technológia menedzsment”
18. L ab
RE
CO
Sequencing and
genomics unit
Epigenetic unit
b
D La
Rn
Se
b
e La
rvic
Biobanking unit
Protein and cell
engeneereing unit
b
D La
Rn
19. Sequencing and genomics unit
Instruments:
•Capillary sequencer
•Affymetrix
•Illumina NGS
•Server system
La b
RE
CO
Wet lab people:
Post docs:
•Beata Scholtz
•Szilárd Póliska
Technicians:
•Sipos Lilla
•Erzsébet Mátyás
Bioinformatics support team:
Endre Barta (leader)
Attila Horvath (system administrator)
Laszlo Steiner (biomathematics and bio statistics)
Gergely Nagy (bioinformatics)
23. GeneChip® 3000 platform
•
•
Hybridisation Oven
Delivers precise
temperature control
during hybridization
• Fluidics stations
• Washing and staining
of hybridized target
probe complexes
• Scanner
• High resolution
scanner for fast
image acquisition
• Autoloader
including barcode
reader for sample
tracking
25. NGS software installed on ngsdeb
Programs used for ChIP-seq,
GRO-seq and RNA-seq analysis
•
HOMER
•
SAMTOOLS
•
BOWTIE
•
ChIPSEEQER
•
BEDTOOLS
•
BAMTOOLS
•
TOPHAT
•
TRINITYRNASEQ
•
BWA
•
MEME
•
MACS
•
FASTX-TOOLKIT
•
PICARD
25
Head Node: 2x6 core, 144GB RAM, 20 Tbyte disk
6x computing nodes: 2x6 core, 48GB RAM 600GB
disk
2012.05.16.
26. ChIP-seq analyze script
•
Aim: To have a simple script that can be used either to analyze local
ChIP-seq sequencing data or to do meta-analysis of ChIP-seq
experiments stored on the NCBI SRA database
•
Command line tool
•
Input: SRA (NCBI reads), fastq (reads), bam (alignments)
•
•
•
•
•
•
•
Downloads SRA format files NCBI
Maps fastq format reads
Peak calling by HOMER and MACS
Peak annotation by HOMER
Known and denovo motif finding by HOMER
GO enrichment analysis by HOMER
Generates bedgraph and bed files for visualization
Barta E
Command line analysis of ChIP-seq results.
EMBNET JOURNAL 17:(1) pp. 13-17. (2011)
27. UPL based miRNS detection system
Czimmerer Zsolt
Astrid
Research
http://genomics.dote.hu:8080/mirnadesigntool/
28. High sensitivity e.g on hsa-mir-181 miRNA gen
family
Hsa-mir-181a:
AACAUUCAACGCUGUCGGUGAGU
Hsa-mir-181b:
AACAUUCAUUGCUGUCGGUGGGU
Hsa-mir-181c:
AACAUUCAAC*CUGUCGGUGAGU
http://genomics.dote.hu:8080/mirnadesigntool/
29. More info:
Balint L. Balint , Head of
Laboratory
Lbalint@med.unideb.hu
http://genomics.med.unideb.hu
Notas do Editor
The „Standard“ System
- every Affymetrix lab in the world uses the same instruments, with the same protocols
=> standardization of results, easy to compare
- point out Fluidics Station is integral component: important for reduction of variability. Competitors dont have their own FS.