Download presentatie - Life Science Technology

Evidence and Translational Medicine
Dr. Andrew Stubbs
Evidence Based Medicine
Adoption of Personalized Medicine
Science Driven PoC’s
Cost-effective Implementation
Scalable Cloud and Big Data Solutions
Secure Privacy Protected Patient Data
Galaxy: Data Analysis Platform.
Galaxy: Repertoire analysis
Science Driven PoC’s
Galaxy: Quantitative Digital Image Analysis
Science Driven PoC’s
Adrenocortical Carcinoma (ACC) Ki67
 Determine best practice for Ki67 evaluation
 Develop Galaxy Digital Image Analysis
Adrenocortical Carcinoma
i-Space: Diagnostic Applications
Science Driven PoC’s
Is it possible to evaluate ?rst trimester brain ventricle
development in human pregnancies using an innovative
virtual reality (VR) application and to analyze the relation
of the embryonic volume (EV) and brain ventricle ?uid
volume (BVFV) with gestational age (GA), crown-rump
length (CRL) and the Carnegie stage?
summary answer: Volumetry and staging of the human
embryo using a VR application make it possible to obtain
unique information about in-vivo embryonic normal and
abnormal development and about the sizes of the
ventricles and body
Diagnostic Sequencing @ Erasmus
NGS: Craniofacial Pathology
Science Driven PoC’s
Whole Genome Sequencing (WGS)
 Variants are responsible for normal variation
 Dominant exonic mutations correlate to clinical
phenotype
 Family based WGS with Complete Genomics
NGS: Huvariome
Scalable Cloud and Big Data Solutions
Functionality
 Whole genome comparison with reference population
 > 1000 reference genomes Q1 2014
 Trio and Family based analysis
Specifications
 Whole genome Sequence (WGS): Complete Genomics,
Illumina
 > 40,000 WGS Samples (replicated)
 Oracle 11g on an Exadata X2 Quarter Rack
Secure Easy Access to Results
Secure Easy Access to Results
Secure Easy Access to Results
NGS: Fusion Gene Detection
Science Driven PoC’s
 Gene fusions in prostate cancer are characterized by 5'
genomic regulatory elements,
commonly controlled by
androgen, fused to members of the Ets family of transcription
factors.
 TMPRSS2–ERG is the most common gene fusion, present in
about half of all localized prostate cancers analysed. TMPRSS2
also fuses to other Ets family genes such as ETV1
NGS: A Galaxy CLOUD
Scalable Cloud and Big Data Solutions
BiGGrid & SARA HPC Cloud
19 x Intel Xeon 32 core processors (608 cores)
 19 x 256 GB RAM (7.75 TB RAM)
 400 TB shared storage
http://galaxy.ctmm-trait.nl
Biosensor: Cardiovascular Disease
Secure Privacy Protected Patient Data
Science Driven PoC’s
Objectives
 Diagnose progression of cardiovascular disease
 Determine Risk of developing clinical manifestations
 Personalized therapy
Biosensor: Cardiovascular Disease
Secure Privacy Protected Patient Data
Science Driven PoC’s
TRC: Translational Research Center
Secure Privacy Protected Patient Data
Scalable Cloud and Big Data Solutions
Science Driven PoC’s
TRC “omics” Data Bank with integrated reference knowledge
Evidence Based To Personalised Medicine
Jensen et al 2012
Availability: Bioinformatics Toolbox
http://bioinformatics.erasmusmc.nl/wiki/index.php/Translational_Bioinformatics
Acknowledgements
Erasmus University Medical Center
Bioinformatics: Saskia Hiltemann, Youri
Hogestra, Karl Brand, Elizabeth McClellan,
Bas Horsman, Sylvia de Does, David van
Zessen, Daphne Hiejsman, Arne Ijpma, Sigrid
Swagemaker, Anton Koning, Ivo Palli, Peter
van der Spek
Exp. Cardiology: Dirk Duncker
NeuroOncology: Pim French
Exp. Urology: Ines Alves, Guido Jenster
Exp. Cardiology (AUMC)
 Yigal Pinto, Esther Creemers
MUMC
 Leon de Windt, Stefanos Leptidis
Department of Nephrology and Einthoven
Laboratory for Experimental Vascular
Medicine (LUMC)
 Anton-Jan van Zonneveld, Jacques Duijs
Erasmus University
 Ken Redekop, Laura Burgers
Department of Clinical Chemistry and
Hematology (UMCU)
 Mark Roest, Thijs van Holten
NBIC
 Haliiang Mei, Jan Bot
Experimental Cardiology (UMCU)
 Imo Hoefer, Gerard Pasterkamp
CTMM
 Jan-Willem Boiten, Erna Erdtsieck-Ernste,
Eelco Soeteman
LACDR/Division of Biopharmaceutics (LU)
 Johan Kuiper, Thijs Zweers
Experimental Cardiology (MUMC)
 Eric Biessen, Marco Manca
Thank you
Any questions ? ….

Download Report