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OncoTrack - Methods for systematic next generation oncology biomarker development

Objective

We propose here an exhaustive analysis of the genome, exome, methylome and transcriptome of primary tumours and metastases from patients with colon carcinoma, based on a combination of deep sequencing and chip based techniques. Dependent on their availability, we shall also perform analyses of tumor stem cells, circulating tumor cells, free tumor DNA in serum and xenografts derived from the same patients. This will be complemented by the development and application of highly sensitive techniques to identify individual mutations, transcripts and proteins/protein complexes both in-situ in pathology slides as well as in patients’ blood or serum. The integration of these results will allow us to address the heterogeneity of the tumor samples, to deduce the genome/epigenome/transcriptome of the different cell types making up or originating from the tumor (e.g. circulating tumor cells, tumour stem cells or xenografts), to establish models able to predict suitable candidates for further biomarker development, and also to predict the effects and side effects of drugs in the treatment of genetically defined groups of patients. Available biomarkers, as well as biomarkers predicted from the work within the project will be validated in patient derived xenograft models and stem cell cultures, and ultimately transferred into a point of care (POC) diagnostic format. In parallel we will explore the use of the global genome and methylome information, e.g. derived from the analysis of free tumor DNA in the serum of the patient, as the ‘ultimate’ biomarker, to model the biology of the tumor (possibly even before any tumor has been localised), and as an independent route to predict clinically relevant parameters. Though sequencing/methylation analysis of the genome of the tumor through free DNA is currently still too costly for use as a routine diagnostic, this is likely to change over the period covered by the grant, due to the extremely rapid progress in the development of large scale sequencing techniques.

Field of science

  • /medical and health sciences/basic medicine/pathology
  • /medical and health sciences/medical biotechnology/cells technologies/stem cells
  • /natural sciences/biological sciences/genetics and heredity/mutation
  • /natural sciences/biological sciences/genetics and heredity/genome

Call for proposal

IMI-JU-02-2009
See other projects for this call

Funding Scheme

JTI-CP-IMI - Joint Technology Initiatives - Collaborative Project (IMI)

Coordinator

Bayer Pharma AG
Address
Muellerstrasse 178
13353 Berlin
Germany
Activity type
Private for-profit entities (excluding Higher or Secondary Education Establishments)
Principal investigator
David Henderson (Dr.)
Administrative Contact
Burkhardt Neumann (Mr.)

Participants (21)

MAX-PLANCK-GESELLSCHAFT ZUR FORDERUNG DER WISSENSCHAFTEN EV
Germany
EU contribution
€ 4 080 739
Address
Hofgartenstrasse 8
80539 Munich
Activity type
Other
Administrative Contact
Anke Badrow (Mrs)
UPPSALA UNIVERSITET
Sweden
EU contribution
€ 1 277 110
Address
Von Kraemers Alle 4
751 05 Uppsala
Activity type
Higher or Secondary Education Establishments
Administrative Contact
Margareta Uvhagen Antoni (Mrs)
University College London
United Kingdom
EU contribution
€ 617 022
Address
Gower Street
WC1E 6BT London
Activity type
Higher or Secondary Education Establishments
Administrative Contact
Greta Borg-Carbott (Ms)
INTERNATIONAL PREVENTION RESEARCH INSTITUT-IPRI MANAGEMENT
France
EU contribution
€ 285 664
Address
Cours Lafayette 95
69006 Lyon
Activity type
Private for-profit entities (excluding Higher or Secondary Education Establishments)
Administrative Contact
Elisabeth Marchi (Mrs)
ALACRIS THERANOSTICS GMBH
Germany
EU contribution
€ 5 698 658
Address
Max Planck Strasse 3
12489 Berlin
Activity type
Private for-profit entities (excluding Higher or Secondary Education Establishments)
Administrative Contact
Ralf Sudbrak (Dr.)
UNIVERSITE PARIS-SUD
France
EU contribution
€ 455 288
Address
Rue Georges Clemenceau 15
91405 Orsay Cedex
Activity type
Higher or Secondary Education Establishments
Administrative Contact
Nicolas LECOMPTE (Mr)
EXPERIMENTELLE PHARMAKOLOGIE UND ONKOLOGIE BERLIN-BUCH GMBH
Germany
EU contribution
€ 697 830
Address
Robert-roessle-strasse 10
13125 Berlin
Activity type
Private for-profit entities (excluding Higher or Secondary Education Establishments)
Administrative Contact
Jens Hoffmann (Dr.)
CHARITE - UNIVERSITAETSMEDIZIN BERLIN
Germany
EU contribution
€ 1 373 584
Address
Chariteplatz 1
10117 Berlin
Activity type
Higher or Secondary Education Establishments
Administrative Contact
Eveline Fräßdorf (Ms.)
MEDIZINISCHE UNIVERSITAT GRAZ
Austria
EU contribution
€ 833 333
Address
Auenbruggerplatz 2
8036 Graz
Activity type
Higher or Secondary Education Establishments
Administrative Contact
Johannes Haybaeck (Dr.)
TECHNISCHE UNIVERSITAET DRESDEN
Germany
EU contribution
€ 259 020
Address
Helmholtzstrasse 10
01069 Dresden
Activity type
Higher or Secondary Education Establishments
Administrative Contact
Sven Kreigenfeld (Mr)
GABO:MI GESELLSCHAFT FUR ABLAUFORGANISATION:MILLIARIUM MBH & CO KG

Participation ended

Germany
EU contribution
€ 618 423
Address
Oskar Von Miller Ring 29
80333 Muenchen
Activity type
Private for-profit entities (excluding Higher or Secondary Education Establishments)
Administrative Contact
Birgit Fuchs (Mrs.)
ASTRAZENECA AB
Sweden
Address
Vastra Maelarhamnen
151 85 Sodertaelje
Activity type
Private for-profit entities (excluding Higher or Secondary Education Establishments)
Administrative Contact
Eva Lindgren (Mrs.)
BOEHRINGER INGELHEIM INTERNATIONALGMBH
Germany
Address
Binger Strasse
55218 Ingelheim
Activity type
Private for-profit entities (excluding Higher or Secondary Education Establishments)
Administrative Contact
Erik Patzelt (Dr.)
JANSSEN PHARMACEUTICA NV
Belgium
Address
Turnhoutseweg 30
2340 Beerse
Activity type
Private for-profit entities (excluding Higher or Secondary Education Establishments)
Administrative Contact
Koen Meeussen (Mr)
Merck KGaA
Germany
Address
Frankfurter Strasse 250
64293 Darmstadt
Activity type
Private for-profit entities (excluding Higher or Secondary Education Establishments)
Administrative Contact
Ninog Peresse (N/A)
PFIZER LIMITED
United Kingdom
Address
Ramsgate Road
CT13 9NJ Sandwich
Activity type
Private for-profit entities (excluding Higher or Secondary Education Establishments)
Administrative Contact
Olga Krylova (Dr)
F. HOFFMANN-LA ROCHE AG
Switzerland
Address
Grenzacherstrasse 124
4070 Basel
Activity type
Private for-profit entities (excluding Higher or Secondary Education Establishments)
Administrative Contact
Jason Hannon (Dr)
Eli Lilly and Company Limited
United Kingdom
Address
Lilly House, Priestley Road
RG24 9NL Basingstoke
Activity type
Private for-profit entities (excluding Higher or Secondary Education Establishments)
Administrative Contact
Birgit Steckel-Hamann (Dr.)
STOCKHOLMS UNIVERSITET
Sweden
EU contribution
€ 518 611
Address
Universitetsvagen 10
10691 Stockholm
Activity type
Higher or Secondary Education Establishments
Administrative Contact
Ann Nielsen (Ms)
FUNDACIO PRIVADA INSTITUT D'INVESTIGACIO ONCOLOGICA DE VALL-HEBRON
Spain
Address
Calle Nazaret 115-117
08035 Barcelona
Activity type
Research Organisations
Administrative Contact
Alejandro Piris (Mr)
Dahlem Centre for Genome Research and Medical Systems Biology
Germany
EU contribution
€ 42 000
Address
Fabeckstr
14195 Berlin
Administrative Contact
Ingrid Stark (-)