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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.

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)

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MAX-PLANCK-GESELLSCHAFT ZUR FORDERUNG DER WISSENSCHAFTEN EV

Germany

EU Contribution

€ 4 080 739

UPPSALA UNIVERSITET

Sweden

EU Contribution

€ 1 277 110

UNIVERSITY COLLEGE LONDON

United Kingdom

EU Contribution

€ 617 022

INTERNATIONAL PREVENTION RESEARCH INSTITUT-IPRI MANAGEMENT

France

EU Contribution

€ 285 664

ALACRIS THERANOSTICS GMBH

Germany

EU Contribution

€ 5 698 658

UNIVERSITE PARIS-SUD

France

EU Contribution

€ 455 288

EXPERIMENTELLE PHARMAKOLOGIE UND ONKOLOGIE BERLIN-BUCH GMBH

Germany

EU Contribution

€ 697 830

CHARITE - UNIVERSITAETSMEDIZIN BERLIN

Germany

EU Contribution

€ 1 373 584

MEDIZINISCHE UNIVERSITAT GRAZ

Austria

EU Contribution

€ 833 333

TECHNISCHE UNIVERSITAET DRESDEN

Germany

EU Contribution

€ 259 020

GABO:MI GESELLSCHAFT FUR ABLAUFORGANISATION:MILLIARIUM MBH & CO KG

Germany

EU Contribution

€ 618 423

ASTRAZENECA AB

Sweden

BOEHRINGER INGELHEIM INTERNATIONALGMBH

Germany

JANSSEN PHARMACEUTICA NV

Belgium

Merck KGaA

Germany

PFIZER LIMITED

United Kingdom

F. HOFFMANN-LA ROCHE AG

Switzerland

Eli Lilly and Company Limited

United Kingdom

STOCKHOLMS UNIVERSITET

Sweden

EU Contribution

€ 518 611

FUNDACIO PRIVADA INSTITUT D'INVESTIGACIO ONCOLOGICA DE VALL-HEBRON

Spain

Dahlem Centre for Genome Research and Medical Systems Biology

Germany

EU Contribution

€ 42 000

Project information

Grant agreement ID: 115234

Status

Closed project

  • Start date

    1 January 2011

  • End date

    31 December 2016

Funded under:

FP7-JTI

  • Overall budget:

    € 30 860 819

  • EU contribution

    € 16 757 282

Coordinated by:

Bayer Pharma AG

Germany