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APERIM: Advanced bioinformatics platform for PERsonalised cancer IMmunotherapy

Objective

Cancer treatment platforms that involve the use of the adaptive immune system have demonstrated profound tumour regressions including complete cure. Importantly, technological advances in next-generation sequencing (NGS) allow for the first time the development of personalised cancer immunotherapies that target patient specific mutations. However, clinical application is currently hampered by specific bottlenecks in bioinformatics, which we aim to address in this proposal.

The overall objective of our trans-disciplinary network of leading experts in bioinformatics and cancer immunology is to develop an Advanced bioinformatics platform for PERrsonalised cancer IMmunotherapy (APERIM). Specifically we aim to develop:

1) database for the integration of NGS data, images of whole tissue slides of tumour sections, and clinical data. To enhance the usability and the data sharing we will use semantic web technologies, and will provide standardised interfaces to a set of analytical tools.

2) tools for automated quantification of tumour-infiltrating lymphocytes using whole tissue slide images and NGS data for patient stratification.

3) analytical pipeline for NGS-guided individualised cancer vaccines including crucial NGS data analysis and epitope selection components for the selection of vaccination targets.

4) a method for deriving T-cell receptor (TCR) sequences from NGS data and predicting TCR specificity.

We will achieve these aims using unique training and validation datasets available to the consortium. We will develop user-friendly software modules as well as analytical standard operating procedures for clinical use, and apply the bioinformatics platform in clinical settings. The bioinformatics platform will considerably accelerate the clinical translation and maximise the accessibility and utility of biomedical data in research and medicine.
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Coordinator

MEDIZINISCHE UNIVERSITAT INNSBRUCK

Address

Christoph Probst Platz 1
6020 Innsbruck

Austria

Activity type

Higher or Secondary Education Establishments

EU Contribution

€ 420 540

Participants (10)

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CENTRO NACIONAL DE INVESTIGACIONESCARDIOVASCULARES CARLOS III (F.S.P.)

Spain

EU Contribution

€ 185 262,50

EBERHARD KARLS UNIVERSITAET TUEBINGEN

Germany

EU Contribution

€ 247 500

UNIVERSITEIT UTRECHT

Netherlands

EU Contribution

€ 249 000

Masarykova univerzita

Czechia

EU Contribution

€ 135 250

INSTITUT NATIONAL DE LA SANTE ET DE LA RECHERCHE MEDICALE

France

EU Contribution

€ 258 000

TRON - TRANSLATIONALE ONKOLOGIE ANDER UNIVERSITATSMEDIZIN DER JOHANNES GUTENBERG-UNIVERSITAT MAINZ GEMEINNUTZIGE GMBH

Germany

EU Contribution

€ 347 250

STICHTING HET NEDERLANDS KANKER INSTITUUT-ANTONI VAN LEEUWENHOEK ZIEKENHUIS

Netherlands

EU Contribution

€ 279 000

DEFINIENS AG

Germany

EU Contribution

€ 327 000

APTAIT GMBH

Germany

EU Contribution

€ 307 125

CENTER OF EXCELLENCE IN MEDICINE AND IT GMBH

Austria

EU Contribution

€ 243 360

Project information

Grant agreement ID: 633592

  • Start date

    1 May 2015

  • End date

    30 April 2018

Funded under:

H2020-EU.3.1.6.

  • Overall budget:

    € 2 999 287,50

  • EU contribution

    € 2 999 287,50

Coordinated by:

MEDIZINISCHE UNIVERSITAT INNSBRUCK

Austria