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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.

Field of science

  • /natural sciences/biological sciences/genetics and heredity/mutation
  • /natural sciences/computer and information sciences/software
  • /natural sciences/computer and information sciences/internet/semantic web
  • /medical and health sciences/basic medicine/immunology
  • /medical and health sciences/clinical medicine/oncology/cancer
  • /natural sciences/computer and information sciences/data science/data analysis
  • /medical and health sciences/basic medicine/pharmacology and pharmacy/pharmaceutical drug/vaccines

Call for proposal

H2020-PHC-2014-two-stage
See other projects for this call

Funding Scheme

RIA - Research and Innovation action

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)

CENTRO NACIONAL DE INVESTIGACIONES CARDIOVASCULARES CARLOS III (F.S.P.)
Spain
EU contribution
€ 185 262,50
Address
Calle Melchor Fernandez Almagro 3
28029 Madrid
Activity type
Research Organisations
EBERHARD KARLS UNIVERSITAET TUEBINGEN
Germany
EU contribution
€ 247 500
Address
Geschwister-scholl-platz
72074 Tuebingen
Activity type
Higher or Secondary Education Establishments
UNIVERSITEIT UTRECHT
Netherlands
EU contribution
€ 249 000
Address
Heidelberglaan 8
3584 CS Utrecht
Activity type
Higher or Secondary Education Establishments
Masarykova univerzita
Czechia
EU contribution
€ 135 250
Address
Zerotinovo Namesti 9
60177 Brno Stred
Activity type
Higher or Secondary Education Establishments
INSTITUT NATIONAL DE LA SANTE ET DE LA RECHERCHE MEDICALE
France
EU contribution
€ 258 000
Address
Rue De Tolbiac 101
75654 Paris
Activity type
Research Organisations
TRON - TRANSLATIONALE ONKOLOGIE ANDER UNIVERSITATSMEDIZIN DER JOHANNES GUTENBERG-UNIVERSITAT MAINZ GEMEINNUTZIGE GMBH
Germany
EU contribution
€ 347 250
Address
Freiligrathstrasse 12
55131 Mainz
Activity type
Research Organisations
STICHTING HET NEDERLANDS KANKER INSTITUUT-ANTONI VAN LEEUWENHOEK ZIEKENHUIS
Netherlands
EU contribution
€ 279 000
Address
Plesmanlaan 121
1066 CX Amsterdam
Activity type
Research Organisations
DEFINIENS AG
Germany
EU contribution
€ 327 000
Address
Bernhard Wicki Str 5
80636 Munchen
Activity type
Private for-profit entities (excluding Higher or Secondary Education Establishments)
APTAIT GMBH
Germany
EU contribution
€ 307 125
Address
Leonhardistrasse 2E
86911 Diessen
Activity type
Private for-profit entities (excluding Higher or Secondary Education Establishments)
CENTER OF EXCELLENCE IN MEDICINE AND IT GMBH
Austria
EU contribution
€ 243 360
Address
Karl Kapferer Strasse 5
6020 Innsbruck
Activity type
Private for-profit entities (excluding Higher or Secondary Education Establishments)