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Opendata, web and dolomites

APERIM

APERIM: Advanced bioinformatics platform for PERsonalised cancer IMmunotherapy

Total Cost €

EC-Contrib. €

Partnership

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Outcomes and
results

APERIM project word cloud

Explore the words cloud of the APERIM project. It provides you a very rough idea of what is the project "APERIM" about.

accessibility immunotherapy first immunology infiltrating biomedical profound aperim integration automated pipeline hampered sections tumour standard software involve predicting generation adaptive personalised sequencing settings maximise semantic usability images immunotherapies perrsonalised tcr cell slide guided mutations considerably regressions slides medicine accelerate utility disciplinary treatment cure clinical ngs tissue sharing complete demonstrated bottlenecks stratification analytical tools vaccines receptor cancer network technological deriving interfaces translation training components individualised modules patient epitope datasets validation immune vaccination quantification specificity technologies time database bioinformatics platform experts trans lymphocytes standardised sequences web platforms data

Project "APERIM" data sheet

The following table provides information about the project.

Coordinator	MEDIZINISCHE UNIVERSITAT INNSBRUCK Organization address address: CHRISTOPH PROBST PLATZ 1 city: INNSBRUCK postcode: 6020 website: www.i-med.ac.at contact info title: n.a. name: n.a. surname: n.a. function: n.a. email: n.a. telephone: n.a. fax: n.a.
Coordinator Country	Austria [AT]
Project website	http://aperim.eu/
Total cost	2˙999˙287 €
EC max contribution	2˙999˙287 € (100%)
Programme	1. H2020-EU.3.1.6. (Health care provision and integrated care)
Code Call	H2020-PHC-2014-two-stage
Funding Scheme	RIA
Starting year	2015
Duration (year-month-day)	from 2015-05-01 to 2018-04-30

Partnership

Take a look of project's partnership.

#	participants	country	role	EC contrib. [€]
1	MEDIZINISCHE UNIVERSITAT INNSBRUCK MEDIZINISCHE UNIVERSITAT INNSBRUCK Organization address address: CHRISTOPH PROBST PLATZ 1 city: INNSBRUCK postcode: 6020 website: www.i-med.ac.at contact info title: n.a. name: n.a. surname: n.a. function: n.a. email: n.a. telephone: n.a. fax: n.a.	AT (INNSBRUCK)	coordinator	420˙540.00
2	TRON - TRANSLATIONALE ONKOLOGIE ANDER UNIVERSITATSMEDIZIN DER JOHANNES GUTENBERG-UNIVERSITAT MAINZ GEMEINNUTZIGE GMBH TRON - TRANSLATIONALE ONKOLOGIE ANDER UNIVERSITATSMEDIZIN DER JOHANNES GUTENBERG-UNIVERSITAT MAINZ GEMEINNUTZIGE GMBH Organization address address: FREILIGRATHSTRASSE 12 city: MAINZ postcode: 55131 website: http://www.tron-mainz.de/ contact info title: n.a. name: n.a. surname: n.a. function: n.a. email: n.a. telephone: n.a. fax: n.a.	DE (MAINZ)	participant	347˙250.00
3	DEFINIENS AG DEFINIENS AG Organization address address: BERNHARD WICKI STR 5 city: MUNCHEN postcode: 80636 website: www.definiens.com contact info title: n.a. name: n.a. surname: n.a. function: n.a. email: n.a. telephone: n.a. fax: n.a.	DE (MUNCHEN)	participant	327˙000.00
4	APTAIT GMBH APTAIT GMBH Organization address address: LEONHARDISTRASSE 2E city: DIESSEN postcode: 86911 website: n.a. contact info title: n.a. name: n.a. surname: n.a. function: n.a. email: n.a. telephone: n.a. fax: n.a.	DE (DIESSEN)	participant	307˙125.00
5	STICHTING HET NEDERLANDS KANKER INSTITUUT-ANTONI VAN LEEUWENHOEK ZIEKENHUIS STICHTING HET NEDERLANDS KANKER INSTITUUT-ANTONI VAN LEEUWENHOEK ZIEKENHUIS Organization address address: PLESMANLAAN 121 city: AMSTERDAM postcode: 1066 CX website: www.nki.nl contact info title: n.a. name: n.a. surname: n.a. function: n.a. email: n.a. telephone: n.a. fax: n.a.	NL (AMSTERDAM)	participant	279˙000.00
6	INSTITUT NATIONAL DE LA SANTE ET DE LA RECHERCHE MEDICALE INSTITUT NATIONAL DE LA SANTE ET DE LA RECHERCHE MEDICALE Organization address address: RUE DE TOLBIAC 101 city: PARIS postcode: 75654 website: www.inserm.fr contact info title: n.a. name: n.a. surname: n.a. function: n.a. email: n.a. telephone: n.a. fax: n.a.	FR (PARIS)	participant	258˙000.00
7	UNIVERSITEIT UTRECHT UNIVERSITEIT UTRECHT Organization address address: HEIDELBERGLAAN 8 city: UTRECHT postcode: 3584 CS website: www.uu.nl contact info title: n.a. name: n.a. surname: n.a. function: n.a. email: n.a. telephone: n.a. fax: n.a.	NL (UTRECHT)	participant	249˙000.00
8	EBERHARD KARLS UNIVERSITAET TUEBINGEN EBERHARD KARLS UNIVERSITAET TUEBINGEN Organization address address: GESCHWISTER-SCHOLL-PLATZ city: TUEBINGEN postcode: 72074 website: www.uni-tuebingen.de contact info title: n.a. name: n.a. surname: n.a. function: n.a. email: n.a. telephone: n.a. fax: n.a.	DE (TUEBINGEN)	participant	247˙500.00
9	CENTER OF EXCELLENCE IN MEDICINE AND IT GMBH CENTER OF EXCELLENCE IN MEDICINE AND IT GMBH Organization address address: KARL KAPFERER STRASSE 5 city: INNSBRUCK postcode: 6020 website: www.cemit.at contact info title: n.a. name: n.a. surname: n.a. function: n.a. email: n.a. telephone: n.a. fax: n.a.	AT (INNSBRUCK)	participant	243˙360.00
10	CENTRO NACIONAL DE INVESTIGACIONESCARDIOVASCULARES CARLOS III (F.S.P.) CENTRO NACIONAL DE INVESTIGACIONESCARDIOVASCULARES CARLOS III (F.S.P.) Organization address address: CALLE MELCHOR FERNANDEZ ALMAGRO 3 city: MADRID postcode: 28029 website: www.cnic.es contact info title: n.a. name: n.a. surname: n.a. function: n.a. email: n.a. telephone: n.a. fax: n.a.	ES (MADRID)	participant	185˙262.00
11	Masarykova univerzita Masarykova univerzita Organization address address: Zerotinovo namesti 9 city: BRNO STRED postcode: 60177 website: http://www.muni.cz contact info title: n.a. name: n.a. surname: n.a. function: n.a. email: n.a. telephone: n.a. fax: n.a.	CZ (BRNO STRED)	participant	135˙250.00

Map

Project 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.

Deliverables

List of deliverables.
digital TILsorter	Other	2019-05-30 17:26:33
CRCclassifier	Documents, reports	2019-05-30 17:26:33
SOPs for TIL quantification	Documents, reports	2019-05-30 17:26:32
TCR2epitope	Documents, reports	2019-03-11 14:16:41
SOP for TCR repertoire	Documents, reports	2019-03-11 14:16:34
Evaluation of the analytical pipeline for cancer vaccines	Documents, reports	2019-02-26 16:05:07
RDF database	Other	2019-02-26 16:05:10
epitopeselector	Other	2019-02-26 16:05:08
Immuno Oncoclogy Suite	Documents, reports	2019-02-26 12:43:14
Webpage	Websites, patent fillings, videos etc.	2019-05-30 11:38:52

Take a look to the deliverables list in detail: detailed list of APERIM deliverables.

Publications

List of publications.
year	authors and title	journal	last update
2018	Mirjana Efremova, Dietmar Rieder, Victoria Klepsch, Pornpimol Charoentong, Francesca Finotello, Hubert Hackl, Natascha Hermann-Kleiter, Martin LÃ¶wer, Gottfried Baier, Anne Krogsdam, Zlatko Trajanoski Targeting immune checkpoints potentiates immunoediting and changes the dynamics of tumor evolution published pages: , ISSN: 2041-1723, DOI: 10.1038/s41467-017-02424-0	Nature Communications 9/1	2019-05-24
2017	Mikhail Shugay, Dmitriy V Bagaev, Ivan V Zvyagin, Renske M Vroomans, Jeremy Chase Crawford, Garry Dolton, Ekaterina A Komech, Anastasiya L Sycheva, Anna E Koneva, Evgeniy S Egorov, Alexey V Eliseev, Ewald VanÂ Dyk, Pradyot Dash, Meriem Attaf, Cristina Rius, Kristin Ladell, James E McLaren, Katherine K Matthews, EÂ Bridie Clemens, Daniel C Douek, Fabio Luciani, Debbie vanÂ Baarle, Katherine Kedzierska, Can Kesmir, Paul G Thomas, David A Price, Andrew K Sewell, Dmitriy M Chudakov VDJdb: a curated database of T-cell receptor sequences with known antigen specificity published pages: D419-D427, ISSN: 0305-1048, DOI: 10.1093/nar/gkx760	Nucleic Acids Research 46/D1	2019-05-24
2017	Bernhard Mlecnik, Marc Van den Eynde, Gabriela Bindea, Sarah E Church, Angela Vasaturo, Tessa Fredriksen, Lucie Lafontaine, Nacilla Haicheur, Florence Marliot, DaphnÃ© Debetancourt, GÃ©raldine Pairet, Anne Jouret-Mourin, Jean-Francois Gigot, Catherine Hubert, Etienne Danse, Cristina Dragean, Javier Carrasco, Yves Humblet, Viia Valge-Archer, Anne Berger, Franck PagÃ¨s, Jean-Pascal Machiels, JÃ©rÃ´me Galon Comprehensive Intrametastatic Immune Quantification and Major Impact of Immunoscore on Survival published pages: 97-108, ISSN: 0027-8874, DOI: 10.1093/jnci/djx123	JNCI: Journal of the National Cancer Institute 110/1	2019-05-24
2017	Pornpimol Charoentong, Francesca Finotello, Mihaela Angelova, Clemens Mayer, Mirjana Efremova, Dietmar Rieder, Hubert Hackl, Zlatko Trajanoski Pan-cancer Immunogenomic Analyses Reveal Genotype-Immunophenotype Relationships and Predictors of Response to Checkpoint Blockade published pages: 248-262, ISSN: 2211-1247, DOI: 10.1016/j.celrep.2016.12.019	Cell Reports 18/1	2019-05-24
2017	Mirjana Efremova, Francesca Finotello, Dietmar Rieder, Zlatko Trajanoski Neoantigens Generated by Individual Mutations and Their Role in Cancer Immunity and Immunotherapy published pages: , ISSN: 1664-3224, DOI: 10.3389/fimmu.2017.01679	Frontiers in Immunology 8	2019-05-24
2018	Christopher Mohr, Andreas Friedrich, David Wojnar, Erhan Kenar, Aydin Can Polatkan, Marius Cosmin Codrea, Stefan Czemmel, Oliver Kohlbacher, Sven Nahnsen qPortal: A platform for data-driven biomedical research published pages: e0191603, ISSN: 1932-6203, DOI: 10.1371/journal.pone.0191603	PLOS ONE 13/1	2019-05-24
2017	Elias Tappeiner, Francesca Finotello, Pornpimol Charoentong, Clemens Mayer, Dietmar Rieder, Zlatko Trajanoski TIminer: NGS data mining pipeline for cancer immunology and immunotherapy published pages: , ISSN: 1367-4803, DOI: 10.1093/bioinformatics/btx377	Bioinformatics	2019-05-27
2017	Francesca Finotello, Zlatko Trajanoski New strategies for cancer immunotherapy: targeting regulatory T cells published pages: , ISSN: 1756-994X, DOI: 10.1186/s13073-017-0402-8	Genome Medicine 9/1	2019-05-27
2017	Mikhail Shugay, Andrew R. Zaretsky, Dmitriy A. Shagin, Irina A. Shagina, Ivan A. Volchenkov, Andrew A. Shelenkov, Mikhail Y. Lebedin, Dmitriy V. Bagaev, Sergey Lukyanov, Dmitriy M. Chudakov MAGERI: Computational pipeline for molecular-barcoded targeted resequencing published pages: e1005480, ISSN: 1553-7358, DOI: 10.1371/journal.pcbi.1005480	PLOS Computational Biology 13/5	2019-05-27
2016	Bernhard Mlecnik, Gabriela Bindea, HelenÂ K. Angell, Pauline Maby, Mihaela Angelova, David Tougeron, SarahÂ E. Church, Lucie Lafontaine, Maria Fischer, Tessa Fredriksen, Maristella Sasso, AmÃ©lieÂ M. Bilocq, Amos Kirilovsky, AnnaÂ C. Obenauf, Mohamad Hamieh, Anne Berger, Patrick Bruneval, Jean-Jacques Tuech, Jean-Christophe Sabourin, Florence LeÂ Pessot, Jacques Mauillon, Arash Rafii, Pierre Laurent-Puig, MichaelÂ R. Speicher, Zlatko Trajanoski, Pierre Michel, Richard SesboÃ¼e, Thierry Frebourg, Franck PagÃ¨s, Viia Valge-Archer, Jean-Baptiste Latouche, JÃ©rÃ´me Galon Integrative Analyses of Colorectal Cancer Show Immunoscore Is a Stronger Predictor of Patient Survival Than Microsatellite Instability published pages: 698-711, ISSN: 1074-7613, DOI: 10.1016/j.immuni.2016.02.025	Immunity 44/3	2019-05-27
2016	E. Stronen, M. Toebes, S. Kelderman, M. M. van Buuren, W. Yang, N. van Rooij, M. Donia, M.-L. Boschen, F. Lund-Johansen, J. Olweus, T. N. Schumacher Targeting of cancer neoantigens with donor-derived T cell receptor repertoires published pages: 1337-1341, ISSN: 0036-8075, DOI: 10.1126/science.aaf2288	Science 352/6291	2019-05-27
2016	B. Mlecnik, G. Bindea, A. Kirilovsky, H. K. Angell, A. C. Obenauf, M. Tosolini, S. E. Church, P. Maby, A. Vasaturo, M. Angelova, T. Fredriksen, S. Mauger, M. Waldner, A. Berger, M. R. Speicher, F. Pages, V. Valge-Archer, J. Galon The tumor microenvironment and Immunoscore are critical determinants of dissemination to distant metastasis published pages: 327ra26-327ra26, ISSN: 1946-6234, DOI: 10.1126/scitranslmed.aad6352	Science Translational Medicine 8/327	2019-05-27
2017	Benjamin Schubert, Luis de la Garza, Christopher Mohr, Mathias Walzer, Oliver Kohlbacher ImmunoNodes â€“ graphical development of complex immunoinformatics workflows published pages: , ISSN: 1471-2105, DOI: 10.1186/s12859-017-1667-z	BMC Bioinformatics 18/1	2019-05-27
2016	Benjamin Schubert, Oliver Kohlbacher Designing string-of-beads vaccines with optimal spacers published pages: 1-10, ISSN: 1756-994X, DOI: 10.1186/s13073-016-0263-6	Genome Medicine 8/1	2019-05-27
2016	Benjamin Schubert, Mathias Walzer, Hans-Philipp Brachvogel, AndrÃ¡s Szolek, Christopher Mohr, Oliver Kohlbacher FRED 2 â€“ An Immunoinformatics Framework for Python published pages: btw113, ISSN: 1367-4803, DOI: 10.1093/bioinformatics/btw113	Bioinformatics	2019-05-27
2017	Dmitriy A. Shagin, Maria A. Turchaninova, Irina A. Shagina, Mikhail Shugay, Andrew R. Zaretsky, Olga I. Zueva, Dmitriy A. Bolotin, Sergey Lukyanov, Dmitriy M. Chudakov Application of nonsense-mediated primer exclusion (NOPE) for preparation of unique molecular barcoded libraries published pages: , ISSN: 1471-2164, DOI: 10.1186/s12864-017-3815-2	BMC Genomics 18/1	2019-05-27
2016	Hubert Hackl, Pornpimol Charoentong, Francesca Finotello, Zlatko Trajanoski Computational genomics tools for dissecting tumourâ€“immune cell interactions published pages: 441-458, ISSN: 1471-0056, DOI: 10.1038/nrg.2016.67	Nature Reviews Genetics 17/8	2019-05-27

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For instance: the website url (it has not provided by EU-opendata yet), the logo, a more detailed description of the project (in plain text as a rtf file or a word file), some pictures (as picture files, not embedded into any word file), twitter account, linkedin page, etc.

Send me an email (fabio@fabiodisconzi.com) and I put them in your project's page as son as possible.

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The information about "APERIM" are provided by the European Opendata Portal: CORDIS opendata.