APERIM: Advanced bioinformatics platform for PERsonalised cancer IMmunotherapy

Risultati finali

Evaluated and implemented SOPs. SOPs for TCR repertoire. Samples used for generating data to develop the tools and validate the software: melanoma, colorectal cancer, and ovarian cancer.

Evaluation of the analytical pipeline for cancer vaccines

Evaluated and implemented SOPs. Samples used for generating data to develop the tools and validate the software: melanoma, glioblastoma, and breast cancer.

CRCclassifier

A decision support model using the clinical parameters and the image descriptors derived from the analyses in task 2.1. The model will be a validated prototype using the available data. Samples used for generating data to develop the tools and validate the software: colorectal cancer.

SOPs for TIL quantification

Evaluated and implemented SOPs. SOPs for routine application in pathology labs. Samples used for generating data to develop the tools and validate the software: colorectal cancer.

TCR2epitope

Software tool for predicting epitope characteristics from the primary sequence information of TCRs. The software will include a method for identifying specificity of TCR-pMHC interaction (UU) as well as a web-database for TCRs with known specificities (MU). The data will be provided by NKI. Samples used for generating data to develop the tools and validate the software: melanoma, colorectal cancer, and ovarian cancer

Immuno Oncoclogy Suite

Database for molecular data (whole-exome sequencing data, microsatellite status, FACS data), clinical data (information about cancer patients, TNM staging, and density values of TILs used for immune score estimation), and imaging data (scanned whole-slide H&E images and stained IHC images) generated from colorectal cancer samples in WP2.

epitopeselector

Software for selecting epitopes from large number of candidates. Samples used for generating data to develop the tools and validate the software: melanoma, glioblastoma, and breast cancer.

RDF database

RDF version of the database ImmunoOncologySuite and SPARQL graphical editor

digital TILsorter

Method and software for TIL reconstruction employing a) deconvolution method (CNIC) and develop the algorithm for enumeration of immune cells, stromal cells, and tumour cells (I-MED). Samples used for generating data to develop the tools and validate the software: colorectal cancer.

Webpage

Institution of APERIM web page: A webpage is an absolute requirement for dissemination Furthermore it supports the communication within the consortium.

Pubblicazioni

Designing string-of-beads vaccines with optimal spacers

Autori: Benjamin Schubert, Oliver Kohlbacher
Pubblicato in: Genome Medicine, Numero 8/1, 2016, Pagina/e 1-10, ISSN 1756-994X
Editore: BioMed Central
DOI: 10.1186/s13073-016-0263-6

FRED 2 – An Immunoinformatics Framework for Python

Autori: Benjamin Schubert, Mathias Walzer, Hans-Philipp Brachvogel, András Szolek, Christopher Mohr, Oliver Kohlbacher
Pubblicato in: Bioinformatics, 2016, Pagina/e btw113, ISSN 1367-4803
Editore: Oxford University Press
DOI: 10.1093/bioinformatics/btw113

qPortal: A platform for data-driven biomedical research

Autori: Christopher Mohr, Andreas Friedrich, David Wojnar, Erhan Kenar, Aydin Can Polatkan, Marius Cosmin Codrea, Stefan Czemmel, Oliver Kohlbacher, Sven Nahnsen
Pubblicato in: PLOS ONE, Numero 13/1, 2018, Pagina/e e0191603, ISSN 1932-6203
Editore: Public Library of Science
DOI: 10.1371/journal.pone.0191603

VDJdb: a curated database of T-cell receptor sequences with known antigen specificity

Autori: 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 Van Dyk, Pradyot Dash, Meriem Attaf, Cristina Rius, Kristin Ladell, James E McLaren, Katherine K Matthews, E Bridie Clemens, Daniel C Douek, Fabio Luciani, Debbie van Baarle, Katherine Kedzier
Pubblicato in: Nucleic Acids Research, Numero 46/D1, 2017, Pagina/e D419-D427, ISSN 0305-1048
Editore: Oxford University Press
DOI: 10.1093/nar/gkx760

Neoantigens Generated by Individual Mutations and Their Role in Cancer Immunity and Immunotherapy

Autori: Mirjana Efremova, Francesca Finotello, Dietmar Rieder, Zlatko Trajanoski
Pubblicato in: Frontiers in Immunology, Numero 8, 2017, ISSN 1664-3224
Editore: Frontiers Media SA
DOI: 10.3389/fimmu.2017.01679

Pan-cancer Immunogenomic Analyses Reveal Genotype-Immunophenotype Relationships and Predictors of Response to Checkpoint Blockade

Autori: Pornpimol Charoentong, Francesca Finotello, Mihaela Angelova, Clemens Mayer, Mirjana Efremova, Dietmar Rieder, Hubert Hackl, Zlatko Trajanoski
Pubblicato in: Cell Reports, Numero 18/1, 2017, Pagina/e 248-262, ISSN 2211-1247
Editore: Cell Press
DOI: 10.1016/j.celrep.2016.12.019

Comprehensive Intrametastatic Immune Quantification and Major Impact of Immunoscore on Survival

Autori: Bernhard Mlecnik, Marc Van den Eynde, Gabriela Bindea, Sarah E Church, Angela Vasaturo, Tessa Fredriksen, Lucie Lafontaine, Nacilla Haicheur, Florence Marliot, Daphné Debetancourt, Géraldine Pairet, Anne Jouret-Mourin, Jean-Francois Gigot, Catherine Hubert, Etienne Danse, Cristina Dragean, Javier Carrasco, Yves Humblet, Viia Valge-Archer, Anne Berger, Franck Pagès, Jean-Pascal Machiels, Jérôm
Pubblicato in: JNCI: Journal of the National Cancer Institute, Numero 110/1, 2017, Pagina/e 97-108, ISSN 0027-8874
Editore: Oxford University Press
DOI: 10.1093/jnci/djx123

Targeting immune checkpoints potentiates immunoediting and changes the dynamics of tumor evolution

Autori: Mirjana Efremova, Dietmar Rieder, Victoria Klepsch, Pornpimol Charoentong, Francesca Finotello, Hubert Hackl, Natascha Hermann-Kleiter, Martin Löwer, Gottfried Baier, Anne Krogsdam, Zlatko Trajanoski
Pubblicato in: Nature Communications, Numero 9/1, 2018, ISSN 2041-1723
Editore: Nature Publishing Group
DOI: 10.1038/s41467-017-02424-0

Computational genomics tools for dissecting tumour–immune cell interactions

Autori: Hubert Hackl, Pornpimol Charoentong, Francesca Finotello, Zlatko Trajanoski
Pubblicato in: Nature Reviews Genetics, Numero 17/8, 2016, Pagina/e 441-458, ISSN 1471-0056
Editore: Nature Publishing Group
DOI: 10.1038/nrg.2016.67

Integrative Analyses of Colorectal Cancer Show Immunoscore Is a Stronger Predictor of Patient Survival Than Microsatellite Instability

Autori: Bernhard Mlecnik, Gabriela Bindea, Helen K. Angell, Pauline Maby, Mihaela Angelova, David Tougeron, Sarah E. Church, Lucie Lafontaine, Maria Fischer, Tessa Fredriksen, Maristella Sasso, Amélie M. Bilocq, Amos Kirilovsky, Anna C. Obenauf, Mohamad Hamieh, Anne Berger, Patrick Bruneval, Jean-Jacques Tuech, Jean-Christophe Sabourin, Florence Le Pessot, Jacques Mauillon, Arash Rafii, Pierre Laure
Pubblicato in: Immunity, Numero 44/3, 2016, Pagina/e 698-711, ISSN 1074-7613
Editore: Cell Press
DOI: 10.1016/j.immuni.2016.02.025

Targeting of cancer neoantigens with donor-derived T cell receptor repertoires

Autori: 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
Pubblicato in: Science, Numero 352/6291, 2016, Pagina/e 1337-1341, ISSN 0036-8075
Editore: American Association for the Advancement of Science
DOI: 10.1126/science.aaf2288

The tumor microenvironment and Immunoscore are critical determinants of dissemination to distant metastasis

Autori: 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
Pubblicato in: Science Translational Medicine, Numero 8/327, 2016, Pagina/e 327ra26-327ra26, ISSN 1946-6234
Editore: American Association for the Advancement of Science
DOI: 10.1126/scitranslmed.aad6352

ImmunoNodes – graphical development of complex immunoinformatics workflows

Autori: Benjamin Schubert, Luis de la Garza, Christopher Mohr, Mathias Walzer, Oliver Kohlbacher
Pubblicato in: BMC Bioinformatics, Numero 18/1, 2017, ISSN 1471-2105
Editore: BioMed Central
DOI: 10.1186/s12859-017-1667-z

New strategies for cancer immunotherapy: targeting regulatory T cells

Autori: Francesca Finotello, Zlatko Trajanoski
Pubblicato in: Genome Medicine, Numero 9/1, 2017, ISSN 1756-994X
Editore: BioMed Central
DOI: 10.1186/s13073-017-0402-8

TIminer: NGS data mining pipeline for cancer immunology and immunotherapy

Autori: Elias Tappeiner, Francesca Finotello, Pornpimol Charoentong, Clemens Mayer, Dietmar Rieder, Zlatko Trajanoski
Pubblicato in: Bioinformatics, 2017, ISSN 1367-4803
Editore: Oxford University Press
DOI: 10.1093/bioinformatics/btx377

Application of nonsense-mediated primer exclusion (NOPE) for preparation of unique molecular barcoded libraries

Autori: 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
Pubblicato in: BMC Genomics, Numero 18/1, 2017, ISSN 1471-2164
Editore: BioMed Central
DOI: 10.1186/s12864-017-3815-2

MAGERI: Computational pipeline for molecular-barcoded targeted resequencing

Autori: 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
Pubblicato in: PLOS Computational Biology, Numero 13/5, 2017, Pagina/e e1005480, ISSN 1553-7358
Editore: Paul P Gardner
DOI: 10.1371/journal.pcbi.1005480

Risultati finali

Pubblicazioni

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