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PanCanRisk

Personalized bioinformatics for global cancer susceptibility identification and clinical management

Total Cost €

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EC-Contrib. €

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Partnership

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Project "PanCanRisk" data sheet

The following table provides information about the project.

Coordinator
FUNDACION PUBLICA GALEGA DE MEDICINA XENOMICA 

Organization address
address: Hospital Clínico Universitario. Edif. consultas planta -2. Choupana s/n
city: Santiago de Compostela
postcode: 15706
website: http://fundacion.xenomica.org/

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 Spain [ES]
 Project website http://www.pancanrisk.eu/
 Total cost 2˙948˙183 €
 EC max contribution 2˙948˙183 € (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 2015-07-01   to  2018-06-30

 Partnership

Take a look of project's partnership.

# participants  country  role  EC contrib. [€] 
1    FUNDACION PUBLICA GALEGA DE MEDICINA XENOMICA ES (Santiago de Compostela) coordinator 558˙350.00
2    FUNDACIO CENTRE DE REGULACIO GENOMICA ES (BARCELONA) participant 881˙410.00
3    EUROPEAN MOLECULAR BIOLOGY LABORATORY DE (HEIDELBERG) participant 508˙080.00
4    PROTEINLOGIC LIMITED UK (CAMBRIDGE CAMBRIDGESHIRE) participant 415˙287.00
5    INSTITUT CURIE FR (PARIS) participant 328˙713.00
6    CONSULTORIO DEXEUS SAP ES (BARCELONA) participant 256˙342.00

Map

 Project objective

Cancer sequencing studies have extensively investigated the landscape of somatic mutations that drive tumor development, however the importance of germline variation for cancer susceptibility has been neglected. We hypothesize that for cancer types affecting a large proportion of the population, a shared set of genes with variants of different levels of penetrance leads to the clinical phenotype. While rare germline variants are not interrogated by array-based genome-wide association studies (GWAS), these can be effectively studied by whole-genome or whole-exome sequencing. Here, we propose in-depth pan-cancer analyses, which will be implemented as part of the International Cancer Genome Consortium (ICGC) initiative, as a model to develop and apply the necessary bioinformatics tools and pipelines to fully exploit the cancer-genome datasets, and to harness the diagnostic power of genome sequencing in day-to-day clinical practice. Our proposal addresses the full chain of computational and statistical tools that are needed for clinically relevant diagnosis and intervention, including discovery in large cohorts, validation of putative causal sites in model systems and development of targeted cancer-risk panels. The consortium combines complementary expertise to extend the computational discovery of novel variants that influence cancer susceptibility to intergenic and regulatory variants; to integrate genomic, molecular phenotype, biomarker and clinical data; and to develop novel statistical methods for variant association and eQTL analysis. The project will deal with essential aspects on how data are collected, stored, organized, integrated, analyzed and exploited in cancer genetic clinics. We aim to provide a concerted, cross-disciplinary framework for a better understanding, integration and use of cancer clinical data in the evaluation of the multitude of genetic variants and mutations involved in cancer susceptibility, for the direct benefit of cancer patients.

 Deliverables

List of deliverables.
Project’s agendas, minutes and all documents related to the organization and running of the meetings of the consortium Documents, reports 2019-10-03 18:23:26
Open-source software for indel and CNV prediction Demonstrators, pilots, prototypes 2019-10-03 18:23:26
Internal satisfaction surveys and “Lessons Learned” document Documents, reports 2019-10-03 18:23:26
Cloud installation of the eDiVA Demonstrators, pilots, prototypes 2019-10-03 18:23:26
Website Websites, patent fillings, videos etc. 2019-10-03 18:23:26
eDiVA Demonstrators, pilots, prototypes 2019-10-03 18:23:26
Material for dissemination and information purposes Websites, patent fillings, videos etc. 2019-10-03 18:23:26
Revision of ethical guidelines Documents, reports 2019-10-03 18:23:26

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

 Publications

year authors and title journal last update
List of publications.
2018 Luis Zapata, Oriol Pich, Luis Serrano, Fyodor A. Kondrashov, Stephan Ossowski, Martin H. Schaefer
Negative selection in tumor genome evolution acts on essential cellular functions and the immunopeptidome
published pages: , ISSN: 1474-760X, DOI: 10.1186/s13059-018-1434-0
Genome Biology 19/1 2019-10-03
2017 Sebastian M. Waszak, Grace Tiao, Bin Zhu, Tobias Rausch, Francesc Muyas, Bernardo Rodriguez-Martin, Raquel Rabionet, Sergei Yakneen, Georgia Escaramis, Yilong Li, Natalie Saini, Steven A. Roberts, German M. Demidov, Esa Pitkanen, Olivier Delaneau, Jose M. Heredia-Genestar, Joachim Weischenfeldt, Suyash S. Shringarpure, Jieming Chen, Hidewaki Nakagawa, Ludmil B. Alexandrov, Oliver Drechsel, L. Jonathan Dursi, Ayellet V. Segre, Erik Garrison, Serap Erkek, Nina Habermann, Lara Urban, Ekta Khurana, Andy Cafferkey, Shuto Hayashi, Seiya Imoto, Lauri A. Aaltonen, Eva G. Alvarez, Adrian Baez-Ortega, Matthew Bailey, Mattia Bosio, Alicia L. Bruzos, Ivo Buchhalter, Carlos D. Bustamante, Claudia Calabrese, Anthony DiBiase, Mark Gerstein, Aliaksei Z. Holik, Xing Hua, Kuan-lin Huang, Ivica Letunic, Leszek J. Klimczak, Roelof Koster, Sushant Kumar, Mike McLellan, Jay Mashl, Lisa Mirabello, Steven Newhouse, Aparna Prasad, Gunnar Raetsch, Matthias Schlesner, Roland Schwarz, Pramod Sharma, Tal Shmaya, Nikos Sidiropoulos, Lei Song, Hana Susak, Tomas Tanskanen, Marta Tojo, David C. Wedge, Mark Wright, Ying Wu, Kai Ye, Venkata D. Yellapantula, Jorge Zamora, Atul J. Butte, Gad Getz, Jared Simpson, Li Ding, Tomas Marques-Bonet, Arcadi Navarro, Alvis Brazma, Peter Campbell, Stephen J. Chanock, Nilanjan Chatterjee, Oliver Stegle, Reiner Siebert, Stephan Ossowski, Olivier Harismendy, Dmitry A. Gordenin, Jose M. C. Tubio, Francisco M. De La Vega, Douglas F. Easton, Xavier Estivill, Jan Korbel, PCAWG Germline Working Group, ICGC/TCGA Pan-Cancer Analysis of Whole Genomes Net
Germline determinants of the somatic mutation landscape in 2,642 cancer genomes
published pages: , ISSN: , DOI: 10.1101/208330
2019-10-03
2018 Luis Zapata, Oriol Pich, Luis Serrano, Fyodor A. Kondrashov, Stephan Ossowski, Martin H. Schaefer
Negative selection in tumor genome evolution acts on essential cellular functions and the immunopeptidome
published pages: , ISSN: 1474-760X, DOI: 10.1186/s13059-018-1434-0
Genome Biology 19/1 2019-10-03
2017 Susak, Hana; Zapata, Luis; Ossowski, Stephan; Estivill, Xavier; Friedlander, Marc; Drechsel, Oliver
Bayesian Inference Of Cancer Driver Genes Using Signatures Of Positive Selection
published pages: , ISSN: , DOI: 10.1101/059360
1 2019-10-03
3400 Francesc Muyas, Mattia Bosio, Anna Puig, Hana Susak, Laura Domènech-Salgado, Georgia Escaramis, Luis Zapata, German Demidov, Xavier Estivill, Raquel Rabionet, Stephan Ossowski
Allele balance bias identifies systematic genotyping errors and false disease associations
published pages: , ISSN: 1059-7794, DOI: 10.1002/humu.23674
Human Mutation 2019-10-03
2017 Luis Zapata, Hana Susak, Oliver Drechsel, Marc R. Friedländer, Xavier Estivill, Stephan Ossowski
Signatures of positive selection reveal a universal role of chromatin modifiers as cancer driver genes
published pages: , ISSN: 2045-2322, DOI: 10.1038/s41598-017-12888-1
Scientific Reports 7/1 2019-10-03
2016 Christof Angermueller, Tanel Pärnamaa, Leopold Parts, Oliver Stegle
Deep learning for computational biology
published pages: 878, ISSN: 1744-4292, DOI: 10.15252/msb.20156651
Molecular Systems Biology 12/7 2019-10-03

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

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