Personalized bioinformatics for global cancer susceptibility identification and clinical management

Project Information

PanCanRisk

Grant agreement ID: 635290

DOI

10.3030/635290

Project closed

EC signature date 7 April 2015

Start date 1 July 2015

End date 30 June 2018

Funded under

• SOCIETAL CHALLENGES - Health, demographic change and well-being

Total cost

€ 2 948 183,75

EU contribution

€ 2 948 183,75

Coordinated by

FUNDACION PUBLICA GALEGA DE MEDICINA XENOMICA
Spain

CORDIS provides links to public deliverables and publications of HORIZON projects.

Links to deliverables and publications from FP7 projects, as well as links to some specific result types such as dataset and software, are dynamically retrieved from OpenAIRE .

Deliverables

Demonstrators, pilots, prototypes (3)

Cloud installation of the eDiVA

Proof-of-concept cloud installation of the eDiVA platform optimized for NGS-based diagnostics in the clinics, with a specific focus on MGTS analysis for cancer risk diagnostics, intuitively accessible interfaces and data views as well as restricted access and data security

eDiVA

A specialised version of the eDiVA NGS analysis platform optimized for distributed analysis of germline variation in large-scale cancer studies

Open-source software for indel and CNV prediction

Release of improved version of open-source software for indel and CNV prediction (ClinDel, ClinCNV, PeSV-Fisher) Note: Month 30 (tentative)

Websites, patent fillings, videos etc. (2)

Material for dissemination and information purposes

Material for dissemination and information purposes (power point presentations, posters, flyers; others) to be presented at international conferences/ events/ workshops (these will be repeated tasks, months 18 and 24)

Website

Project website online

Documents, reports (3)

Project’s agendas, minutes and all documents related to the organization and running of the meetings of the consortium
Revision of ethical guidelines

Revision of ethical guidelines for the PanCanRisk

Internal satisfaction surveys and “Lessons Learned” document

Publications

Other (4)

Germline determinants of the somatic mutation landscape in 2,642 cancer genomes

Author(s): 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. Jona
Published in: 2017
Publisher: Cold Spring Harbor Laboratory
DOI: 10.1101/208330

Assessing the Gene Regulatory Landscape in 1,188 Human Tumors

Author(s): Claudia Calabrese, Kjong-Van Lehmann, Lara Urban, Fenglin Liu, Serap Erkek, Nuno Fonseca, Andre Kahles, Leena Helena Kilpinen-Barrett, Julia Markowski, PCAWG-3, Sebastian Waszak, Jan Korbel, Zemin Zhang, Alvis Brazma, Gunnar Raetsch, Roland Schwarz, Oliver Stegle
Published in: 2019
Publisher: Cold Spring Harbour Lab
DOI: 10.1101/225441

Combined single cell profiling of expression and DNA methylation reveals splicing regulation and heterogeneity

Author(s): Stephanie Maria Linker, View ORCID ProfileLara Urban, View ORCID ProfileStephen Clark, Mariya Chhatriwala, Shradha Amatya, View ORCID ProfileDavis McCarthy, View ORCID ProfileIngo Ebersberger, View ORCID ProfileLudovic Vallier, View ORCID ProfileWolf Reik, View ORCID ProfileOliver Stegle, View ORCID ProfileMarc Jan Bonder
Published in: 2018
Publisher: Cold Spring Harbour
DOI: 10.1101/328138

Bayesian Inference Of Cancer Driver Genes Using Signatures Of Positive Selection

Author(s): Susak, Hana; Zapata, Luis; Ossowski, Stephan; Estivill, Xavier; Friedlander, Marc; Drechsel, Oliver
Published in: Issue 1, 2017
Publisher: Cold Spring Harbor Laboratory
DOI: 10.1101/059360

Peer reviewed articles (4)

Signatures of positive selection reveal a universal role of chromatin modifiers as cancer driver genes

Author(s): Luis Zapata, Hana Susak, Oliver Drechsel, Marc R. Friedländer, Xavier Estivill, Stephan Ossowski
Published in: Scientific Reports, Issue 7/1, 2017, ISSN 2045-2322
Publisher: Nature Publishing Group
DOI: 10.1038/s41598-017-12888-1

Negative selection in tumor genome evolution acts on essential cellular functions and the immunopeptidome

Author(s): Luis Zapata, Oriol Pich, Luis Serrano, Fyodor A. Kondrashov, Stephan Ossowski, Martin H. Schaefer
Published in: Genome Biology, Issue 19/1, 2018, ISSN 1474-760X
Publisher: BMC
DOI: 10.1186/s13059-018-1434-0

Deep learning for computational biology

Author(s): Christof Angermueller, Tanel Pärnamaa, Leopold Parts, Oliver Stegle
Published in: Molecular Systems Biology, Issue 12/7, 2016, Page(s) 878, ISSN 1744-4292
Publisher: Nature Publishing Group
DOI: 10.15252/msb.20156651

Allele balance bias identifies systematic genotyping errors and false disease associations

Author(s): Francesc Muyas, Mattia Bosio, Anna Puig, Hana Susak, Laura Domènech, Georgia Escaramis, Luis Zapata, German Demidov, Xavier Estivill, Raquel Rabionet, Stephan Ossowski
Published in: Human Mutation, Issue 40/1, 2019, Page(s) 115-126, ISSN 1059-7794
Publisher: John Wiley & Sons Inc.
DOI: 10.1002/humu.23674