Personalized bioinformatics for global cancer susceptibility identification and clinical management

Livrables

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)

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

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

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

Auteurs: 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
Publié dans: 2017
Éditeur: Cold Spring Harbor Laboratory
DOI: 10.1101/208330

Assessing the Gene Regulatory Landscape in 1,188 Human Tumors

Auteurs: 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
Publié dans: 2019
Éditeur: Cold Spring Harbour Lab
DOI: 10.1101/225441

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

Auteurs: 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
Publié dans: 2018
Éditeur: Cold Spring Harbour
DOI: 10.1101/328138

Bayesian Inference Of Cancer Driver Genes Using Signatures Of Positive Selection

Auteurs: Susak, Hana; Zapata, Luis; Ossowski, Stephan; Estivill, Xavier; Friedlander, Marc; Drechsel, Oliver
Publié dans: Numéro 1, 2017
Éditeur: Cold Spring Harbor Laboratory
DOI: 10.1101/059360

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

Auteurs: Luis Zapata, Hana Susak, Oliver Drechsel, Marc R. Friedländer, Xavier Estivill, Stephan Ossowski
Publié dans: Scientific Reports, Numéro 7/1, 2017, ISSN 2045-2322
Éditeur: Nature Publishing Group
DOI: 10.1038/s41598-017-12888-1

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

Auteurs: Luis Zapata, Oriol Pich, Luis Serrano, Fyodor A. Kondrashov, Stephan Ossowski, Martin H. Schaefer
Publié dans: Genome Biology, Numéro 19/1, 2018, ISSN 1474-760X
Éditeur: BMC
DOI: 10.1186/s13059-018-1434-0

Deep learning for computational biology

Auteurs: Christof Angermueller, Tanel Pärnamaa, Leopold Parts, Oliver Stegle
Publié dans: Molecular Systems Biology, Numéro 12/7, 2016, Page(s) 878, ISSN 1744-4292
Éditeur: Nature Publishing Group
DOI: 10.15252/msb.20156651

Allele balance bias identifies systematic genotyping errors and false disease associations

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

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