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Personalized bioinformatics for global cancer susceptibility identification and clinical management

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.

Call for proposal

H2020-PHC-2014-2015

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Sub call

H2020-PHC-2014-two-stage

Coordinator

FUNDACION PUBLICA GALEGA DE MEDICINA XENOMICA
Net EU contribution
€ 558 350,00
Address
Hospital Clínico Universitario. Edif. Consultas Planta -2. Choupana S/n
15706 Santiago De Compostela
Spain

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Region
Galicia A Coruña
Activity type
Research Organisations
Other funding
€ 558 350,00

Participants (5)

CONSULTORIO DEXEUS SAP
Spain
Net EU contribution
€ 256 342,50
Address
Gran Via Carlos Iii 71-75
08028 Barcelona

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Region
Este Cataluña Barcelona
Activity type
Private for-profit entities (excluding Higher or Secondary Education Establishments)
Other funding
€ 256 342,50
INSTITUT CURIE
France
Net EU contribution
€ 328 713,75
Address
Rue D'ulm 26
75231 Paris

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Region
Ile-de-France Ile-de-France Paris
Activity type
Research Organisations
Other funding
€ 328 713,75
EUROPEAN MOLECULAR BIOLOGY LABORATORY
Germany
Net EU contribution
€ 508 080,00
Address
Meyerhofstrasse 1
69117 Heidelberg

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Region
Baden-Württemberg Karlsruhe Heidelberg, Stadtkreis
Activity type
Research Organisations
Other funding
€ 508 080,00
FUNDACIO CENTRE DE REGULACIO GENOMICA
Spain
Net EU contribution
€ 881 410,00
Address
Carrer Doctor Aiguader 88
08003 Barcelona

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Region
Este Cataluña Barcelona
Activity type
Research Organisations
Other funding
€ 881 410,00
PROTEINLOGIC LIMITED
United Kingdom
Net EU contribution
€ 415 287,50
Address
Shakespeare House 42 Newmarket Road
CB5 8EP Cambridge Cambridgeshire

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SME

The organization defined itself as SME (small and medium-sized enterprise) at the time the Grant Agreement was signed.

Yes
Region
East of England East Anglia Cambridgeshire CC
Activity type
Private for-profit entities (excluding Higher or Secondary Education Establishments)
Other funding
€ 415 287,50