Section: Partnerships and Cooperations

Regional Initiatives

SysMics

Participants : Jean-Marc Menaud, Mario Südholt [coordinator] .

The SysMics project aims at federating the NExT scientific community toward a common objective: anticipate the emergence of systems medicine by co-developing 3 approaches in population-scale genomics: genotyping by sequencing, cell-by-cell profiling and microbiome analysis. STACK investigates new means for secure and privacy-aware computations in the context of personalized medecine, notably genetic analyses.

This project is financed by the Nantes excellency initiative in Medecine and Informatics (NExT) from 2018-22.

SHLARC

Participants : Mario Südholt [coordinator] , Sirine Sayadi.

The SHLARC project is an international network involving more than 20 partners from more than 15 countries located on four continents. The network aims at improving HLA imputation techniques in the domain of immunobiology, notably by investigation better computational methods for the correspoding biomedical analyses.

The ambition of the SHLARC is to bring together international expertise to solve essential questions on immune-related pathologies through innovative algorithms and powerful computation tool development. To achieve this goal, we determined 3 main objectives

• Data. By bringing together scientists from around the world, we will collectively increase the amount of SNP+HLA data available, both in terms of quantity and diversity.

• Applied mathematical and computer sciences. We will further optimize SNP-HLA imputation methods using the attribute-bagging HIBAG tool, and particularly for genetically diverse and admixed populations.

• Accessibility and service to the scientific community. Following the Haplotype Reference Consortium (HRC) initiative, the network envisions building a free, user-friendly webserver where researchers can access improved imputation protocols by simply uploading their data and obtaining the best possible HLA imputation for their dataset.

In this context, the STACK team is working on improved analysis techniques that harness distributed infrastructures.

This project is financed by the Nantes excellency initiative in Medecine and Informatics (NExT) from 2019-22.

Oncoshare

Participant : Mario Südholt [coordinator] .

The ONCOSHARe project (ONCOlogy big data SHAring for Research) will demonstrate, through a multidisciplinary cooperation within the Western CANCEROPOLE network, the feasibility and the added value of a Cancer Patient Centered Information Common for in-silico research. The STACK team will work on challenges to the security and the privacy of user data in this context.

This project is financed by three French regions from 2018-2021.