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Related projects (13)

A long-term mission for an assigned CIH-embedded bioinformatician to provide bioinformatic support to the CIH community

The Center for Human Immunology (CIH) supports researchers involved in translational research projects by providing access to 16 different cutting edge technologies. Currently, the CIH hosts over 60 scientific projects coming from 8 departments of the Institut Pastuer and 5 external teams. In order to respond to the growing needs of these projects in the area of single cell analysis, the CIH has introduced a significant number of single-cell/single-molecule technologies over the past 2-3 years. These new technologies, such as the Personal Genome Machine (PGM) and Ion Proton sequencers, iSCAN microarray scanner, Nanostring technology for transcriptomics profiling and real-time PCR machine BioMark, give rise to large datasets with high dimensionality. Such trend, in terms of data complexity, is also true for flow cytometry technologies (currently reaching over 20 parameters per cell). The exploration of this data is generally beyond the scope of scientists involved in translational research projects. In order to maximize the research outcomes obtained from the analysis of these rich datasets, and to ensure that the full potential of our technologies can be served to the users of the CIH, we would require a proximity bioinformatics support. A CIH-embedded bioinformatician would: 1) design and implement standard analysis pipelines for each of the data-rich technologies of the CIH; 2) provide regular ‘bioinformatics clinics’ to allow scientists the possibility to customize standard pipelines to their specific needs; 3) run trainings on the ‘R software’ platform and other data analysis tools (such as Qlucore) of interest for the CIH users. The objective would be to empower the users to run exploratory analysis by themselves, and to teach good practices in terms of data management and data analysis.    

Project status : In Progress

DNA encapsulation of human resources for research projects on immune system and inflammatory diseases

Freezing is the most commonly used method for storing DNA extracts. However, that method is non-practical and expensive, since requiring freezers and back-up generators for storage, and specific conditions/reagents for transport. In addition, even when adequate procedures are followed, the frozen extracts integrity might suffer from repeated freeze-thaw cycles or residual microorganism activity. The Institut Pasteur’s ICAReB platform hosts the biological collection related to the CoSImmGEn cohorts (Cohort and Collection to Study the Immune System with its Genetic and Environmental determinants) since 2011 (see related team publication 1). Those cohorts have been designed for providing large, duly annotated, qualified blood-derived bio-resources such as blood peripheral mononuclear cells, DNA and RNA from healthy subjects or cases suffering from diseases such as Hidradenitis Suppurativa to support genetic studies linked to the immune system (see related team publication 2 et 3). To provide over the long term genomic DNA for any kind of future genetic studies searching for immune system etio-pathogenesis, the ICAReB platform has used a newly developed DNAshells® (Imagene) which ensure nondestructive, reliable and long-term stability of DNA at low-cost (Clermont et coll, Biopreserv Biobank, 2014). That technology involves encapsulation of the genomic material such that it can be stored dry at room temperature, in small, watertight, oxidation-proof metal capsules. The first aim of the present project is to determine if SNP genotyping allows the detection of DNA damage during storage in various conditions. The second aim of the project is to demonstrate that encapsulation allows an optimal storage of human blood derived DNA at room temperature.

Project status : Closed