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Section: Research Program

High dimensional data

With the availability of omics data such as genomics (DNA), transcriptomics (RNA) or proteomics (proteins), but also other types of data, such as those arising from the combination of large observational databases (e.g. in pharmacoepidemiology or environmental epidemiology), high-dimensional data have became increasingly common. Use of molecular biological technics such as Polymerase Chain Reaction (PCR) allows for amplification of DNA or RNA sequences. Nowadays, microarray and Next Generation Sequencing (NGS) techniques give the possibility to explore very large portions of the genome. Furthermore, other assays have also evolved, and traditional measures such as cytometry or imaging have became new sources of big data. Therefore, in the context of HIV research, the dimension of the datasets has much grown in term of number of variables per individual than in term of number of included patients although this latter is also growing thanks to the multi-cohort collaborations such as CASCADE or COHERE organized in the EuroCoord network (see online at As an exemple, in a recent phase 1/2 clinical trial evaluating the safety and the immunological response to a dendritic cell-based HIV vaccine, 19 infected patients were included. Bringing together data on cell count, cytokine production, gene expression and viral genome change led to a 20 Go database [56]. This is far from big databases faced in other areas but constitutes a revolution in clinical research where clinical trials of hundred of patients sized few hundred of Ko at most. Therefore, more than the storage and calculation capacities, the challenge is the comprehensive analysis of these datasets.

The objective is either to select the relevant information or to summarize it for understanding or prediction purposes. When dealing with high dimensional data, the methodological challenge arises from the fact that datasets typically contain many variables, much more than observations. Hence, multiple testing is an obvious issue that needs to be taken into account [54]. Furthermore, conventional methods, such as linear models, are inefficient and most of the time even inapplicable. Specific methods have been developed, often derived from the machine learning field, such as regularization methods [58]. The integrative analysis of large datasets is challenging. For instance, one may want to look at the correlation between two large scale matrices composed by the transcriptome in the one hand and the proteome on the other hand [47]. The comprehensive analysis of these large datasets concerning several levels from molecular pathways to clinical response of a population of patients needs specific approaches and a very close collaboration with the providers of data that is the immunologists, the virologists, the clinicians...