RADIANT

Rapid development and distribution of statistical tools for high-throughput sequencing data

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 Obiettivo del progetto (Objective)

'High-throughput sequencing (HTS) is a powerful and rapidly evolving family of technologies with a multitude of applications. They include genetics of rare and common diseases, understanding of disease mechanism and progression through transcriptome and epigenome profiling, cancer stratification, personalised medicine and molecular systems biology of gene regulation. The genome, epigenome, transcriptome and interactome are all intricately connected, and modern HTS technology can probe all of these -omic levels. Statistical analysis is a crucial component of many experiments and studies, and the quality and efficiency of the analysis often determines the success of a project.

In this collaborative project we will develop a range of new statistical analysis tools to solve open problems in HTS data analysis, ranging from low-level processing of sequence reads up to systems-level modelling of disease associated and cellular processes. We will provide to a wide audience an integrated computational framework for HTS data analysis and interpretation that is robust, efficient and user-friendly. We will establish improved procedures for the publishing of statistical software as an integral part of the scientific publication process, within the framework of the Bioconductor project. We will provide tools to benchmark experimental protocols and statistical methods, and we will provide training materials and a extensive training programme to rapidly disseminate these new tools to the broader biomedical community.

SME partners will integrate these new tools within their analysis pipelines with associated user-friendly commercial software providing access to their additional proprietary tools. SMEs will benefit from basic methodology development done in a public, pre-competitive arena and will be able to use these technologies to enhance their products and services.'

Introduzione (Teaser)

High-throughput sequencing (HTS) has transformed the way scientists extract genetic information from biological systems. For the analysis of hundreds of gigabytes of data produced in a single sequencing run, EU-funded researchers are developing a series of statistical tools.

Descrizione progetto (Article)

In HTS, fragments of DNA are sequentially identified from signals emitted as each fragment is re-synthesised from a template DNA strand. This technology allows rapid sequencing of large stretches of base pairs spanning entire genomes. However, to extract meaningful biological signals, HTS experiments require powerful and computationally efficient statistical tools.

The EU-funded project 'Rapid development and distribution of statistical tools for high-throughput sequencing data' (http://radiant-project.eu/ (RADIANT)) supports improvements of the most popular statistical tools. Its ultimate objective is to integrate software packages developed by researchers in France, Germany, Italy, Switzerland and the United Kingdom into a single computational framework.

Among them is the Python library HTSeq that pre-processes RNA sequencing data for differential expression genes' analysis. The package DESeq2 provides methods to detect differentially expressed genes by means of generalised linear models. On the other hand, the BitSeq package implements a Bayesian approach to inferring the concentration of messenger RNA transcripts.

Research within the RADIANT project covers all aspects of HTS data analysis, from quality control to data visualisation. For gene expression time series, a hierarchical Bayesian modelling was proposed that can impute data missing both systematically and randomly. The RADIANT genome browser is the first visualisation application to be developed for DNA methylation data.

Thanks to its ability to reveal limitless insight into the human genome, HTS has permeated virtually all branches of biological research. With the newly developed RADIANT platform for HTS data analysis, it will become firmly entrenched as an indispensable tool. The applications hosted can transform genomic studies, surpassing boundaries and unlocking information never before imaginable.