Computational genomics

A developing network

Genopole is building a strategy on three pillar sectors, each contributing to its ambition of transforming life sciences technologies into tomorrow’s therapeutic and industrial solutions. The computational genomics sector lends its fundamental support to the two other sectors: innovative therapies and the bioeconomy. It takes on the challenge of valorizing the "Big Data" resulting from large-scale sequencing. This involves standardizing those data, aggregating them with others, and interpreting the information within to better understand biological mechanisms, improve disease diagnostics & treatments, and conceptualize biological—and thus more sustainable—processes for the manufacture of medicines, materials, energies and more.

In this still-emerging sector, Genopole has the advantage of counting six laboratories for research in bioinformatics, biomathematics and genomics, nine businesses developing applications in bioinformatics and artificial intelligence, and five shared-use platforms, two of which provide informatics tools. In 2021, Genopole financed the outfitting of the CEA premises housing the National Center of Human Genomics Research (CNRGH) and CRefIX, the reference center responsible for sequencing processes harmonization.

The biocluster constructed a network of academic and industrial partners and foreshadowed a proposed project for an institute responding to their needs in computational genomics. That project, the objective of which is to federate a community of biologists mathematicians, informaticians and researchers in human and social sciences, was submitted by Genopole and the University of Évry as an "interdisciplinary object" in a call for expression of interest by Paris-Saclay University. The operational model and offer of this future computational genomics institute will be consolidated in 2022.

In 2021, to accompany the emergence of a computational genomics sector, Genopole pursued its initiatives to energize initial bioinformatics training with the territory’s higher learning facilities. As part of those initiatives, the IBISC laboratory provided training to students at the Grande Écoles Télécom SudParis and ENSIIE. Strengthening the offer of high-level, two-axis training in biology and data sciences is a major issue in computational genomics. To successfully address it, new concepts and innovative methods need to be invented in mathematics, statistics and informatics, all in synergy with biological sciences

Training for computational genomics in healthcare

Genopole’s Bioinformatics and Biostatistical Tools in Genomics for the Summer School accompanies the growth of the computational genomics sector by offering a yearly program of conferences and practical training with the support of the University of Évry-Paris Saclay, the Jean Dausset Foundation and the French Institute of Bioinformatics. The various sessions of its fourth edition, held 18–21 October, were led by 12 experts from major French and European research centers (UPSay, INRAE, EBI-EMBL, Inserm, Institut Curie, U-Sheffield UK) and two representatives of international industrial research (GSK UK and Agency for Science, Technology and Research, Singapore).

Genomics and bioinformatics: two weapons to fight COVID-19

Underlining the need for a national COVID-19 surveillance network

Several Genopole laboratories remained in the fight while COVID-19 continued its pernicious course in 2021. In an opinion piece published 14 January in the newspaper Figaro, 13 scientific personalities, including Jean-François Deleuze, Director of the National Center of Human Genomics Research (CNRGH/CEA), underlined the urgent need to create a national network for coronavirus variant surveillance via the mobilization of the large-scale DNA sequencing expertise available in private companies, academia and hospitals.

POSCOVD: A project for mass diagnoses of COVID-19

Marco Mendoza, laureate of the special project call launched within the Île-de-France Region’s DIM (Domain of Main Interest) Elicit, was present on 20 January for a colloquium held under the banner "Innovative technologies to Fight SARS-CoV-2." There, he presented his project POSCOVD, intended to replace individual COVID-19 testing by grouped testing of thousands of patient samples, which should reduce per-patient time and cost. POSCOVD includes the integration of a molecular barcode in each sample, thus making it possible to massively sequence the pool of samples then extract individual results by informatics analysis.

A digital map of COVID-19 biological mechanisms

The digital COVID-19 Disease Map, which gathers all known molecular mechanisms of the coronavirus pathology, was published 19 October in Molecular Systems Biology. Anna Niarakis, teaching researcher in computational systems biology at the GenHotel laboratory, was one of the four coordinators of this international project involving nearly 300 biologists, bioinformaticians and clinicians in 30 countries.

International project involving

300

biologists, bioinformaticians and clinicians in

countries

A mobile application to fight antibiotic resistance

Researchers from LaMME (Évry Mathematics and Modeling Laboratory) and the Genomics Metabolics unit have developed a mobile, artificial intelligence application for the automated analysis of antibiogram images. Google provided a grant for the project, carried out in partnership with Médecins Sans Frontières and the Bacteriology-Virology Department of the Henri-Mondor Hospital. Freely available to health professionals across the globe, the tool facilitates the reasoned choice of the specific antibiotic to be used as a function of the susceptibility/resistance profile of the bacterium in question. It thus contributes to slowing the progression of antibiotic resistance, which, if left unchecked, could become the world’s leading cause of mortality.

Watch the demo

AI for gene therapies

The Genopole company WhiteLab Genomics, a specialist in artificial intelligence for gene and cell therapies, has teamed with two of Genopole’s major actors in gene therapy: Genethon and the Genomic Therapy Technology Research Accelerator (ART-TG). Within this partnership supported by the Île-de-France Region, WhiteLab Genomics is providing its Catalyst™ platform, its machine learning algorithms and public and propriety databases to the research teams so that they can optimize their experimental protocols. With that access, Genethon will accelerate the development of AAV vectors with improved specificity to targeted tissues and thus greater efficacy and safety. ART-TG will be able to improve the quality and yield of lentiviral vector biomanufacturing. The expected time savings and efficacy gains will contribute to lowering treatment costs.

Virtual reality to train future surgeons

The French National Research Agency retained the Show-Me virtual reality surgical training program forwarded by the Genopole lab IBISC. The program aims within the next four years to provide teaching surgeons with a virtual patient via which they will be able to transmit their knowledge. Show-Me will build upon improved knowledge on learning processes and virtual reality technologies associating images, gestures and the spoken word. The project saw the day thanks to researcher-physician interactions impulsed by Genopole.

A dataset to train artificial intelligence

The AROB@S team at IBISC (Computer Science, Bio-informatics and Complex Systems) has brought together an initial, standardized, non-coding RNA dataset that can be used to train machine learning models. This powerful artificial intelligence method will accelerate discoveries in the small RNA sequences involved in gene expression normally and major pathologies such as cancer abnormally. Automatically updated from public sources, the dataset is available to the scientific community via the EvryRNA platform’s website.

Multilayer digitizes organs

Created with the support of a Genopole Atige grant, the Sysfate team at the Genomics Metabolics mixed research unit has developed an algorithm, called MULTILAYER, that furnishes images of activities in biological tissues. Their technology takes inspiration from imaging analysis, replacing pixels by expression data from thousands of genes, point by point, in tissue slices. With its ability to reveal various functional zones in tissues and organs, MULTILAYER may contribute to a better understanding of diseases and their molecular diagnosis.