Genomics analysis tools for university hospitals

Changed on 31/03/2020
Academic research has led to the development of many first-rate software applications for genome data processing. Enancio, a new start-up established out of the Inria Rennes – Bretagne Atlantique research centre, is preparing to roll out a platform to facilitate the use and joint development of these applications. The service was created for hospital researchers and practitioners, particularly to help diagnose cancer.
jennifer del giudice
Jean-Michel Prima pour Inria
Jean-Michel Prima for Inria
Jean-Michel Prima for Inria

So is it as simple as a blood test? Not exactly, but almost. Genome sequencing is becoming more accessible as it becomes cheaper and more accurate, with new-generation sequencers giving hospitals the ability to decipher each patient’s 22,000 genes. The study of genetic alterations is advancing clinical diagnosis and contributing to medical research.

Today, the challenge is not just collecting but also using mass data. Analysis requires the development of a myriad of specialised tools to draw out knowledge. Many of theses tools are software components that are built into larger processing chains – workflows. Various players can be involved in their creation, based on a transparent joint development model.
Joint development, transparency and user-friendliness are the cornerstones of Enancio , which was founded by five researchers and engineers seeking to optimise the research of GenScale , an IT research team, whose work focuses on processing large-scale genomic data, and the GenOuest platform , which overseas the CPER CeSGO project for the development of an e-science centre in western France.

Pooling tools developed in university hospitals

“Enancio offers a software platform that optimises and pools the tools developed in different university hospitals, and makes them easier to use, ” says Jennifer Del Giudice , CEO of the start-up. “The corporate vision is consistent with national objectives to create a genomic sector in France, as set out in the government strategy France Médecine Génomique 2025 for large-scale sequencing. ”

In practice, Enancio’s services are geared towards hospital practitioners. The goal is to help them decide on the best treatments to use. “The platform hosts all workflows jointly developed with university hospitals. Doctors are provided with a search engine to access the workflow that matches the pathology to be treated. They launch the workflow by inputting raw sequencing data and then obtain the list of biomarkers to help them with their diagnosis. ”

Applications have improved in recent years through the work of the Genscale team. “Enancio optimises these search results, which reduce IT resource needs. This is key because the volume of data to be processed will continue to increase over time. Today, analysis is mainly conducted on a sample of around thirty genes, but in the future, it will be on several thousand genes. ” Enancio is working to prepare for this transition.

Making components more modular and interoperable

The company is currently establishing contacts with university hospitals. “We hope to gradually create synergies around the diversity of analytical components. Workflows currently function as silos. It is difficult to replace one part with another. Our aim is to make these components more modular and interoperable. This would improve the overall performance of the tools available to practitioners. ”

In the long run, the software platform will be used to “analyse the entire human genome using tools designed by experts in the field, while protecting the sovereignty of patient data. ”