Technologies NGS (Ion Torrent PGM)Expertise d'un pipeline d'annotation automatisé de variations génétiquesCréation automatisée de rapports PDFPython - Perl - PHP

La société Genexpath, basée à Rouen, développe et produit des kits de diagnostic des cancers.Basés sur des technologies innovantes et brevetées, ces produits permettent d’établir des diagnostics fiables et rapides, sans achat de matériel supplémentaire.Genexpath est née de la volonté de mettre à disposition du plus grand nombre les travaux de recherche ayant montré leur efficacité dans la caractérisation de plusieurs cancers dont les sarcomes et les lymphomes. La prise en charge du patient en est ainsi améliorée.

Développement du logiciel EVA V3.0 "Exome Variation Analyzer""Whole exome sequencing (WES) has become the strategy of choice to identify a coding allelic variant for a rare human monogenic disorder. This approach is a revolution in medical genetics history, impacting both fundamental research, and diagnostic methods leading to personalized medicine. A plethora of efficient algorithms has been developed to ensure the variant discovery. They generally lead to ~20,000 variations that have to be narrow down to find the potential pathogenic allelic variant(s) and the affected gene(s). For this purpose, commonly adopted procedures which implicate various filtering strategies have emerged: exclusion of common variations, type of the allelics variants, pathogenicity effect prediction, modes of inheritance and multiple individuals for exome comparison. To deal with the expansion of WES in medical genomics individual laboratories, new convivial and versatile software tools have to implement these filtering steps. Non-programmer biologists have to be autonomous combining themselves different filtering criteria and conduct a personal strategy depending on their assumptions and study design."EVA: Exome Variation Analyzer, an efficient and versatile tool for filtering strategies in medical genomics - Sophie Coutant,1,2,3 Chloé Cabot,2,3 Arnaud Lefebvre,2,3 Martine Léonard,2,3 Elise Prieur-Gaston,2,3 Dominique Campion,1,3 Thierry Lecroq,2,3 and Hélène Dauchel

Développement du logiciel FunEVA "Functionnal Effect Variation Analyzer""The current bottleneck in genetic studies is no more acquiring sequences but the challenging complete NGS data management workflow, including efficient bioinformatics algorithms, reliable analytic pipelines and effective tools to help the final biological interpretation. FunEVA is a user-friendly application designed for the functional interpretation in batch of the coding human genetic variations and their prioritization. The quick aggregation of multiple analyses of the potential functional impact of variations on corresponding proteins should help the biologist to distinguish causal mutations among many variations identified by whole or targeted exome sequencing. "