Orateur : Daniel Gautheret, Institute for Integrative Biology of the Cell, CNRS, CEA, Université Paris-Sud, Orsay
Lieu : Centre de Génomique Fonctionnelle (salle des conférences, 1ème étage)
Titre: "RNA discovery in tumor samples through k-mer analysis"
Abstract: I will present the use of k-mer tools for reference-free analysis of RNA-seq samples. Applying this approach to cancer datasets, we identify a wide variety of mRNA isoforms, retrotransposons and even bacterial RNAs that are related to patient status or clinical outcome. We show that some of these non-canonical RNAs are candidates for neoantigen production. We also show that ribodepleted total RNA sequencing reveals unexpected layers of pervasive and repeat-associated RNAs that are relevant to patient response to immune checkpoint therapy.