GenerateReports: an Ion Torrent plugin summarizing a whole NGS experiment for clinical interpretation

Pierre Julien Viailly (1, 2) , Sylvain Mareschal (1, 2) , Philippe Bertrand (1, 2) , Sydney Dubois (1, 2) , Elodie Bohers (1, 2) , Catherine Maingonnat (1, 2) , Thierry Lecroq (3, 4) , Hélène Dauchel (3, 4) , Herve Tilly (2, 1) , Fabrice Jardin (2, 1)

1 GPL - Groupe d'étude des proliférations lymphoïdes
2 GPMCND - Génomique et Médecine Personnalisée du Cancer et des Maladies Neuropsychiatriques
3 IRIB - Institute for Research and Innovation in Biomedicine
4 TIBS - LITIS - Equipe Traitement de l'information en Biologie Santé

The increasing arrival of Next Generation Sequencing technologies in diagnostic laboratories creates a need to develop tools for rapid data interpretation. For example, targeted cancer sequencing allows biologists to focus on a selected range of known cancer-relevant genes and has become a choice strategy to quickly screen patients' mutational profiles. Although these profiles can aid in developing personalized therapy, their interpretation remains difficult. The aim is now to develop tools to provide a quick understanding of mutation profiles, highlighting the most impactful anomalies. Here, we present an open-source integrated IonTorrent plugin called GenerateReports. This tool aggregates data in a single clinical report, enabling the clear visualization of the main results for each sample sequenced. GenerateReports is based on CoverageAnalysis and VariantCaller Torrent Suite plugins results but goes even further by performing annotation of single nucleotide variants and searching for copy-number variations (CNVs). Thus, the biologist has access to sample identification, run and sample quality metrics, annotated and stratified variants, CNVs detected with statistical relevance and information about experimental and informatics traceability, all in a single PDF report for each sample sequenced. An associated interfaced database allows for further statistical studies. It could help to identify sequencing artifacts by Sanger validation storing and to stratify thousands of anomalies in several runs. We illustrate the results obtained using this plugin through the sequencing of a patient suffering from Diffuse Large B-Cell Lymphoma.

Domaines: Sciences du Vivant [q-bio]

Pierre Julien Viailly, Sylvain Mareschal, Philippe Bertrand, Sydney Dubois, Elodie Bohers, et al.. GenerateReports: an Ion Torrent plugin summarizing a whole NGS experiment for clinical interpretation. JOBIM, Jul 2015, Clermont-Ferrand, France. ⟨hal-02896717⟩