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Section: New Software and Platforms
Vidjil
High-Throughput Analysis of V(D)J Immune Repertoire
Keywords: Cancer - Indexation - NGS - Bioinformatics - Drug development
Scientific Description: Vidjil is made of three components: an algorithm, a visualization browser and a server that allow an analysis of lymphocyte populations containing V(D)J recombinations.
Vidjil high-throughput algorithm extracts V(D)J junctions and gathers them into clones. This analysis is based on a spaced seed heuristics and is fast and scalable, as, in the first phase, no alignment is performed with database germline sequences. Each sequence is put in a cluster depending on its V(D)J junction. Then a representative sequence of each cluster is computed in time linear in the size of the cluster. Finally, we perform a full alignment using dynamic programming of that representative sequence against the germline sequences.
Vidjil also contains a dynamic browser (with D3JS) for visualization and analysis of clones and their tracking along the time in a MRD setup or in an immunological study.
Functional Description: Vidjil is an open-source platform for the analysis of high-throughput sequencing data from lymphocytes. V(D)J recombinations in lymphocytes are essential for immunological diversity. They are also useful markers of pathologies, and in leukemia, are used to quantify the minimal residual disease during patient follow-up. High-throughput sequencing (NGS/HTS) now enables the deep sequencing of a lymphoid population with dedicated Rep-Seq methods and software.
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Participants: Florian Thonier, Marc Duez, Mathieu Giraud, Mikaël Salson, Ryan Herbert and Tatiana Rocher
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Publications: High-Throughput Immunogenetics for Clinical and Research Applications in Immunohematology: Potential and Challenges. - High-throughput sequencing in acute lymphoblastic leukemia: Follow-up of minimal residual disease and emergence of new clones - Diagnostic et suivi des leucémies aiguës lymphoblastiques (LAL) par séquençage haut-débit (HTS) - Multiclonal Diagnosis and MRD Follow-up in ALL with HTS Coupled with a Bioinformatic Analysis - A dataset of sequences with manually curated V(D)J designations - Vidjil: A Web Platform for Analysis of High-Throughput Repertoire Sequencing - Multi-loci diagnosis of acute lymphoblastic leukaemia with high-throughput sequencing and bioinformatics analysis - Fast multiclonal clusterization of V(D)J recombinations from high-throughput sequencing - The predictive strength of next-generation sequencing MRD detection for relapse compared with current methods in childhood ALL.