Titre :

Fast multiclonal clusterization of V(D)J recombinations from high-throughput sequencing

Auteur(s) :

Giraud, Mathieu [Auteur correspondant]
Bioinformatics and Sequence Analysis [BONSAI]
Laboratoire d'Informatique Fondamentale de Lille [LIFL]
Salson, Mikael [Auteur correspondant]
Bioinformatics and Sequence Analysis [BONSAI]
Laboratoire d'Informatique Fondamentale de Lille [LIFL]
Duez, Marc [Auteur]
Bioinformatics and Sequence Analysis [BONSAI]
Laboratoire d'Informatique Fondamentale de Lille [LIFL]
Site de Recherche Intégrée en Cancérologie [SIRIC-ONCOLille]
Villenet, Céline [Auteur]
Plateforme de génomique fonctionnelle et structurelle [Lille]
Quief, Sabine [Auteur]
Institut pour la recherche sur le cancer de Lille [Lille] [IRCL]
Plateforme de génomique fonctionnelle et structurelle [Lille]
Caillault, Aurélie [Auteur]
Service d'Hématologie Cellulaire [Lille]
Grardel, Nathalie [Auteur]
Service d'Hématologie Cellulaire [Lille]
Roumier, Christophe [Auteur]
Institut de recherche sur le cancer
Service d'Hématologie Cellulaire [Lille]
Preudhomme, Claude [Auteur]
Institut de recherche sur le cancer
Service d'Hématologie Cellulaire [Lille]
Figeac, Martin [Auteur]
Plateforme de génomique fonctionnelle et structurelle [Lille]

Titre de la revue :

Bmc Genomics

Pagination :

409

Éditeur :

BioMed Central

Date de publication :

2014

ISSN :

1471-2164

Mot(s)-clé(s) en anglais :

Sequence analysis
High-throughput sequencing
V(D)J recombinations
Repertoire sequencing (Rep-Seq)
Immunology
Leukemia
Minimal residual disease follow-up

Discipline(s) HAL :

Informatique [cs]/Bio-informatique [q-bio.QM]
Sciences du Vivant [q-bio]/Bio-Informatique, Biologie Systémique [q-bio.QM]
Sciences du Vivant [q-bio]/Génétique
Sciences du Vivant [q-bio]/Immunologie
Informatique [cs]/Bibliothèque électronique [cs.DL]

Résumé en anglais : [en]

BACKGROUND: V(D)J recombinations in lymphocytes are essential for immunological diversity. They are also usefulmarkers of pathologies. In leukemia, they are used to quantify the minimal residual disease duringpatient ...
Lire la suite >BACKGROUND: V(D)J recombinations in lymphocytes are essential for immunological diversity. They are also usefulmarkers of pathologies. In leukemia, they are used to quantify the minimal residual disease duringpatient follow-up. However, the full breadth of lymphocyte diversity is not fully understood. RESULTS: We propose new algorithms that process high-throughput sequencing (HTS) data to extract unnamedV(D)J junctions and gather them into clones for quantification. This analysis is based on a seedheuristic and is fast and scalable because in the first phase, no alignment is performed with germlinedatabase sequences. The algorithms were applied to TR HTS data from a patient with acutelymphoblastic leukemia, and also on data simulating hypermutations. Our methods identified themain clone, as well as additional clones that were not identified with standard protocols. CONCLUSIONS: The proposed algorithms provide new insight into the analysis of high-troughput sequencing data forleukemia, and also to the quantitative assessment of any immunological profile. The methodsdescribed here are implemented in a C++ open-source program called Vidjil.Lire moins >

Langue :

Anglais

Comité de lecture :

Oui

Audience :

Internationale

Vulgarisation :

Non

Collections :

• Centre de Recherche en Informatique, Signal et Automatique de Lille (CRIStAL) - UMR 9189

Source :

Harvested from HAL