Title :

Frugal alignment-free identification of FLT3-internal tandem duplications with FiLT3r

Author(s) :

Boudry, Augustin [Auteur]
Hétérogénéité, Plasticité et Résistance aux Thérapies des Cancers = Cancer Heterogeneity, Plasticity and Resistance to Therapies - UMR 9020 - U 1277 [CANTHER]
Darmon, Sasha [Auteur]
École normale supérieure de Lyon [ENS de Lyon]
Centre de Recherche en Informatique, Signal et Automatique de Lille - UMR 9189 [CRIStAL]
Duployez, Nicolas [Auteur]
Hétérogénéité, Plasticité et Résistance aux Thérapies des Cancers = Cancer Heterogeneity, Plasticity and Resistance to Therapies - UMR 9020 - U 1277 [CANTHER]
Figeac, Martin [Auteur]
Plateformes Lilloises en Biologie et Santé - UAR 2014 - US 41 [PLBS]
Geffroy, Sandrine [Auteur]
Bucci, Maxime [Auteur]
Celli-Lebras, Karine [Auteur]
Service d'Hémato-oncologie [CHU Saint-Louis]
Joudinaud, Romane [Auteur]
Hétérogénéité, Plasticité et Résistance aux Thérapies des Cancers = Cancer Heterogeneity, Plasticity and Resistance to Therapies - UMR 9020 - U 1277 [CANTHER]
Fenwarth, Laurène [Auteur]
Hétérogénéité, Plasticité et Résistance aux Thérapies des Cancers = Cancer Heterogeneity, Plasticity and Resistance to Therapies - UMR 9020 - U 1277 [CANTHER]
Nibourel, Olivier [Auteur]
Goursaud, Laure [Auteur]
Itzykson, Raphael [Auteur]
Service d'Hémato-oncologie [CHU Saint-Louis]
Génomes, biologie cellulaire et thérapeutiques [GenCellDis (U944 / UMR7212)]
Dombret, Hervé [Auteur]
Service d'Hémato-oncologie [CHU Saint-Louis]
Hunault, Mathilde [Auteur]
Centre de Recherche en Cancérologie et Immunologie Intégrée Nantes-Angers [CRCI2NA ]
Preudhomme, Claude [Auteur]
Hétérogénéité, Plasticité et Résistance aux Thérapies des Cancers = Cancer Heterogeneity, Plasticity and Resistance to Therapies - UMR 9020 - U 1277 [CANTHER]
Salson, Mikael [Auteur]
Centre de Recherche en Informatique, Signal et Automatique de Lille - UMR 9189 [CRIStAL]
Duchmann, Matthieu [Auteur]
Hopital Saint-Louis [AP-HP] [AP-HP]
Génomes, biologie cellulaire et thérapeutiques [GenCellDis (U944 / UMR7212)]

Journal title :

BMC Bioinformatics

Pages :

448

Publisher :

BioMed Central

Publication date :

2022-12

ISSN :

1471-2105

HAL domain(s) :

Informatique [cs]/Bio-informatique [q-bio.QM]
Informatique [cs]/Algorithme et structure de données [cs.DS]

English abstract : [en]

Abstract Background Internal tandem duplications in the FLT3 gene, termed FLT3 -ITDs, are useful molecular markers in acute myeloid leukemia (AML) for patient risk stratification and follow-up. FLT3 -ITDs are increasingly ...
Show more >Abstract Background Internal tandem duplications in the FLT3 gene, termed FLT3 -ITDs, are useful molecular markers in acute myeloid leukemia (AML) for patient risk stratification and follow-up. FLT3 -ITDs are increasingly screened through high-throughput sequencing (HTS) raising the need for robust and efficient algorithms. We developed a new algorithm, which performs no alignment and uses little resources, to identify and quantify FLT3 -ITDs in HTS data. Results Our algorithm (FiLT3r) focuses on the k -mers from reads covering FLT3 exons 14 and 15. We show that those k -mers bring enough information to accurately detect, determine the length and quantify FLT3 -ITD duplications. We compare the performances of FiLT3r to state-of-the-art alternatives and to fragment analysis, the gold standard method, on a cohort of 185 AML patients sequenced with capture-based HTS. On this dataset FiLT3r is more precise (no false positive nor false negative) than the other software evaluated. We also assess the software on public RNA-Seq data, which confirms the previous results and shows that FiLT3r requires little resources compared to other software. Conclusion FiLT3r is a free software available at https://gitlab.univ-lille.fr/filt3r/filt3r . The repository also contains a Snakefile to reproduce our experiments. We show that FiLT3r detects FLT3-ITDs better than other software while using less memory and time.Show less >

Language :

Anglais

Peer reviewed article :

Oui

Audience :

Internationale

Popular science :

Non

Collections :

• Cancer Heterogeneity, Plasticity and Resistance to Therapies (CANTHER) - UMR 9020 - UMR 1277

Source :

Harvested from HAL