Frugal alignment-free identification of FLT3-internal tandem duplications with FiLT3r - Université de Lille Accéder directement au contenu
Article Dans Une Revue BMC Bioinformatics Année : 2022

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

Augustin Boudry
  • Fonction : Auteur
Sasha Darmon
  • Fonction : Auteur
Nicolas Duployez
  • Fonction : Auteur
Sandrine Geffroy
  • Fonction : Auteur
Maxime Bucci
  • Fonction : Auteur
Karine Celli-Lebras
  • Fonction : Auteur
Matthieu Duchmann
  • Fonction : Auteur
Romane Joudinaud
  • Fonction : Auteur
Laurène Fenwarth
  • Fonction : Auteur
Olivier Nibourel
  • Fonction : Auteur
Laure Goursaud
  • Fonction : Auteur
Raphael Itzykson
  • Fonction : Auteur
Hervé Dombret
  • Fonction : Auteur
Mathilde Hunault
  • Fonction : Auteur
Claude Preudhomme
  • Fonction : Auteur
Mikaël Salson
  • Fonction : Auteur

Résumé

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.

Dates et versions

hal-04435109 , version 1 (02-02-2024)

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Citer

Augustin Boudry, Sasha Darmon, Nicolas Duployez, Martin Figeac, Sandrine Geffroy, et al.. Frugal alignment-free identification of FLT3-internal tandem duplications with FiLT3r. BMC Bioinformatics, 2022, 23 (1), pp.448. ⟨10.1186/s12859-022-04983-6⟩. ⟨hal-04435109⟩
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