TRIT1 deficiency: Two novel patients with four novel variants - Université de Lille Accéder directement au contenu
Article Dans Une Revue European Journal of Medical Genetics Année : 2022

TRIT1 deficiency: Two novel patients with four novel variants

Thomas Smol
Perrine Brunelle
  • Fonction : Auteur
Roseline Caumes
  • Fonction : Auteur
Odile Boute-Benejean
  • Fonction : Auteur
Caroline Thuillier
  • Fonction : Auteur
Emilie Ait-Yahya
  • Fonction : Auteur
Fabrice Bonte
  • Fonction : Auteur
Frederic Tran Mau-Them
  • Fonction : Auteur
Christel Thauvin-Robinet
  • Fonction : Auteur
Laurence Faivre
  • Fonction : Auteur
Catherine Roche-Lestienne
  • Fonction : Auteur
Sylvie Manouvrier-Hanu
  • Fonction : Auteur
Florence Petit
  • Fonction : Auteur
Jamal Ghoumid
  • 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-04435095 , version 1 (02-02-2024)

Identifiants

Citer

Thomas Smol, Perrine Brunelle, Roseline Caumes, Odile Boute-Benejean, Caroline Thuillier, et al.. TRIT1 deficiency: Two novel patients with four novel variants. European Journal of Medical Genetics, 2022, 65 (11), pp.104603. ⟨10.1016/j.ejmg.2022.104603⟩. ⟨hal-04435095⟩
17 Consultations
0 Téléchargements

Altmetric

Partager

Gmail Mastodon Facebook X LinkedIn More