title: Fast multiclonal clusterization of V(D)J recombinations from high-throughput sequencing.
abstract: BACKGROUND
  V(D)J recombinations in lymphocytes are essential for immunological diversity. They are also useful markers of pathologies. In leukemia, they are used to quantify the minimal residual disease during patient 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 unnamed V(D)J junctions and gather them into clones for quantification. This analysis is based on a seed heuristic and is fast and scalable because in the first phase, no alignment is performed with germline database sequences. The algorithms were applied to TR γ HTS data from a patient with acute lymphoblastic leukemia, and also on data simulating hypermutations. Our methods identified the main 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-throughput sequencing data for leukemia, and also to the quantitative assessment of any immunological profile. The methods described here are implemented in a C++ open-source program called Vidjil.
authors.affiliation: Laboratoire d'Informatique Fondamentale de Lille (LIFL, UMR CNRS 8022, Université Lille 1) and Inria Lille - Cité scientifique - Bâtiment M3, 59655 Villeneuve d'Ascq, France. mathieu.giraud@vidjil.org.
authors.forename: Mathieu
authors.initials: M
authors.lastname: Giraud
authors.forename: Mikaël
authors.initials: M
authors.lastname: Salson
authors.forename: Marc
authors.initials: M
authors.lastname: Duez
authors.forename: Céline
authors.initials: C
authors.lastname: Villenet
authors.forename: Sabine
authors.initials: S
authors.lastname: Quief
authors.forename: Aurélie
authors.initials: A
authors.lastname: Caillault
authors.forename: Nathalie
authors.initials: N
authors.lastname: Grardel
authors.forename: Christophe
authors.initials: C
authors.lastname: Roumier
authors.forename: Claude
authors.initials: C
authors.lastname: Preudhomme
authors.forename: Martin
authors.initials: M
authors.lastname: Figeac
mesh_terms: D000465:Algorithms; D059014:High-Throughput Nucleotide Sequencing / Q000379:methods*; D006801:Humans; D018365:Neoplasm, Residual / Q000175:diagnosis; D054198:Precursor Cell Lymphoblastic Leukemia-Lymphoma / Q000175:diagnosis* / Q000235:genetics; D017422:Sequence Analysis, DNA / Q000379:methods*; D012984:Software; D060152:V(D)J Recombination