Service interruption on Monday 11 July from 12:30 to 13:00: all the sites of the CCSD (HAL, EpiSciences, SciencesConf, AureHAL) will be inaccessible (network hardware connection).
Skip to Main content Skip to Navigation
Journal articles

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 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.
Complete list of metadata
Contributor : Mathieu Giraud Connect in order to contact the contributor
Submitted on : Friday, June 20, 2014 - 7:31:26 AM
Last modification on : Thursday, May 5, 2022 - 8:36:04 AM
Long-term archiving on: : Saturday, September 20, 2014 - 10:41:51 AM



Mathieu Giraud, Mikaël Salson, Marc Duez, Céline Villenet, Sabine Quief, et al.. Fast multiclonal clusterization of V(D)J recombinations from high-throughput sequencing. BMC Genomics, BioMed Central, 2014, 15 (1), pp.409. ⟨10.1186/1471-2164-15-409⟩. ⟨hal-01009173⟩



Record views


Files downloads