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.
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https://hal.archives-ouvertes.fr/hal-01009173
Contributeur : Mathieu Giraud <>
Soumis le : vendredi 20 juin 2014 - 07:31:26
Dernière modification le : vendredi 8 janvier 2016 - 01:06:54
Document(s) archivé(s) le : samedi 20 septembre 2014 - 10:41:51

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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>

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