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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.
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https://hal.archives-ouvertes.fr/hal-01009173
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

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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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