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. © 2014 Giraud et al.; licensee BioMed Central Ltd.
CITATION STYLE
Giraud, M., Salson, M., Duez, M., Villenet, C., Quief, S., Caillault, A., … Figeac, M. (2014). Fast multiclonal clusterization of V(D)J recombinations from high-throughput sequencing. BMC Genomics, 15(1). https://doi.org/10.1186/1471-2164-15-409
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