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BMC Genomics. 2014 May 28;15:409. doi: 10.1186/1471-2164-15-409.

Fast multiclonal clusterization of V(D)J recombinations from high-throughput sequencing.

Author information

1
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.

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.

PMID:
24885090
PMCID:
PMC4070559
DOI:
10.1186/1471-2164-15-409
[Indexed for MEDLINE]
Free PMC Article

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