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

Mathieu Giraud,Sabine Quief,Céline Villenet,Nathalie Grardel,Martin Figeac,Claude Preudhomme,Mikaël Salson,Christophe Roumier,Aurélie Caillault,Marc Duez

doi:10.1186/1471-2164-15-409

Abstract

BackgroundV(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.ResultsWe 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.ConclusionsThe 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.Electronic supplementary materialThe online version of this article (doi:10.1186/1471-2164-15-409) contains supplementary material, which is available to authorized users.

Highlights

V(D)J recombinations in lymphocytes are essential for immunological diversity
VDJ recombinations occur in B-cell heavy chains (IgH) and T-cell β and δ chains (TRβ and δ), whereas VJ recombinations occur in B-cell light chains κ (Igκ) and λ (Igλ), and T-cell α and γ chains (TRα and γ )
DNA extraction and PCR We sequenced the bone-marrow samples taken from a patient with B-cell acute lymphoblastic leukemia (B-at junctionAcute lymphoblastic leukemia (ALL))

Summary

Introduction

V(D)J recombinations in lymphocytes are essential for immunological diversity In leukemia, they are used to quantify the minimal residual disease during patient follow-up. V(D)J recombinations in lymphocytes are essential for immunological diversity because they influence the production of antibodies and antigen receptors [1,2]. In more than 90% of cases, a recombined Ig or TR junction fingerprint of the blastic cells can be identified at diagnosis. This clonality marker is used during patient follow-up to quantify the minimal residual disease [3,5]

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