Fast multiclonal clusterization of V(D)J recombinations from high-throughput sequencing
Related Experiment Video
Updated: Apr 28, 2026

VDJ-Seq: Deep Sequencing Analysis of Rearranged Immunoglobulin Heavy Chain Gene to Reveal Clonal Evolution Patterns of B Cell Lymphoma
Published on: December 28, 2015
Mathieu Giraud1, Mikaël Salson, Marc Duez
1Laboratoire 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.
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.
Related Concept Videos
RNA-seq
Before the discovery of RNA-seq, microarray-based methods and Sanger sequencing were used for transcriptome analysis. However, while...
Next-generation Sequencing
Next-Generation Sequencing Methods
Although all next-generation methods use different technologies, they all share a set of standard features....
Homologous Recombination
Homologous Recombination
Viral Recombination
Sanger Sequencing

