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Updated: Feb 18, 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
HashClone: a new tool to quantify the minimal residual disease in B-cell lymphoma from deep sequencing data
Marco Beccuti1, Elisa Genuardi2, Greta Romano1
1Department of Computer Science, University of Torino, Via Pesinetto 12, Turin, 10149, Italy.
Insights
HashClone is a new bioinformatics tool for analyzing next-generation sequencing data to detect B-cell clones and monitor minimal residual disease (MRD) in Mantle Cell Lymphoma patients. It offers improved accuracy and ease of use compared to existing methods.
Area of Science:
- Oncology
- Bioinformatics
- Immunology
Background:
- Mantle Cell Lymphoma (MCL) is an aggressive B-cell neoplasm.
- ImmunoGlobulin Heavy chain (IGH) rearrangement is a key marker for B-cell clonality and Minimal Residual Disease (MRD) monitoring.
- Current MRD monitoring relies on Polymerase Chain Reaction (PCR), but deep sequencing offers potential advantages in sensitivity and feasibility.
Purpose of the Study:
- To introduce HashClone, a novel bioinformatics tool for B-cell clonality assessment and MRD monitoring using Next-Generation Sequencing (NGS) data.
- To provide a user-friendly solution for analyzing IGH rearrangements in MCL patients.
- To evaluate HashClone's performance in detecting B-cell clones and monitoring MRD.
Main Methods:
- HashClone employs a three-step strategy involving alignment-free prediction and alignment-based identification of IGH rearrangements.
- It utilizes data from Next-Generation Sequencing (NGS).
- A graphical user interface (GUI) facilitates tool execution and visualization of clonality over time.
Main Results:
- HashClone successfully identified major B-cell clones in diagnostic samples from MCL patients.
- The tool accurately monitored MRD in both real and artificial follow-up samples.
- Performance was evaluated on NGS data from MCL patients.
Conclusions:
- HashClone accurately detects major B-cell clones and precisely monitors them over time.
- The tool demonstrates superior accuracy compared to state-of-the-art methods in experimental settings.
- HashClone offers a reliable and user-friendly solution for IGH-based MRD monitoring in MCL.
Background:
Mantle Cell Lymphoma (MCL) is a B cell aggressive neoplasia accounting for about the 6% of all lymphomas. The most common molecular marker of clonality in MCL, as in other B lymphoproliferative disorders, is the ImmunoGlobulin Heavy chain (IGH) rearrangement, occurring in B-lymphocytes. The patient-specific IGH rearrangement is extensively used to monitor the Minimal Residual Disease (MRD) after treatment through the standardized Allele-Specific Oligonucleotides Quantitative Polymerase Chain Reaction based technique. Recently, several studies have suggested that the IGH monitoring through deep sequencing techniques can produce not only comparable results to Polymerase Chain Reaction-based methods, but also might overcome the classical technique in terms of feasibility and sensitivity. However, no standard bioinformatics tool is available at the moment for data analysis in this context.
Results:
In this paper we present HashClone, an easy-to-use and reliable bioinformatics tool that provides B-cells clonality assessment and MRD monitoring over time analyzing data from Next-Generation Sequencing (NGS) technique. The HashClone strategy-based is composed of three steps: the first and second steps implement an alignment-free prediction method that identifies a set of putative clones belonging to the repertoire of the patient under study. In the third step the IGH variable region, diversity region, and joining region identification is obtained by the alignment of rearrangements with respect to the international ImMunoGenetics information system database. Moreover, a provided graphical user interface for HashClone execution and clonality visualization over time facilitate the tool use and the results interpretation. The HashClone performance was tested on the NGS data derived from MCL patients to assess the major B-cell clone in the diagnostic samples and to monitor the MRD in the real and artificial follow up samples.
Conclusions:
Our experiments show that in all the experimental settings, HashClone was able to correctly detect the major B-cell clones and to precisely follow them in several samples showing better accuracy than the state-of-art tool.
