HashClone

HashClone assesses B-cell clonality and monitors Minimal Residual Disease (MRD) using Next-Generation Sequencing (NGS) data for applications in Mantle Cell Lymphoma (MCL) research and clinical monitoring.

Key Features:

• Clonality Assessment: Analyzes IGH rearrangements to identify major B-cell clones as molecular markers of clonality in MCL and other B lymphoproliferative disorders.
• MRD Monitoring: Monitors MRD over time using deep sequencing (NGS) data as an alternative to Allele-Specific Oligonucleotides Quantitative Polymerase Chain Reaction (ASO-qPCR) for enhanced sensitivity and feasibility.
• Alignment-Free Prediction Method: Employs an alignment-free prediction method in the initial steps to identify putative clones within a patient’s B-cell repertoire.
• IGH Region Identification: Aligns identified rearrangements with the IMGT database to determine IGH variable regions, diversity regions, and joining regions.
• Performance Validation: Validated on NGS data from MCL patients, detecting major diagnostic B-cell clones and monitoring MRD in real and artificial follow-up samples, with reported superior accuracy versus existing methods.

Scientific Applications:

• MCL Research and Treatment Monitoring: Enables identification of the major B-cell clone at diagnosis and longitudinal MRD tracking during follow-up in Mantle Cell Lymphoma studies.
• Benchmarking and Method Comparison: Serves for comparative evaluation against state-of-the-art methods for detecting and tracking B-cell clones across samples.

Methodology:

Three computational steps: (1) alignment-free prediction to identify putative clones from NGS-derived B-cell repertoires, (2) a further alignment-free clonal analysis to refine and confirm putative clones, and (3) alignment of identified rearrangements to the IMGT database to identify IGH variable, diversity, and joining regions.