VDJSeq-Solver

VDJSeq-Solver identifies clonal lymphocyte populations and characterizes predominant V(D)J rearrangements from paired-end RNA sequencing reads to enable clonal analysis in neoplastic tissues.

Key Features:

• Clonal Detection: Identifies the predominant clonal population in neoplastic samples by detecting the most abundant V(D)J rearrangement.
• Sequence Identification: Reconstructs the exact nucleotide sequence of the predominant clone and accounts for enzymatic modifications introduced during RNA sequencing.
• High-Throughput Compatibility: Processes high-throughput paired-end RNA-seq data rather than analyzing single sequences individually.
• Application and Validation: Validated on Mantle Cell Lymphoma (five cases) and on twelve Diffuse Large B-Cell Lymphoma samples, accurately detecting and characterizing the main clone in those datasets.

Scientific Applications:

• Lymphoma Clonality Analysis: Assessment of clonal lymphocyte populations in lymphomas such as Mantle Cell Lymphoma and Diffuse Large B-Cell Lymphoma.
• Tumor Heterogeneity and Evolution: Characterization of clonal architecture to study tumor heterogeneity and clonal evolution.
• Diagnostic Clonality Assessment: Support for diagnostic clonality assessment by providing exact V(D)J sequences of predominant clones.
• Therapeutic Development: Inform targeted therapy development by identifying dominant clone sequences.

Methodology:

Processes paired-end RNA sequencing reads to detect and extract predominant V(D)J recombination sequences, accounting for enzymatic modifications introduced during RNA-seq.