ViCloD

ViCloD analyzes Adaptive Immune Receptor Repertoire (AIRR-seq) B cell receptor (BCR) data to visualize clonal lineages and quantify intraclonal diversity for studies of somatic hypermutation and affinity maturation.

Key Features:

• Clonal grouping: Groups AIRR-seq BCR sequences into clonal lineages.
• Intraclonal diversity visualization: Provides visual representations of clonal lineages to inspect intraclonal diversity.
• Evolutionary tree reconstruction: Reconstructs evolutionary trees of clonal lineages to infer antigen-driven antibody evolution.
• Somatic hypermutation analysis: Examines somatic hypermutations in immunoglobulin (IG) genes to study affinity maturation.
• High-throughput processing: Processes large AIRR-seq datasets, scaling to hundreds of thousands of sequences.

Scientific Applications:

• Antibody maturation studies: Facilitates analysis of somatic hypermutation and affinity maturation in B cell repertoires.
• Broadly neutralizing antibody discovery: Aids elucidation of the generation of high-affinity or broadly neutralizing antibodies.
• Vaccine response analysis: Enables study of B cell clonal dynamics following vaccination.
• Pathogen exposure and humoral immunity: Assesses effects of pathogen exposure on humoral immune repertoires.
• B cell malignancy clonal architecture: Characterizes the clonal architecture of B cell tumors.

Methodology:

Performs clonal grouping, reconstructs evolutionary trees, and analyzes somatic hypermutations in immunoglobulin (IG) genes on AIRR-seq BCR datasets and is optimized for processing hundreds of thousands of sequences.