Immcantation

Immcantation identifies B cell clonal families from next-generation sequencing (NGS)-based adaptive immune receptor repertoire sequencing (AIRR-Seq) data to infer B cell receptor (BCR) relationships and track clonal expansions in adaptive immune responses.

Key Features:

• Clonal Family Identification: Groups BCR sequences that share a common ancestor to identify B cell clonal families despite sequence variation.
• Somatic Hypermutation Analysis: Incorporates somatic hypermutations (SHMs) in V and J segments and the junction region when assessing clonal relationships.
• Distance Functions and Clustering: Uses independent distance functions that capture junction similarity and shared mutations integrated into a spectral clustering framework (SCOPer) to infer clonal partitions.
• Data Compatibility and Validation: Has been validated using both simulated and experimental datasets.

Scientific Applications:

• Tracking Immune Responses: Identifies clonal expansions to monitor B cell responses to infections or vaccinations.
• Autoimmune Disease Research: Analyzes aberrant B cell clonal expansions associated with autoimmune conditions.
• Cancer Immunotherapy Research: Supports investigation of B cell behavior in patients undergoing cancer immunotherapies.

Methodology:

Analyzes BCR sequences from NGS/AIRR-Seq, computes independent distance functions for junction similarity and shared mutations, and integrates these distances into a spectral clustering framework (SCOPer) to infer clonal relationships.