IgIDivA: immunoglobulin intraclonal diversification analysis

Abstract

Intraclonal diversification (ID) within the immunoglobulin (IG) genes expressed by B cell clones arises due to ongoing somatic hypermutation (SHM) in a context of continuous interactions with antigen(s). Defining the nature and order of appearance of SHMs in the IG genes can assist in improved understanding of the ID process, shedding light into the ontogeny and evolution of B cell clones in health and disease. Such endeavor is empowered thanks to the introduction of high-throughput sequencing in the study of IG gene repertoires. However, few existing tools allow the identification, quantification and characterization of SHMs related to ID, all of which have limitations in their analysis, highlighting the need for developing a purpose-built tool for the comprehensive analysis of the ID process. In this work, we present the immunoglobulin intraclonal diversification analysis (IgIDivA) tool, a novel methodology for the in-depth qualitative and quantitative analysis of the ID process from high-throughput sequencing data. IgIDivA identifies and characterizes SHMs that occur within the variable domain of the rearranged IG genes and studies in detail the connections between identified SHMs, establishing mutational pathways. Moreover, it combines established and new graph-based metrics for the objective determination of ID level, combined with statistical analysis for the comparison of ID level features for different groups of samples. Of importance, IgIDivA also provides detailed visualizations of ID through the generation of purpose-built graph networks. Beyond the method design, IgIDivA has been also implemented as an R Shiny web application. IgIDivA is freely available at https://bio.tools/igidiva

ViCloD, an interactive web tool for visualizing B cell repertoires and analyzing intraclonal diversities: application to human B-cell tumors

“…IgIDivA ( 40 ) differs from the above tools and ViCloD since it assumes that SHMs are acquired sequentially. It first identifies all nucleotide variants (here termed as clonotypes) inside a sub-clone.…”

“…IgIDivA ( 41 ) is a dedicated tool for intraclonal analysis; it first identifies all nucleotide variants (here termed as clonotypes) inside a subclone. Second, it constructs a network/graph centered on the most abundant clonotype rather than a tree from the HAUS.…”

“…Several web servers devoted to analyzing AIRR data have been recently reported, most of them for pre-processing, V(D)J gene annotation, clonal grouping, repertoire diversity, and mutation analysis (26)(27)(28)(29)(30)(31)(32)(33)(34)(35)(36)(37). However, only some tools permit the analysis of intraclonal diversities and the investigation of the mutational architecture of an individual repertoire and its evolution (36,38,40,41). Most existing tools require some computational skills to manage installations and resolve dependencies.…”

“…Such tools quantify the diversity of a BCR repertoire by estimating clonal group sizes, characterizing CDR3 regions, identifying the most used V, D, and J genes (alleles), and the most frequent VJ combinations. However, few tools allow the investigation of intraclonal diversity/evolution of a Bcell repertoire (38)(39)(40)(41)(42). Such analyses can potentially reconstruct antibodies' evolutionary (clonal) development and identify mutable positions that correlate with antigen-binding sites.…”

“…Users' data are stored temporarily, but they can be downloaded in a pre-defined format that allows re-analyzing posteriorly. Additional features will be implemented in the future, such as (i) intra-clonal analysis at the amino acid level, including Physico-chemical properties, (ii) diversity measures, such as the species richness, and the Shannon index, and gene usage plots, (iii) metrics to measure the intra-clonal diversity level (40), (iv) the possibility of visualizing evolutionary events within a give sub-clone, (v) comparisons of several repertoires, which will allow users to analyze repertoires from the same individual at various time points or to compare repertoires of different individuals. ViCloD's flexibility offers the possibility of further extensions, including the estimation of B cell migration and differentiation (41).…”