IGHV allele similarity clustering improves genotype inference from adaptive immune receptor repertoire sequencing data

Abstract

In adaptive immune receptor repertoire analysis, determining the germline variable (V) allele associated with each T- and B-cell receptor sequence is a crucial step. This process is highly impacted by allele annotations. Aligning sequences, assigning them to specific germline alleles, and inferring individual genotypes are challenging when the repertoire is highly mutated, or sequence reads do not cover the whole V region. Here, we propose an alternative naming scheme for the V alleles as well as a novel method to infer individual genotypes. We demonstrate the strength of the two by comparing their outcomes to other genotype inference methods and validated the genotype approach with independent genomic long read data. The naming scheme is compatible with current annotation tools and pipelines. Analysis results can be converted from the proposed naming scheme to the nomenclature determined by the International Union of Immunological Societies (IUIS). Both the naming scheme and the genotype procedure are implemented in a freely available R package (PIgLET). To allow researchers to explore further the approach on real data and to adapt it for their future uses, we also created an interactive website (https://yaarilab.github.io/IGHV_reference_book).

Biophysical cartography of the native and human-engineered antibody landscapes quantifies the plasticity of antibody developability

“…To this end, we first examined the pairwise correlation of antibody developability profiles ( d evelopability p rofile c orrelation: DPC) alongside the pairwise sequence similarity score (see Methods) for a random sample of 100 natural antibodies from the human IgM dataset that share the IGHV gene family annotation (Figure 5A). This is to eliminate the role of the V-gene as a factor of variance in our analysis, as up to 80% of sequence similarity can be expected among antibodies that belong to the same IGHV gene family ( 61 , 62 ). Sequence-level DPC clusters were often, but not always, accompanied by sequence similarity clusters, while structure-level DPC clusters were independent in regards to sequence similarity clusters (Figure 5A, Supp.…”

“…Figure 9C (computationally intensive process; 12,500,000 data points for each ED and LD calculation). We ensured that these sampled antibodies belong to the same IGHV gene family to exclude the effect of IGHV family variance on the LD computations ( 61 , 62 ). Antibody pairs with ED ≥ 15 were considered as outliers and were excluded from this analysis (forming 0.8% of total data points).…”

Addressing technical pitfalls in pursuit of molecular factors that mediate immunoglobulin gene regulation

“…Variation in the BCR/antibody (Ab) repertoire has been linked to differential immune responses in a variety of disease contexts including infection, cancer, and autoimmunity [1][2][3][4][5][6]. This has prompted interest to better understand the development of the BCR repertoire and factors that contribute to variation in the circulating Ab repertoire in both healthy and disease states [1,[7][8][9][10][11][12]. BCRs and Abs are composed of two identical heavy and light chains, which are encoded by genes at the immunoglobulin (IG) heavy (IGH) and light chain (kappa, IGK; lambda, IGL) loci.…”

De novo antibody discovery in human blood from full-length single B cell transcriptomics and matching haplotyped-resolved germline assemblies

“…However, individual single-cell transcriptomes have so far not been paired with germline assemblies from the same donor. Haplotyped structural variants and heterogeneity of immunoglobulin V, D, J, and C gene segments may affect the antibody repertoire of a given individual, representing the potential of future precision medicine based on individual variation (Kidd et al 2016; Kenter et al 2021; Peres et al 2023).…”