Automated analysis of immunosequencing datasets reveals novel immunoglobulin D genes across diverse species

Abstract

Immunoglobulin genes are formed through V(D)J recombination, which joins the variable (V), diversity (D), and joining (J) germline genes. Since variations in germline genes have been linked to various diseases, personalized immunogenomics focuses on finding alleles of germline genes across various patients. Although reconstruction of V and J genes is a well-studied problem, the more challenging task of reconstructing D genes remained open until the IgScout algorithm was developed in 2019. In this work, we address limitations of IgScout by developing a probabilistic MINING-D algorithm for D gene reconstruction, apply it to hundreds of immunosequencing datasets from multiple species, and validate the newly inferred D genes by analyzing diverse whole genome sequencing datasets and haplotyping heterozygous V genes.

Population matched (pm) germline allelic variants of immunoglobulin (IG) loci: Relevance in infectious diseases and vaccination studies in human populations

“…Also, a very small false-negative rate of 5% for the known alleles and 0% for the novel alleles was observed. We also found that the novel pmIG IGHD3-10 and IGHD3-16 alleles were profiled in a recent study [ 58 ]. Apart from profiling the alleles for genes, we could further identify conserved heptamer sequences adjacent to the genes and also pseudogenes.…”

Diversity in immunogenomics: the value and the challenge

“…Efforts to improve germline databases are therefore critical for improved coverage of diversity in immune repertoire analysis. Computational methods to infer germline TCR and immunoglobulin genes from AIRR-seq data are expected to accelerate these efforts [19][20][21][22][23][24] (Table 1). Comparisons are also needed between results obtained from methods for inferring germline gene variants from AIRR-seq repertoires 25 and from direct sequencing of genomic DNA 15 , such as the sequencing and assembly of large-insert clones (for example, bacterial artificial chromosome (BAC) and fosmid clones) 16 and, more recently, whole-genome sequencing and targeted long-read sequencing 26 .…”

Immunoglobulin germline gene variation and its impact on human disease

“…Due to the large complexity of the Ig loci, the options to study these genomic regions have been somehow limited. High-throughput Ig repertoire studies have been central in characterising germline variants of Ig V genes (and recently also IGHD [ 131 ] and TCRβ [ 132 ] genes), however, such studies have their limitations. Since repertoire studies utilise mRNA (transcribed to cDNA) and not genomic DNA, they only provide information about the coding parts of the Ig loci.…”