Genome Biology: ImmuSeeker: deep mining of immune-related gene family signatures through lineage reconstruction
First tool to extract immune gene family signatures - including HLA and KIR activity, diversity, and binding - from standard sequencing data, validated in MS and neuromyelitis optica cohorts across eight institutions.
Abstract
HLA typing from sequencing data is crucial for studying immune gene families, but high allele similarity challenges existing tools. We present ImmuSeeker, comprehensive software for extracting HLA genotypes, expression, and diversity at gene, one-field, and two-field allele levels, with improved Bayesian zygosity inference and graphical phylogenetic visualization. ImmuSeeker was benchmarked against nine established tools using gold-standard HLA datasets, repeated RNA sequencing (RNA-seq) and Isoform Sequencing (Iso-Seq) data, and a longitudinal patient cohort, demonstrating superior accuracy, consistency, and analytical utility. ImmuSeeker provides a scalable, robust framework for comprehensive HLA typing and immune system analyses.
Read the full article at: https://link.springer.com/article/10.1186/s13059-026-04039-5#Fun
