ArticleAnimal bioscience2026
NGSMHC: a simple bioinformatics tool for comprehensively typing major histocompatibility complex genes in non-human species using next-generation sequencing data.
Article in Animal bioscience, 2026. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Not yet cited in PubMed.
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Abstract
objectiveUnderstanding the individual- and population-level polymorphisms of major histocompatibility complex (MHC) genes is crucial for identifying associations between MHC variations and immune phenotypes. To support this, we developed NGSMHC, a streamlined bioinformatics tool for efficient and accurate MHC genotyping using nextgeneration sequencing (NGS) data in non-human species.
methodsNGSMHC constructs phased haplotype contigs of selected MHC genes from BAM-format mapping data and determines the best matching MHC alleles and genotypes via nucleotide BLAST analysis against a user-provided reference set of MHC alleles. We evaluated NGSMHC using short-read whole-genome sequencing (WGS) data from 12 pigs, focusing on swine leukocyte antigen (SLA) genes. The typing results from NGSMHC were compared to those obtained using polymerase chain reaction sequence-based typing (PCR-SBT). In addition, we tested NGSMHC on a publicly available long-read WGS dataset with known SLA genotypes.
resultsThe short-read WGS data showed an average read depth of 20.9× across the SLA region, enabling typing of SLA-2, SLA-3, SLA-DRB1, and SLA-DQB1 using NGSMHC. The concordance rates between NGSMHC and PCR-SBT were 88% for SLA-3, 92% for SLA-DRB1, and 100% for SLA-DQB1. However, SLA-2 typing showed lower concordance (58%), likely due to its high sequence similarity with other SLA class I genes and complex intra-locus polymorphisms. In contrast, NGSMHC accurately identified all tested SLA genotypes-including SLA-1, SLA-2, SLA-3, SLA-DRA, SLA-DRB1, SLA-DQA, and SLADQB1-when applied to the long-read WGS data.
conclusionNGSMHC is a simple and effective tool for MHC genotyping using NGS data, particularly for non-human species. Its accuracy is significantly improved by longread sequencing, underscoring the importance of read length in precise MHC allele determination.
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