HLA/MHC and KIR characterization in humans and non‐human primates using Oxford Nanopore Technologies and Pacific Biosciences sequencing platforms

Abstract

The gene products of the HLA/MHC and KIR multigene families are important modulators of the immune system and are associated with health and disease. Characterization of the genes encoding these receptors has been integrated into different biomedical applications, including transplantation and reproduction biology, immune therapies and in fundamental research into disease susceptibility or resistance. Conventional short‐read sequencing strategies have shown their value in high throughput typing, but are insufficient to uncover the entire complexity of the highly polymorphic HLA/MHC and KIR gene systems. The implementation of single‐molecule and real‐time sequencing platforms, offered by Pacific Biosciences (PacBio) and Oxford Nanopore Technologies (ONT), revolutionized the fields of genomics and transcriptomics. Using fundamentally distinct principles, these platforms generate long‐read data that can unwire the plasticity of the HLA/MHC and KIR genes, including high‐resolution characterization of genes, alleles, phased haplotypes, transcription levels and epigenetics modification patterns. These insights might have profound clinical relevance, such as improved matching of donors and patients in clinical transplantation, but could also lift disease association studies to a higher level. Even more, a comprehensive characterization may refine animal models in preclinical studies. In this review, the different HLA/MHC and KIR characterization approaches using PacBio and ONT platforms are described and discussed.

The effect of immune cell traits on efficacy and adverse drug reactions of platinum drugs： A Mendelian randomization analysis

“…Human Leukocyte Antigen (HLA), also known as major histocompatibility complex (MHC), is a protein molecule that exists on the surface of antigen presenting cells and is responsible for antigen presentation (Bruijnesteijn et al 2023). It mainly includes three categories: HLA-I, HLA-II and HLA-III.…”

Advancements in HLA Typing Techniques and Their Impact on Transplantation Medicine

“…Regarding accuracy, PacBio exhibits a raw error rate of 13–15%, exceeded by Illumina. Leveraging circular consensus sequencing and error correction methods enhances PacBio accuracy up to 99.999% [ 88 , 89 ]. ONT sequencing shows varying raw error rates (10–15% for MinION, 5–10% for PromethION) [ 81 , 90 , 91 ].…”

“…Despite higher error rates, PacBio and ONT’s long-read capabilities offer effective solutions for complex alleles [ 81 , 92 ]. Incorporating error correction and bioinformatics pipelines mitigates sequencing errors’ impact on HLA typing precision [ 89 ]. Processing ONT sequencing data involves various computational tools like Guppy, Metrichor, Nanonet, Albacore, Scrappie, Flappie, Taiyaki, and Bonito for base calling.…”

“…The evolving focus on Killer Cell Immunoglobulin-like Receptor (KIR) genes in transplantation biology highlights their crucial role in immune surveillance. The extensive polymorphism of KIR genes and their interactions with HLA molecules drive investigations into the impact of KIR gene matching on transplantation outcomes, emphasizing their significance in this field [ 89 , 107 ]. High-resolution characterization of HLA/MHC and KIR genes is vital in transplantation biology.…”

“…High-resolution characterization of HLA/MHC and KIR genes is vital in transplantation biology. It ensures accurate donor-recipient matching, lowers the risk of immune-related complications, and improves long-term outcomes for transplant recipients [ 89 ]. Several studies have underscored the influence of KIR gene matching between donors and recipients on the success of hematopoietic cell transplantation.…”