Human leukocyte antigen super-locus: nexus of genomic supergenes, SNPs, indels, transcripts, and haplotypes

The human Major Histocompatibility Complex (MHC) or Human Leukocyte Antigen (HLA) super-locus is a highly polymorphic genomic region that encodes more than 140 coding genes including the transplantation and immune regulatory molecules. It receives special attention for genetic investigation because of its important role in the regulation of innate and adaptive immune responses and its strong association with numerous infectious and/or autoimmune diseases. In recent years, MHC genotyping and haplotyping using Sanger sequencing and next-generation sequencing (NGS) methods have produced many hundreds of genomic sequences of the HLA super-locus for comparative studies of the genetic architecture and diversity between the same and different haplotypes. In this special issue on ‘The Current Landscape of HLA Genomics and Genetics’, we provide a short review of some of the recent analytical developments used to investigate the SNP polymorphisms, structural variants (indels), transcription and haplotypes of the HLA super-locus. This review highlights the importance of using reference cell-lines, population studies, and NGS methods to improve and update our understanding of the mechanisms, architectural structures and combinations of human MHC genomic alleles (SNPs and indels) that better define and characterise haplotypes and their association with various phenotypes and diseases. Immunity: Crucial cell surface proteins New genetic sequencing and bioinformatic analysis techniques are improving our understanding of the human major histocompatibility complex (MHC), a large and complicated group of genes that encode cell surface proteins crucial to the human immune system. In a review, Jerzy Kulski and co-workers at the Tokai University School of Medicine in Isehara, Japan report that new sequencing technologies have now allowed researchers to map fine-scale and large-scale differences between different subgroups of genes within the MHC that are inherited together, called haplotypes. Study of haplotypes has illuminated the relatedness and evolutionary history of various human ethnic groups. Large-scale bioinformatic studies have revealed associations between MHC genes and disease. These advances will potentially provide better diagnosis or treatment for many diseases, both infectious and autoimmune, and may help improve transplant donor selection.