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Nomenclature for Factors of the Swine Leukocyte Antigen (SLA) System
Chak-Sum Ho1, Joan K. Lunney2, Asako Ando3, Claire Rogel-Gaillard4, Jun-Heon Lee5, Lawrence B. Schook6, Sabine E. Hammer7.
1Histocompatibility Laboratory, Gift of Life Michigan, Ann Arbor, MI, United States; 2Animal Parasitic Diseases Laboratory, BARC, ARS, USDA, Beltsville, MD, United States; 3Department of Molecular Life Science, Division of Basic Medical Science and Molecular Medicine, Tokai University School of Medicine, Isehara, Japan; 4GABI, INRA, AgroParisTech, Université Paris-Saclay, Jouy-en-Josas, France; 5Division of Animal and Dairy Science, College of Agriculture and Life Sciences, Chungnam National University, Daejeon, Korea; 6Institute for Genomic Biology, University of Illinois, Urbana, IL, United States; 7Institute of Immunology, Department of Pathobiology, University of Veterinary Medicine Vienna, Vienna, Austria
Introduction: The Swine Leukocyte Antigen (SLA) system is among the most well characterized major histocompatibility complex (MHC) systems in non-human animal species.
Methods: The SLA Nomenclature Committee, which is affiliated with the International Society for Animal Genetics (ISAG) and the Veterinary Immunology Committee of the International Union of Immunological Societies (IUIS-VIC), was established 15 years ago with the primary objectives: 1) to validate newly identified SLA sequences according to the guidelines established for maintaining high quality standards of the accepted sequences; 2) to assign appropriate nomenclatures for new alleles as they are validated; and 3) to serve as a curator of the Immuno Polymorphism Database (IPD)-MHC SLA Sequence Database (www.ebi.ac.uk/ipd/mhc/group/SLA), which is the repository for all recognized SLA genes, their allelic sequences and haplotypes. The committee currently consists of 7 members from 5 countries with various areas of expertise related to swine histocompatibility and immunogenetics.
Results: Allele designation of the SLA Nomenclature System primarily adopted that of the HLA Nomenclature System with up to 4 sets of digits separated by colons (e.g. SLA-1*04:01:01:01). As serological specificity of SLA antigens and alleles is largely unknown due to the lack of serologic typing reagents, phylogenetic analysis is the primary approach for assigning alleles of the classical class I (SLA-1, -2, -3) and class II (DRA, DRB1, DQA, DQB1) loci into allele groups (the first field, e.g. SLA-1*04) based on sequence similarity in the exon(s) encoding the peptide binding domain(s). Alleles of the non-classical class I loci (SLA-6, -7, -8, -12) and the class II loci encoding the non-cell surface bound antigens (DMA, DMB, DOA, DOB1), as well as the pseudogenes (SLA-5, DRB2, DRB3, DRB4, DRB5) are designated sequentially as they are discovered, whereas the naming convention for alleles of other loci (SLA-4, -9, -11, DQB2, DOB2, DYB, MIC1, MIC2, TAP1, TAP2) remains to be determined as sequences accumulate. To date, there are 223 class I, 214 class II and 2 SLA-related (MIC1 and MIC2) alleles officially designated. SLA-2 and DRB1 each represents the most polymorphic class I and class II locus, respectively, with 87 and 89 alleles designated. There are also 61 class I (SLA-1-3-2) and 49 class II (DRB1-DQB1) haplotypes designated at allele level resolution.
Conclusion: The systematic nomenclature for SLA genes is essential to the understanding of their involvement in allo- or xenogeneic immune responses in transplantation research, as well as in swine diseases and vaccine development.
BBSRC Bioinformatics and Biological Resources Fund: “Securing and developing the IPD-MHC database to enhance research into livestock diseases”.
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