The Swine Leukocyte Antigen (SLA) Nomenclature System of the International Society for Animal Genetics (ISAG) and the International Union of Immunological Societies (IUIS): Update 2016

C.-S. Ho, J.-H. Lee, A. Ando, C. Rogel-Gaillard, L.B. Schook, D.M. Smith, J.K. Lunney, S.E. Hammer
35th International Society for Animal Genetics Conference, July 23-27, 2016, Salt Lake City, UT

The SLA system is among the most well characterized MHC systems in non-human animal species. The ISAG/IUIS-VIC SLA Nomenclature Committee was formed in 2002, 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 IPD-MHC SLA sequence database (, which is the repository for all recognized SLA genes, their allelic sequences and haplotypes.

The IPD-MHC Database is currently undergoing major revisions on its infrastructure and website, aiming to significantly improve the performance and allow for a simpler submission process and more frequent update. To date, there are 176 class Ia (SLA-1, SLA-2, SLA-3), 16 class Ib (SLA-6, SLA-7 and SLA-8), 5 class I-like SLA-12 and 190 class II (DRA, DRB1, DQA, DQB1, DMA, DMB, DOA and DOB1) alleles officially designated. Additionally, there are 43 class I and 33 class II haplotypes designated at the allele level resolution.

Recent evidence has suggested other loci in the SLA system, previously recognized as pseudogenes (e.g. SLA-9, SLA-11, DQB2 and DOB2), may be expressed at the transcript level for some haplotypes. Specifically, alignment of transcripts to the genomic sequence showed that SLA-11 appears to be a protein coding gene with alternative splicing. Its full length transcript appears to encode a canonical class I-like protein with 8 exons while two other variants encode proteins either lacking exon 3 (alpha 2 domain) or exons 3 and 4 (alpha 2 and 3 domains).

These data suggest that SLA-11 could be an expressed class Ib-like gene within the class Ia gene cluster. The committee will consider reclassifying SLA-11 as a putative functional gene as additional evidence accumulates. A systematic nomenclature for the genes, alleles and haplotypes of the swine MHC is critical to the research in swine genetic diversity, immunology, health, vaccinology, and organ or cell transplantation. Continuous efforts on characterizing SLA alleles and haplotypes and studying of their diversity in various pig populations will further our understanding of the architecture and polymorphism of the SLA system and their role in disease, vaccine and allo- or xeno-graft responses.