title: Expanded dog leukocyte antigen (DLA) single nucleotide polymorphism (SNP) genotyping reveals spurious class II associations.
abstract: The dog leukocyte antigen (DLA) system contains many of the functional genes of the immune system, thereby making it a candidate region for involvement in immune-mediated disorders. A number of studies have identified associations between specific DLA class II haplotypes and canine immune hemolytic anemia, thyroiditis, immune polyarthritis, type I diabetes mellitus, hypoadrenocorticism, systemic lupus erythematosus-related disease complex, necrotizing meningoencephalitis (NME) and anal furunculosis. These studies have relied on sequencing approximately 300 bases of exon 2 of each of the DLA class II genes: DLA-DRB1, DLA-DQA1 and DLA-DQB1. In the present study, an association (odds ratio=4.29) was identified by this method between Weimaraner dogs with hypertrophic osteodystrophy (HOD) and DLA-DRB1∗01501. To fine map the association with HOD, a genotyping assay of 126 coding single nucleotide polymorphisms (SNPs) from across the entire DLA, spanning a region of 2.5 Mb (3,320,000-5,830,000) on CFA12, was developed and tested on Weimaraners with HOD, as well as two additional breeds with diseases associated with DLA class II: Nova Scotia duck tolling retrievers with hypoadrenocorticism and Pug dogs with NME. No significant associations were found between Weimaraners with HOD or Nova Scotia duck tolling retrievers with hypoadrenocorticism and SNPs spanning the DLA region. In contrast, significant associations were found with NME in Pug dogs, although the associated region extended beyond the class II genes. By including a larger number of genes from a larger genomic region, a SNP genotyping assay was generated that provides coverage of the extended DLA region and may be useful in identifying and fine mapping DLA associations in dogs.
authors: School of Veterinary Medicine, University of California, Davis, USA. nsafra@ucdavis.edu
authors: N
authors: N
authors: Safra
authors: N C
authors: NC
authors: Pedersen
authors: Z
authors: Z
authors: Wolf
authors: E G
authors: EG
authors: Johnson
authors: H W
authors: HW
authors: Liu
authors: A M
authors: AM
authors: Hughes
authors: A
authors: A
authors: Young
authors: D L
authors: DL
authors: Bannasch
mesh_terms: D000224:Addison Disease / Q000235:genetics / Q000276:immunology / Q000662:veterinary*; D000818:Animals; D001851:Bone Diseases, Metabolic / Q000235:genetics / Q000276:immunology / Q000662:veterinary*; D004283:Dog Diseases / Q000235:genetics* / Q000276:immunology; D004285:Dogs; D005091:Exons; D005802:Genes, MHC Class II; D020022:Genetic Predisposition to Disease; D055106:Genome-Wide Association Study / Q000662:veterinary; D060005:Genotyping Techniques / Q000379:methods*; D006239:Haplotypes; D000949:Histocompatibility Antigens Class II / Q000235:genetics* / Q000276:immunology; D008590:Meningoencephalitis / Q000235:genetics / Q000276:immunology / Q000662:veterinary*; D016017:Odds Ratio; D010375:Pedigree; D020641:Polymorphism, Single Nucleotide; D013045:Species Specificity
chemical_list: D000949:Histocompatibility Antigens Class II