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. An association (odds ratio = 4.29) was identified by this method between Weimaraner dogs with hypertrophic osteodystrophy (HOD) and DLA-DRB1*01501. In the present study, 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.

Autoinflammatory bone disorders

“…In Safra’s review of clinical disease in 53 affected Weimaraners, ~ 50% of the dogs had at least one affected littermate (36). Linkage to the DLA-DRB1*01501 (DLA is the dog equivalent of the HLA) was reported by Abeles et al (38) but no association could be found with the DLA locus when expanded DLA SNP analysis was performed (39) nor in another study assessing the role of DLA-DQA1 locus(40). The search for the disease causing gene is ongoing using a next generation sequencing approach.…”

Autoinflammatory Diseases Predominantly Affecting Bone and Joints

“…34À36 Largebreed dogs, particularly Weimeraners, develop a disease that is phenotypically similar to human CRMO called hypertrophic osteodystrophy (HOD). 37,38 This disease clusters in litters and in specific breeds, strongly supporting a genetic component. 38 There are also two autosomal recessive human disorders that have CRMO as a subphenotype, including Majeed syndrome, which is due to mutations in LPIN2, and deficiency of the interleukin-1 receptor antagonist (DIRA), which is due to mutations in IL1RN.…”

“…37,38 This disease clusters in litters and in specific breeds, strongly supporting a genetic component. 38 There are also two autosomal recessive human disorders that have CRMO as a subphenotype, including Majeed syndrome, which is due to mutations in LPIN2, and deficiency of the interleukin-1 receptor antagonist (DIRA), which is due to mutations in IL1RN. 39À41 Pathogenesis Innate immune system dysfunction is responsible for the chronic bone and skin inflammation seen in these disorders.…”

Putative candidate genes for canine hypoadrenocorticism (Addison's disease) in multiple dog breeds

“…The canine MHC (dog leucocyte antigen, DLA) has been associated with hypoadrenocorticism (Massey and others 2013) although this was based on DRB1/DQA1/DQB1 exon 2 typing and could be subjected to population stratification as reported by Safra and others for Nova Scotia duck tolling retrievers with hypoadrenocorticism and Weimaraners with hypertrophic osteodystrophy (Safra and others 2011). There is, however, a reported genetic basis in a number of breeds (Shaker and others 1988, Burton and others 1997, Oberbauer and others 2002, 2006, Famula and others 2003, Chase and others 2006, Hughes and others 2007, 2009, Short and others 2013) with anecdotal reports in others (West Highland white terrier, great dane and soft coated wheaten terrier).…”

“…This dog population may also exhibit clinical heterogeneity between breeds but it is likely that the cause of hypoadrenocorticism within a breed is the same; further DLA analysis, in particular, extended DLA analysis (Safra and others 2011) should enable us to identify breeds that have a strong autoimmune component.…”