Expanded dog leukocyte antigen (DLA) single nucleotide polymorphism (SNP) genotyping reveals spurious class II associations

Abeles, 1999, Hypertrophic osteodystrophy in six Weimaraner puppies associated with systemic signs, Veterinary Record, 145, 130, 10.1136/vr.145.5.130 Angles, 2005, Uveodermatologic (VKH-like) syndrome in American Akita dogs is associated with an increased frequency of DQA1∗00201, Tissue Antigens, 66, 656, 10.1111/j.1399-0039.2005.00508.x Angles, 2005, Frequency and distribution of alleles of canine MHC-II DLA-DQB1, DLA-DQA1 and DLA-DRB1 in 25 representative American Kennel Club breeds, Tissue Antigens, 66, 173, 10.1111/j.1399-0039.2005.00461.x Barnes, 2009, Association of canine anal furunculosis with TNFA is secondary to linkage disequilibrium with DLA-DRB1∗, Tissue Antigens, 73, 218, 10.1111/j.1399-0039.2008.01188.x Barrett, 2005, Haploview: Analysis and visualization of LD and haplotype maps, Bioinformatics, 21, 263, 10.1093/bioinformatics/bth457 Bellah, 1993, Hypertrophic osteopathy, 858 Bland, 2000, Statistics notes. The odds ratio, British Medical Journal, 320, 1468, 10.1136/bmj.320.7247.1468 Catchpole, 2008, Canine diabetes mellitus: From phenotype to genotype, Journal of Small Animal Practice, 49, 4 Cheung, 2011, Conditional meta-analysis stratifying on detailed HLA genotypes identifies a novel type 1 diabetes locus around TCF19 in the MHC, Human Genetics, 129, 161, 10.1007/s00439-010-0908-2 Coenen, 2009, Rheumatoid arthritis: A view of the current genetic landscape, Genes and Immunity, 10, 101, 10.1038/gene.2008.77 Dieudé, 2011, Immunogenetics of systemic sclerosis, Autoimmunity Reviews, 10, 282, 10.1016/j.autrev.2010.09.017 Eike, 2009, Conditional analyses on the T1DGC MHC dataset: Novel associations with type 1 diabetes around HLA-G and confirmation of HLA-B, Genes and Immunity, 10, 56, 10.1038/gene.2008.74 Ettinger, 2006, Allelic variation in key peptide-binding pockets discriminates between closely related diabetes-protective and diabetes-susceptible HLA-DQB1∗06 alleles, Journal of Immunology, 176, 1988, 10.4049/jimmunol.176.3.1988 Falorni, 2008, Association of genetic polymorphisms and autoimmune Addison’s disease, Expert Review of Clinical Immunology, 4, 441, 10.1586/1744666X.4.4.441 Farasat, 2008, Autoinflammatory diseases: Clinical and genetic advances, Archives of Dermatology, 144, 392, 10.1001/archderm.144.3.392 Feder, 1996, A novel MHC class I-like gene is mutated in patients with hereditary haemochromatosis, Nature Genetics, 13, 399, 10.1038/ng0896-399 Fugger, 2000, HLA-DR4 and rheumatoid arthritis: Studies in mice and men, Arthritis Research, 2, 208, 10.1186/ar89 Klein, 1986 Gombos, 2007, Analysis of extended human leukocyte antigen haplotype association with Addison’s disease in three populations, European Journal of Endocrinology, 157, 757, 10.1530/EJE-07-0290 Gorodezky, 2006, HLA and autoimmune diseases: Type 1 diabetes (T1D) as an example, Autoimmunity Reviews, 5, 187, 10.1016/j.autrev.2005.06.002 Greer, 2009, Heritability and transmission analysis of necrotizing meningoencephalitis in the Pug, Research in Veterinary Science, 86, 438, 10.1016/j.rvsc.2008.10.002 Greer, 2010, Necrotizing meningoencephalitis of Pug dogs associates with dog leukocyte antigen class II and resembles acute variant forms of multiple sclerosis, Tissue Antigens, 76, 110 Grondalen, 1976, Metaphyseal osteopathy (hypertrophic osteodystrophy) in growing dogs: A clinical study, Journal of Small Animal Practice, 17, 721, 10.1111/j.1748-5827.1976.tb06936.x Harrus, 2002, Development of hypertrophic osteodystrophy and antibody response in a litter of vaccinated Weimaraner puppies, Journal of Small Animal Practice, 43, 27, 10.1111/j.1748-5827.2002.tb00006.x Hinds, 2004, Matching strategies for genetic association studies in structured populations, American Journal of Human Genetics, 74, 317, 10.1086/381716 Holmdahl, 2000, Association of MHC and rheumatoid arthritis: Why is rheumatoid arthritis associated with the MHC genetic region? An introduction, Arthritis Research, 2, 203, 10.1186/ar87 Horton, 2008, Variation analysis and gene annotation of eight MHC haplotypes: The MHC Haplotype Project, Immunogenetics, 60, 1, 10.1007/s00251-007-0262-2 Hughes, 2010, Association of a dog leukocyte antigen class II haplotype with hypoadrenocorticism in Nova Scotia duck tolling retrievers, Tissue Antigens, 75, 684, 10.1111/j.1399-0039.2010.01440.x Hughes, 2007, Clinical features and heritability of hypoadrenocorticism in Nova Scotia duck tolling retrievers: 25 cases (1994–2006), Journal of the American Veterinary Medical Association, 231, 407, 10.2460/javma.231.3.407 Ilonen, 2010, Novel gene associations in type 1 diabetes, Current Diabetes Reports, 10, 338, 10.1007/s11892-010-0133-3 Irion, 2003, Analysis of genetic variation in 28 dog breed populations with 100 microsatellite markers, Journal of Heredity, 94, 81, 10.1093/jhered/esg004 Jawaheer, 2002, Dissecting the genetic complexity of the association between human leukocyte antigens and rheumatoid arthritis, American Journal of Human Genetics, 71, 585, 10.1086/342407 Karlsson, 2007, Efficient mapping of Mendelian traits in dogs through genome-wide association, Nature Genetics, 39, 1321, 10.1038/ng.2007.10 Kennedy, 2006, Identification of susceptibility and protective major histocompatibility complex haplotypes in canine diabetes mellitus, Tissue Antigens, 68, 467, 10.1111/j.1399-0039.2006.00716.x Kennedy, 2006, Association of a common dog leucocyte antigen class II haplotype with canine primary immune-mediated haemolytic anaemia, Tissue Antigens, 68, 502, 10.1111/j.1399-0039.2006.00715.x Kennedy, 2006, Association of canine hypothyroidism with a common major histocompatibility complex DLA class II allele, Tissue Antigens, 68, 82, 10.1111/j.1399-0039.2006.00614.x Kennedy, 2007, 14th International HLA and immunogenetics workshop: Report on joint study on canine DLA diversity, Tissue Antigens, 69, 269, 10.1111/j.1399-0039.2006.00778.x Kennedy, 2007, Canine DLA diversity: 1. New alleles and haplotypes, Tissue Antigens, 69, 272, 10.1111/j.1399-0039.2006.00779.x Kennedy, 2007, Canine DLA diversity: 2. Family studies, Tissue Antigens, 69, 289, 10.1111/j.1399-0039.2006.00780.x Kennedy, 2007, Canine DLA diversity: 3. Disease studies, Tissue Antigens, 69, 292, 10.1111/j.1399-0039.2006.00781.x Kennedy, 2008, Risk of anal furunculosis in German shepherd dogs is associated with the major histocompatibility complex, Tissue Antigens, 71, 51 Kumánovics, 2002, QUOD ERAT FACIENDUM: Sequence analysis of the H2-D and H2-Q regions of 129/SvJ mice, Immunogenetics, 54, 479, 10.1007/s00251-002-0494-0 LaFond, 2002, Breed susceptibility for developmental orthopedic diseases in dogs, Journal of the American Animal Hospital Association, 38, 467, 10.5326/0380467 Lie, 1999, The predisposition to type 1 diabetes linked to the human leukocyte antigen complex includes at least one non-class II gene, American Journal of Human Genetics, 64, 793, 10.1086/302283 Lie, 1999, A gene telomeric of the HLA class I region is involved in predisposition to both type 1 diabetes and coeliac disease, Tissue Antigens, 54, 162, 10.1034/j.1399-0039.1999.540207.x Lindblad-Toh, 2005, Genome sequence, comparative analysis and haplotype structure of the domestic dog, Nature, 438, 803, 10.1038/nature04338 Malfroy, 1997, Heterogeneity in rates of recombination in the 6-Mb region telomeric to the human major histocompatibility complex, Genomics, 43, 226, 10.1006/geno.1997.4800 Munjar, 1998, Comparison of risk factors for hypertrophic osteodystrophy, craniomandibular osteopathy and canine distemper virus infection, Veterinary and Comparative Orthopaedics and Traumatology, 11, 42 Ollier, 2001, Dog MHC alleles containing the human RA shared epitope confer susceptibility to canine rheumatoid arthritis, Immunogenetics, 53, 669, 10.1007/s002510100372 Ota, 2001, A second susceptibility gene for developing rheumatoid arthritis in the human MHC is localized within a 70-kb interval telomeric of the TNF genes in the HLA class III region, Genomics, 71, 263, 10.1006/geno.2000.6371 Purcell, 2007, PLINK: A tool set for whole-genome association and population-based linkage analyses, American Journal of Human Genetics, 81, 559, 10.1086/519795 Ramagopalan, 2009, Multiple sclerosis: Major histocompatibility complexity and antigen presentation, Genome Medicine, 1, 105, 10.1186/gm105 Raymond, 2005, Ancient haplotypes of the HLA class II region, Genome Research, 15, 1250, 10.1101/gr.3554305 Robinson, 2005, IPD – The immuno polymorphism database, Nucleic Acids Research, 33, D523, 10.1093/nar/gki032 Roudier, 2000, Association of RA with HLA-DR4: The role of repertoire selection, Arthritis Research, 2, 217, 10.1186/ar91 Seddon, 2010, Evolutionary history of DLA class II haplotypes in canine diabetes mellitus through single nucleotide polymorphism genotyping, Tissue Antigens, 75, 218, 10.1111/j.1399-0039.2009.01426.x Sutter, 2004, Extensive and breed-specific linkage disequilibrium in Canis familiaris, Genome Research, 14, 2388, 10.1101/gr.3147604 Svejgaard, 2008, The immunogenetics of multiple sclerosis, Immunogenetics, 60, 275, 10.1007/s00251-008-0295-1 Thomsen, 1975, MLC typing in juvenile diabetes mellitus and idiopathic Addison’s disease, Immunological Reviews, 22, 125, 10.1111/j.1600-065X.1975.tb01555.x Thorsby, 2005, HLA associated genetic predisposition to autoimmune diseases: Genes involved and possible mechanisms, Transplant Immunology, 14, 175, 10.1016/j.trim.2005.03.021 Turner, 2002, HLA-B27 and pathogenesis of spondyloarthropathies, Current Opinion in Rheumatology, 14, 367, 10.1097/00002281-200207000-00006 Undlien, 1999, HLA associations in type 1 diabetes among patients not carrying high-risk DR3-DQ2 or DR4-DQ8 haplotypes, Tissue Antigens, 54, 543, 10.1034/j.1399-0039.1999.540602.x Undlien, 2001, HLA complex genes in type 1 diabetes and other autoimmune diseases, Which genes are involved? Trends in Genetics, 17, 93, 10.1016/S0168-9525(00)02180-6 Vandiedonck, 2005, Genetics of autoimmune myasthenia gravis: The multifaceted contribution of the HLA complex, Journal of Autoimmunity, 25, 6, 10.1016/j.jaut.2005.09.010 Wagner, 1995, Nucleotide sequence and polymorphism analysis of canine DRA cDNA clones, Tissue Antigens, 45, 284, 10.1111/j.1399-0039.1995.tb02454.x Wallace, 2010, The imprinted DLK1-MEG3 gene region on chromosome 14q32. 2 Alters susceptibility to type 1 diabetes, Nature Genetics, 42, 68, 10.1038/ng.493 Wang, 2009, Testing for genetic association in the presence of population stratification in genome-wide association studies, Genetic Epidemiology, 33, 637, 10.1002/gepi.20415 Watson, 1973, Hypertrophic osteodystrophy in the dog, Australian Veterinary Journal, 49, 433, 10.1111/j.1751-0813.1973.tb06853.x Weyand, 2000, HLA polymorphisms in phenotypic variants of rheumatoid arthritis, Arthritis Research, 2, 212, 10.1186/ar90 Wilbe, 2009, MHC class II polymorphism is associated with a canine SLE-related disease complex, Immunogenetics, 61, 557, 10.1007/s00251-009-0387-6 Wilbe, 2010, Increased genetic risk or protection for canine autoimmune lymphocytic thyroiditis in Giant Schnauzers depends on DLA class II genotype, Tissue Antigens, 75, 712, 10.1111/j.1399-0039.2010.01449.x Woodard, 1982, Canine hypertrophic osteodystrophy, a study of the spontaneous disease in littermates, Veterinary Pathology, 19, 337, 10.1177/030098588201900401 Wu, 2011, A comparison of association methods correcting for population stratification in case-control studies, Annals of Human Genetics, 75, 418, 10.1111/j.1469-1809.2010.00639.x Zanelli, 2000, HLA association with autoimmune disease: A failure to protect?, Rheumatology, 39, 1060, 10.1093/rheumatology/39.10.1060