title: Next generation sequencing reveals the association of DRB3*02:02 with type 1 diabetes.
abstract: The primary associations of the HLA class II genes, HLA-DRB1 and HLA-DQB1, and the class I genes, HLA-A and HLA-B, with type 1 diabetes (T1D) are well established. However, the role of polymorphism at the HLA-DRB3, HLA-DRB4, and HLA-DRB5 loci remains unclear. In two separate studies, one of 500 subjects and 500 control subjects and one of 366 DRB1*03:01-positive samples from selected multiplex T1D families, we used Roche 454 sequencing with Conexio Genomics ASSIGN ATF 454 HLA genotyping software analysis to analyze sequence variation at these three HLA-DRB loci. Association analyses were performed on the two HLA-DRB loci haplotypes (DRB1-DRB3, -DRB4, or -DRB5). Three common HLA-DRB3 alleles (*01:01, *02:02, *03:01) were observed. DRB1*03:01 haplotypes carrying DRB3*02:02 conferred a higher T1D risk than did DRB1*03:01 haplotypes carrying DRB3*01:01 in DRB1*03:01/*03:01 homozygotes with two DRB3*01:01 alleles (odds ratio [OR] 3.4 [95% CI 1.46-8.09]), compared with those carrying one or two DRB3*02:02 alleles (OR 25.5 [3.43-189.2]) (P = 0.033). For DRB1*03:01/*04:01 heterozygotes, however, the HLA-DRB3 allele did not significantly modify the T1D risk of the DRB1*03:01 haplotype (OR 7.7 for *02:02; 6.8 for *01:01). These observations were confirmed by sequence analysis of HLA-DRB3 exon 2 in a targeted replication study of 281 informative T1D family members and 86 affected family-based association control (AFBAC) haplotypes. The frequency of DRB3*02:02 was 42.9% in the DRB1*03:01/*03:01 patients and 27.6% in the DRB1*03:01/*04 (P = 0.005) compared with 22.6% in AFBAC DRB1*03:01 chromosomes (P = 0.001). Analysis of T1D-associated alleles at other HLA loci (HLA-A, HLA-B, and HLA-DPB1) on DRB1*03:01 haplotypes suggests that DRB3*02:02 on the DRB1*03:01 haplotype can contribute to T1D risk.
authors: Roche Molecular Systems, Pleasanton, California, USA. henry.erlich@roche.com
authors: Henry A
authors: HA
authors: Erlich
authors: Ana Maria
authors: AM
authors: Valdes
authors: Shana L
authors: SL
authors: McDevitt
authors: Birgitte B
authors: BB
authors: Simen
authors: Lisbeth A
authors: LA
authors: Blake
authors: Kim R
authors: KR
authors: McGowan
authors: John A
authors: JA
authors: Todd
authors: Stephen S
authors: SS
authors: Rich
authors: Janelle A
authors: JA
authors: Noble
mesh_terms: D000328:Adult; D000483:Alleles; D003922:Diabetes Mellitus, Type 1 / Q000235:genetics* / Q000276:immunology; D005260:Female; D005787:Gene Frequency; D056726:Genetic Association Studies; D020022:Genetic Predisposition to Disease; D005838:Genotype; D059826:HLA-DRB3 Chains / Q000235:genetics*; D006239:Haplotypes; D006801:Humans; D008297:Male; D011110:Polymorphism, Genetic
chemical_list: D059826:HLA-DRB3 Chains; C553544:HLA-DRB3*02:02:02 antigen