Next Generation Sequencing Reveals the Association of DRB3*02:02 with Type I Diabetes

  1. Janelle Noble3
  1. 1Roche Molecular Systems, Pleasanton, CA
  2. 2King’s College London, London, UK
  3. 3Children’s Hospital Oakland Research Institute, Oakland, CA
  4. 4454 Life Sciences – a Roche Company Branford, CT
  5. 5Department of Medical Genetics, Cambridge Institute of Medical Research, Juvenile Diabetes Research Foundation/Wellcome Trust Diabetes and Inflammation Laboratory, NIHR Cambridge Biomedical Research Centre, University of Cambridge, Addenbrooke’s Hospital, Cambridge
  6. 6Center for Public Health Genomics, University of Virginia, Charlottesville, Virginia
  1. Corresponding author: Henry A. Erlich, henry.erlich{at}roche.com

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 cases and 500 controls and one of 366 DRB1*03:01–positive samples from selected multiplex T1D families, we used Roche 454 sequencing with Conexio Genomics ASSIGN™ATF HLA genotyping software analysis to analyze sequence variation at these three HLA-DRB loci. Association analyses were performed on the two HLA-DRB locus (DRB1-DRB3, -DRB4, or -DRB5) haplotypes. Three common HLA-DRB3 alleles (*01:01, *02:02, *03:01) were observed. DRB1*03:01 haplotypes carrying DRB3*02:02 conferred a higher (p=0.033) T1D risk than did DRB1*03:01 haplotypes carrying DRB3*01:01, primarily in DRB1*03:01/*03:01 homozygotes with two DRB3*01:01 alleles (OR = 3.4 95% CI= 1.46-8.09), compared with those carrying one or two DRB3*02:02 alleles (OR = 25.5; 95% CI – 3.43-189.2). 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; OR = 6.8 for *01:01). These observations were confirmed by sequence analysis of HLA-DRB3 exon 2 in a targeted replication study of 280 informative T1D family members and 86 Affected Family Based 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 to 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.

  • Received October 5, 2012.
  • Accepted February 26, 2013.

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  1. Diabetes
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