Next Generation Sequencing Reveals the Association of DRB3*02:02 with Type I Diabetes
- Henry A. Erlich1,
- Ana Maria Valdes2,
- Shana McDevitt3,
- Birgitte B. Simen4,
- Lisbeth A. Blake4,
- Kim R. McGowan4,
- John A. Todd5,
- Stephen S. Rich6 and
- Janelle Noble3
- 1Roche Molecular Systems, Pleasanton, CA
- 2King’s College London, London, UK
- 3Children’s Hospital Oakland Research Institute, Oakland, CA
- 4454 Life Sciences – a Roche Company Branford, CT
- 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
- 6Center for Public Health Genomics, University of Virginia, Charlottesville, Virginia
- Corresponding author: Henry A. Erlich,
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.
- © 2013 by the American Diabetes Association.
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