Next Generation Sequencing Reveals the Association of DRB3*02:02 With Type 1 Diabetes
- Henry A. Erlich1⇑,
- Ana Maria Valdes2,
- Shana L. McDevitt3,
- Birgitte B. Simen4,
- Lisbeth A. Blake4,
- Kim R. McGowan4,
- John A. Todd5,
- Stephen S. Rich6,
- Janelle A. Noble3,
- for the Type 1 Diabetes Genetics Consortium (T1DGC)*
- 1Roche Molecular Systems, Pleasanton, California
- 2King’s College London, London, U.K.
- 3Children’s Hospital Oakland Research Institute, Oakland, California
- 4454 Life Sciences–a Roche Company, Branford, Connecticut
- 5Department of Medical Genetics, Cambridge Institute of Medical Research, JDRF/Wellcome Trust Diabetes and Inflammation Laboratory, National Institute for Health Research Cambridge Biomedical Research Centre, University of Cambridge, Addenbrooke’s Hospital, Cambridge, U.K.
- 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 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.
This article contains Supplementary Data online at http://diabetes.diabetesjournals.org/lookup/suppl/doi:10.2337/db12-1387/-/DC1.
H.A.E. is currently affiliated with the Children's Hospital Oakland Research Institute, Oakland, California.
*A complete list of the members of the T1DGC can be found in the Supplementary Data online.
- Received October 5, 2012.
- Accepted February 27, 2013.
- © 2013 by the American Diabetes Association.
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