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Genotype effects and epistasis in type 1 diabetes and HLA-DQ trans dimer associations with disease

Abstract

Alleles of HLA class II genes DQB1, DQA1, and DRB1 in the MHC region are major determinants of genetic predisposition to type 1 diabetes (T1D). Several alleles of each of these three loci are associated with susceptibility or protection from disease. In addition, relative risks for some DR-DQ genotypes are not simply the sum or product of the single haplotype relative risks. For example, the risk of the DRB1*03-DQB1*02/DRB1*0401-DQB1*0302 genotype is often found to be higher than for the individual DRB1*03-DQB1*02 and DRB1*0401-DQB1*0302 homozygous genotypes. It has been hypothesized that this synergy or epistasis occurs through formation of highly susceptible trans-encoded HLA-DQ(α1, β1) heterodimers. Here, we evaluated this hypothesis by estimating the disease associations of the range of DR-DQ genotypes and their inferred dimers in a large collection of nuclear families. We determined whether the risk of haplotypes in DRB1*0401-DQB1*0302-positive genotypes relative to the DRB1*03-DQB1*02-positive genotypes is different from that of DRB1*01-DQB1*0501, which we used as a baseline reference. Several haplotypes showed a different risk compared to DRB1*01-DQB1*0501, which correlated with their ability to form certain trans-encoded DQ dimers. This result provides new evidence for the potential importance of trans-encoded HLA DQ molecules in the determination of HLA-associated risk in T1D.

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Abbreviations

OR:

Odds ratio

CETDT:

Conditional Extended Transmission Disequilibrium Test

RTP:

Relative Transmission Probability

RR:

Relative Risk for disease.

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Acknowledgements

We thank the Juvenile Diabetes Research Foundation (JDRF), the Wellcome Trust, Dutch Diabetes Research Foundation (97.137,2001.10.004), The Netherlands Organisation for Health Research and Development (ZonMW) and The Juvenile Diabetes Research Foundation International (JDRF) (2001.10.004), and the Italian Telethon for financial support. We gratefully acknowledge the participation of all patients and family members, including provision of samples from T1D families from the Human Biological Data Interchange and Diabetes UK repositories, and sample collections by The Norwegian Study Group for Childhood Diabetes, and Italy. We thank Sarah Nutland and Helen Rance for DNA preparation and HLA typing.

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Correspondence to B P C Koeleman.

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Koeleman, B., Lie, B., Undlien, D. et al. Genotype effects and epistasis in type 1 diabetes and HLA-DQ trans dimer associations with disease. Genes Immun 5, 381–388 (2004). https://doi.org/10.1038/sj.gene.6364106

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