Haplotype-based search for SNPs associated with differential type 1 diabetes risk among chromosomes carrying a specific HLA DRB1-DQA1-DQB1 haplotype

A re-formulation of generalized linear mixed models to fit family data in genetic association studies

The generalized linear mixed model (GLMM) is a useful tool for modeling genetic correlation among family data in genetic association studies. However, when dealing with families of varied sizes and diverse genetic relatedness, the GLMM has a special correlation structure which often makes it difficult to be specified using standard statistical software. In this study, we propose a Cholesky decomposition based re-formulation of the GLMM so that the re-formulated GLMM can be specified conveniently via “proc nlmixed” and “proc glimmix” in SAS, or OpenBUGS via R package BRugs. Performances of these procedures in fitting the re-formulated GLMM are examined through simulation studies. We also apply this re-formulated GLMM to analyze a real data set from Type 1 Diabetes Genetics Consortium (T1DGC).

HLA-associated phenotypes in youth with autoimmune diabetes

OBJECTIVES

To examine human leukocyte antigen HLA DRB1-DQB1 haplotypes within a multi-ethnic cohort and assess their association with characteristics of diabetes onset.

METHODS

The sample included 1662 participants from the SEARCH for Diabetes in Youth Study who tested positive for GADA and/or IA-2A autoantibodies. Blood drawn at the study visit was used to measure fasting C-peptide (FCP) and genotype HLA DRB1 and DQB1 loci. Diabetic ketoacidosis (DKA) at diagnosis was determined from medical records. Multivariable linear and logistic regression models stratified by race/ethnicity were used to assess associations with DRB1-DQB1 haplotypes.

RESULTS

The frequency of DRB1*03 susceptibility haplotypes ranged 27.5-28.9% in all racial/ethnic groups. The frequency of susceptibility DRB1*04-DQB1*0302 was higher in non-Hispanic White (NHW; 34.1%) and Hispanic (38.9%) compared to non-Hispanic Black (NHB; 20.8%) youth. Neutral and protective haplotypes were low frequency in all groups. DBR1*03 haplotypes were associated with younger age at diagnosis in NHW and positivity for multiple autoantibodies in Hispanics. DRB1*04-DQB1*0302 haplotypes were associated with multiple autoantibody positivity in NHW and Hispanics, and lower FCP and higher odds of DKA in Hispanics only. Although protective DRB1*04-DQB1*0301 haplotypes were associated with older age at diagnosis in NHW, they were also associated with multiple autoantibody positivity in these youth. Protective DRB1*13 haplotypes were associated with decreased odds of multiple autoantibody positivity in NHB youth.

CONCLUSIONS

The distribution of DRB1-DQB1 haplotypes and their association with onset-related characteristics of autoimmune diabetes varies across major racial/ethnic groups in the USA. This may contribute to variation in clinical presentation of autoimmune diabetes by race/ethnicity.