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Two Single Nucleotide Polymorphisms Identify the Highest-Risk Diabetes HLA Genotype

Potential for Rapid Screening

From the Barbara Davis Center for Childhood Diabetes, University of Colorado at Denver, Denver, Colorado

Corresponding author: Jennifer M. Barker, jennifer.barker{at}uchsc.edu

OBJECTIVE—People with the HLA genotype DRB1*0301-DQA1*0501-DQB1*0201/DRB1*04-DQA1*0301-DQB1*0302 (DR3/4-DQ8) are at the highest risk of developing type 1 diabetes. We sought to find an inexpensive, rapid test to identify DR3/4-DQ8 subjects using two single nucleotide polymorphisms (SNPs).

RESEARCH DESIGN AND METHODS—SNPs rs2040410 and rs7454108 were associated with DR3-DQB1*0201 and DR4-DQB1*0302. We correlated these SNPs with HLA genotypes and with publicly available data on 5,019 subjects from the Type 1 Diabetes Genetic Consortium (T1DGC). Additionally, we analyzed these SNPs in samples from 143 HLA-typed children who participated in the Diabetes Autoimmunity Study of the Young (DAISY) using Taqman probes (rs7454108) and restriction digest analysis (rs2040410).

RESULTS—With a simple combinatorial rule, the SNPs of interest identified the presence or absence of the DR3/4-DQ8 genotype. A wide variety of genotypes were tested for both SNPs. In T1DGC samples, the two SNPs were 98.5% (1,173 of 1,191) sensitive and 99.7% (3,815 of 3,828) specific for DR3/4-DQ8. In the DAISY population, the test was 100% (69 of 69) sensitive and 100% (74 of 74) specific. Overall, the sensitivity and specificity for the test were 98.57 and 99.67%, respectively.

CONCLUSIONS—A two-SNP screening test can identify the highest risk heterozygous genotype for type 1 diabetes in a time- and cost-effective manner.

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				J. Romanos and C. Wijmenga Comment on: Barker et al. (2008) Two Single Nucleotide Polymorphisms Identify the Highest-Risk Diabetes HLA Genotype: Diabetes 57:3152-3155, 2008 Diabetes, January 1, 2009; 58(1): e1 - e1. [Full Text] [PDF]

				J. M. Barker, T. M. Triolo, and G. S. Eisenbarth Response to Comment on: Barker et al. (2008) Two Single Nucleotide Polymorphisms Identify the Highest-Risk Diabetes HLA Genotype: Diabetes 57:3152-3155, 2008 Diabetes, January 1, 2009; 58(1): e2 - e2. [Full Text] [PDF]