Effective Detection of Human Leukocyte Antigen Risk Alleles in Celiac Disease Using Tag Single Nucleotide Polymorphisms

Abstract

BackgroundThe HLA genes, located in the MHC region on chromosome 6p21.3, play an important role in many autoimmune disorders, such as celiac disease (CD), type 1 diabetes (T1D), rheumatoid arthritis, multiple sclerosis, psoriasis and others. Known HLA variants that confer risk to CD, for example, include DQA1*05/DQB1*02 (DQ2.5) and DQA1*03/DQB1*0302 (DQ8). To diagnose the majority of CD patients and to study disease susceptibility and progression, typing these strongly associated HLA risk factors is of utmost importance. However, current genotyping methods for HLA risk factors involve many reactions, and are complicated and expensive. We sought a simple experimental approach using tagging SNPs that predict the CD-associated HLA risk factors.MethodologyOur tagging approach exploits linkage disequilibrium between single nucleotide polymorphism (SNPs) and the CD-associated HLA risk factors DQ2.5 and DQ8 that indicate direct risk, and DQA1*0201/DQB1*0202 (DQ2.2) and DQA1*0505/DQB1*0301 (DQ7) that attribute to the risk of DQ2.5 to CD. To evaluate the predictive power of this approach, we performed an empirical comparison of the predicted DQ types, based on these six tag SNPs, with those executed with current validated laboratory typing methods of the HLA-DQA1 and -DQB1 genes in three large cohorts. The results were validated in three European celiac populations.ConclusionUsing this method, only six SNPs were needed to predict the risk types carried by >95% of CD patients. We determined that for this tagging approach the sensitivity was >0.991, specificity >0.996 and the predictive value >0.948. Our results show that this tag SNP method is very accurate and provides an excellent basis for population screening for CD. This method is broadly applicable in European populations.

Search for DQ2.5 and DQ8 alleles using a lower cost technique in patients with type 1 diabetes and celiac disease in a population of southern Brazil

“…The performance of genotyping using the Tag SNP technique has been validated in individuals with T1DM and CD, being considered effective and less costly, allowing the performance of population screening studies (9,21,22). Our study aimed to perform the genotyping of HLA DQ2.5 and DQ8 using the Tag SNP technique in individuals with T1DM and individuals with CD in a population of southern Brazil, which confirmed the high negative predictive value of the test in the group with T1DM.…”

Analysis of 17 autoimmune disease-associated variants in type 1 diabetes identifies 6q23/TNFAIP3 as a susceptibility locus

“…Finally, we tested for an interaction with HLA using the SNPs rs7454108 and rs2187668 to tag the HLA-DRB1*04 and HLA-DRB1*03 alleles. 24 None of the genes showed any evidence for an interaction (data not shown) except for ITGAM, rs9888739 (P ¼ 3.29 Â 10 À5 for interaction test) which in a case-only analysis (7825 cases), the minor allele of which showed a protective effect in DR3/4 positive cases, OR for minor allele T ¼ 0.88 (95% CI ¼ 0.79-0.92), P ¼ 3.00 Â 10 À5 , and susceptibility in DR3/4 negative cases, OR for minor allele T ¼ 1.09 (95% CI ¼ 1.00-1.17), P ¼ 1.71 Â 10 À4 . This observation requires further support in additional datasets before we can make any conclusions.…”

The shared CTLA4-ICOS risk locus in celiac disease, IgA deficiency and common variable immunodeficiency

“…37,47 Genotyping was performed using the On Demand assay by Applied Biosystems, assay number C_58662585_10 (Applied Biosystems, Foster City, CA, USA). Samples were genotyped using the standard protocol provided by Applied Biosystems.…”