Cost-effective HLA typing with tagging SNPs predicts celiac disease risk haplotypes in the Finnish, Hungarian, and Italian populations.

Human leukocyte antigen (HLA) genes, located on chromosome 6p21.3, have a crucial role in susceptibility to various autoimmune and inflammatory diseases, such as celiac disease and type 1 diabetes. Certain HLA heterodimers, namely DQ2 (encoded by the DQA1*05 and DQB1*02 alleles) and DQ8 (DQA1*03 and DQB1*0302), are necessary for the development of celiac disease. Traditional genotyping of HLA genes is laborious, time-consuming, and expensive. A novel HLA-genotyping method, using six HLA-tagging single-nucleotide polymorphisms (SNPs) and suitable for high-throughput approaches, was described recently. Our aim was to validate this method in the Finnish, Hungarian, and Italian populations. The six previously reported HLA-tagging SNPs were genotyped in patients with celiac disease and in healthy individuals from Finland, Hungary, and two distinct regions of Italy. The potential of this method was evaluated in analyzing how well the tag SNP results correlate with the HLA genotypes previously determined using traditional HLA-typing methods. Using the tagging SNP method, it is possible to determine the celiac disease risk haplotypes accurately in Finnish, Hungarian, and Italian populations, with specificity and sensitivity ranging from 95% to 100%. In addition, it predicts homozygosity and heterozygosity for a risk haplotype, allowing studies on genotypic risk effects. The method is transferable between populations and therefore suited for large-scale research studies and screening of celiac disease among high-risk individuals or at the population level.

The prevalence of celiac disease among family members of celiac disease patients.

INTRODUCTION: Celiac disease (CD) is more common in certain risk groups. Family members of known celiac patients represent the most important group. Serological screening enables us to detect patients before they develop serious complications. HLA typing has also proven to be a valuable diagnostic tool, especially in excluding the disease. METHODS: To assess the prevalence of CD among family members, we screened 106 first-degree relatives (73 parents, 33 siblings; mean age 27.9 years) of 45 celiac patients in NE Slovenia. We analysed antigliadin (AGA) and antiendomysium (EMA) antibodies. Levels of IgG and IgAAGA were determined using the ELISA method, and EMA using indirect immunofluorescence. Serologically positive patients were recalled for intestinal biopsy and were HLA typed. Intestinal biopsy was performed by peroral aspiration capsule or during upper GI endoscopy. Biopsy specimens were examined histologically. RESULTS: Six family members (5.67%) were both AGA IgG and EMA positive, and one (0.94%) was only EMA positive. All were either HLA DQ2 or DQ8 positive. Nine family members (8.49%) were only AGA IgG positive, two of them lacked the HLA DQ susceptibility alleles. Intestinal biopsy was performed in six family members, and the diagnosis of CD confirmed in five. All were both AGA IgG and EMA positive. They were either symptom-free or had only mild gastrointestinal symptoms, and carried the known HLA DQ risk alleles. The minimum prevalence of CD among family members in NE Slovenia can therefore be estimated at 4.72%. DISCUSSION: The prevalence of CD among first-degree relatives is much higher than the prevalence of the disease in the general population. Most of these patients have an atypical form of the disease and would therefore be overlooked without an active search. Serological testing is recommended for all first-degree relatives of CD patients; they should also undergo HLA typing to detect those whose HLA phenotype is consistent with CD. This approach can also help in excluding individuals who do not need further diagnostic procedures for CD.

HLA types in celiac disease patients not carrying the DQA1*05-DQB1*02 (DQ2) heterodimer: results from the European Genetics Cluster on Celiac Disease.

Genetic susceptibility to celiac disease is strongly associated with HLA-DQA1*05-DQB1*02 (DQ2) and HLA-DQA1*03-DQB1*0302 (DQ8). Study of the HLA associations in patients not carrying these heterodimers has been limited by the rarity of such patients. This European collaboration has provided a unique opportunity to study a large series of such patients. From 1008 European coeliacs, 61 were identified who neither carry the DQ2 nor DQ8 heterodimers. Fifty seven of these encoded half of the DQ2 heterodimer. The remaining 4 patients had a variety of clinical presentations. Three of them carried the DQA1*01-DQB*05 haplotype as did 20/61 of those carrying neither DQ2 nor DQ8. This may implicate a role of the DQA1*01-DQB*05 haplotype. None of these four patients carried the DQB1*06 allele that has previously been reported in this sub-group of patients. Of the 16 DQ2 heterodimer negative patients without DRB1*04 or DRB1*07 haplotypes, it was inferred that none encoded the previously implicated DRB4 gene as none had a DRB1*09 haplotype. These results underline the primary importance of HLA-DQ alleles in susceptibility to celiac disease, and the extreme rarity of celiac patients carrying neither the DQ2 or DQ8 heterodimers nor one half of the DQ2 heterodimer alone.

A collaborative European search for non-DQA1*05-DQB1*02 celiac disease loci on HLA-DR3 haplotypes: analysis of transmission from homozygous parents.

The HLA-DQA1*05 with DQB1*02 alleles are a major risk factor for celiac disease (CD). To search for additional human leukocyte antigen (HLA) risk factors, we looked on the DR3-DQ2 risk haplotype, selected because it carries both DQ risk alleles in cis and is the more represented among CD patients. In a European consortium, we identified 109 families with a parent homozygous for DQA1*05-DQB1*02. We typed ten microsatellites in the extended HLA complex, and applied the homozygous-parent transmission disequilibrium test (HPTDT) and extended-TDT to transmissions from homozygous parents. These methods eliminate confounding due to linkage disequilibrium between candidate disease loci and the known risk factor DQA1*05-DQB1*02, and are favorable when sufficient families are available. We did not find evidence of association with any single marker or allele, although weak evidence for additional risk was observed, represented by preferential transmission of six adjacent markers. We tested the largest ever reported HPTDT population in CD, providing unprecedented power. We did not find significant evidence of additional risk-modifying factors on the DR3 haplotype, independent of DQA1*05-DQB1*02, although a weak tendency was observed for the B8-DR3 haplotype. This effect should be tested in large populations with significant representations of both B8-DR3 and non-B8 DR3 haplotypes.