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

Lotta Koskinen, Jihane Romanos, Katri Kaukinen, Kirsi Mustalahti, Ilma Korponay-Szabo, Donatella Barisani, Maria Teresa Bardella, Fabiana Ziberna, Serena Vatta, György Széles, Zsuzsa Pocsai, Kati Karell, Katri Haimila, Róza Ádány, Tarcisio Not, Alessandro Ventura, Markku Mäki, Jukka Partanen, Cisca Wijmenga, Päivi Saavalainen

Research output: Contribution to journalArticlepeer-review


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.

Original languageEnglish
Pages (from-to)247-256
Number of pages10
Issue number4
Publication statusPublished - Apr 2009


  • Celiac disease
  • HLA
  • Human leukocyte antigen
  • Tagging SNP

ASJC Scopus subject areas

  • Immunology
  • Genetics


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