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

... DQ2.2 but also included the relatively infrequent DQ4 allele. We therefore decided to tag DQ4 as well (rs4713586) making it possible to call a person DQ2.2 when the alleles were positive for DQ2.2 and negative for DQ4. This led to three tag SNPs being needed for the prediction of DQ2.2, with an overall sensitivity of 0.992, a specificity of 0.998 and a PPV of 0.977. Only four of the 1448 tested chromosomes gave false results (0.28%). The tag SNP selected for prediction of DQ2.5 (rs2187668) showed an

... Positive predicting allele(s) (freqCEU) tag SNP Negative predicting allele DQ2.2 0201 0202 7 rs2395182, rs7775228 T (0.71), G (0.10) rs4713586 G (0.025) DQ2.5 0501 0201 3 rs2187668 T (0.09) DQ7 0505 0301 5 rs4639334 A (0.09) DQ8 0301 0302 4 rs7454108 G (0.18) a) DQ molecules, the corresponding HLA-DQA1 * and -DQB1 * alleles, with the DR type and the tag SNPs. A person that has the T,G,A haplotype for rs2395182, rs7775228, rs4713586, is a DQ2.2. A person that has the T,G,G haplotype for rs2395182, rs7775228, rs4713586, is not a DQ2.2 but a DQ4. Freq(CEU) frequency of annotated alleles in CEU HapMap population Tag SNP selection was based on genotype data collected in the classical HLA genes and >7,500 common SNP and deletion-insertion polymorphisms across the extended human MHC region [20] . We used Tagger [29] to derive SNP-based tests to capture each DQ type in the extended CEU analysis panel (Utah residents with northern and western European ancestry). We first found the SNPs that have the

... (rs2395182, rs4713586, rs4639334) or Assay by Design (rs7454108, rs7775228, rs2187668) from Applied Biosystems (Applied Biosystems, Foster City, California, USA) (see Table S1 for assay numbers or primer sequences and their allele labeling). Samples were genotyped using the manufacturer's instructions and analyzed on an ABI PRISM 7900 HT system (Applied Biosystems). All SNPs were typed using the standard amplification protocol as supplied by Applied Biosystems. We obtained end-point measurements for the

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SNP: rs4713586

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