Association of rs10272724 (T>C) near IKZF1 in 8,333 type 1 diabetes cases, 9,947 control subjects, and 3,997 families with type 1 diabetes

Sample setNo. casesNo. controlsMAF casesMAF controlsOR (95% CI)P*
Full case-control set8,3339,9470.250.280.87 (0.83–0.91)4.8 × 10−9
Analysis of genotypes generated in the current report, within sample sets used by published GWA studies
 Set 1 (T1DGC)3,8503,7720.250.280.85 (0.79–0.91)1.6 × 10−5
 Set 2 (WTCCC)1,8271,5070.250.280.84 (0.76–0.92)0.0014
 Set 3 (Swafford)2,6664,6680.260.280.90 (0.83–0.98)0.011
No. familiesMAF unaffected parentsNo. transmittedNo. not transmittedRR (95% CI)P
Families with type 1 diabetes3,9970.271,4231,6420.87 (0.81–0.93)7.6 × 10−5
Overall1.1 × 10−11
  • MAF, minor allele frequency; RR, relative risk.

  • *No evidence of deviation from a multiplicative allelic effects model was obtained (P = 0.33), so P values assuming multiplicative allelic effects are reported.

  • The overall P value was obtained by combining the P value from the case-control sets and the family transmission disequilibrium test using Fisher’s method for combined probability.

  • †This OR is subject to winner’s curse. ‡Barrett et al. (10) analyzed three datasets in their GWA study, two of which overlap with the samples in the current study. Barrett et al. used the Illumina 550 K SNP chip to genotype rs10272724 in set 1 (4). Genotypes were 99.6% concordant between the Illumina platform and TaqMan in the 3,850 cases and 3,772 controls genotyped using both technologies. Affymetrix 500 K Mapping Array genotypes for neighboring SNPs were used to impute rs10272724 genotypes in set 2 by Barrett et al. because rs10272724 was not genotyped by Affymetrix. T1DGC, Type 1 Diabetes Genetics Consortium; WTCCC, Wellcome Trust Case-Control Consortium.