A 2 stage genome-wide meta analysis including 6 T1D cohorts was conducted. In the discovery phase, using imputation (Mach 1.0) with HapMap CEU population, a total of ~2.4M variants were analysed using logistic regression on Affymetrix platforms and ~2M using Ilumina platforms. PLINK was utilised to combine samples across platforms using inverse-variance meta-analysis. After QC and a fixed effect meta-analysis , 53 variants were chosen for replication in a parent trio cohort using TDT as implemented in PLINK. Having combined discovery and replication meta-analysis p-values using Fisher's method (Haploview),three variants achieved genome-wide significance (P <10-8) and identified genomic regions of T1D susceptibility that had not been previously reported.
- Genotyping call rate < 98%
- Cryptic relatedness
- MAF < 1%
- Genotyping call rate < 95 %
- Deviation from HWE P <= 0.00001
GDXHsS00001 meets the following criteria: