An association study using 12,041 individuals with celiac disease and 12,228 controls genotyped using ImmunoChip platform. Of those variants assayed 139,553 were found to be polymorphic (at least 2 defined genotype groups). After extensive QC, logistic regression analysis was carried out using PLINK v1.07 and 13 new celiac disease risk loci were identified bringing total number of risk loci to 40. 29 of the 54 fine-mapped signals localised to single genes or gene regulatory elements.
Samples were excluded due to :-
- Low call rate(<99.5%).
- Incompatible recorded and genotype-inferred gender.
- Evidence for a first or second-degree relative within the dataset.
Markers were excluded due to :-
- Low call rate (<99.5%).
- Deviation from Hardy-Weinberg equilibrium in controls (P< 0.0001)
- Differential missingness in no-call genotypes between cases and controls (P<0.001).
- Non-polymorphism, where only one of three expected genotype clouds were observed.
GDXHsS00009 meets the following criteria: