GDXHsS00026
ImmunoChip
Overview
High-density genotyping study involving 10,619 individuals with ankylosing spondylitis and 15,145 controls of European, East Asian and Latin American ancestry using the Illumina ImmunoChip platform. A total of 128,935 SNPs were available for analysis after the QC process. For relatedness analysis, PLINK (v1.07) was used to calculate identity-by-descent. Association analysis and population stratification control was perfomed using linear mixed models as implemented in FaST-LMM(v1.05). Imputation was carried out with MACH and Minimac. Association at genome-wide significance (P < 5x10-8) was observed for 25 loci, including the MHC, out of which 13 were novel.
Study Paper
Study Type
Case-Control Study
Samples
| Group | Phenotype | Population | Cases | Controls | Families | Trios |
|---|---|---|---|---|---|---|
| Discovery | AS | 10619 | 15145 | - | - |
Exclusion Criteria
Samples were excluded due to:-
- Low call rate (<95%) - before merging data sets
- Low call rate (<98%) - after merging data sets
- Duplication
Markers were excluded due to:-
- Low call rate(<95%) - before merging data sets
- Low call rate(<98%) - after merging data sets
- Deviation from Hardy-Weinberg equilibrium in controls (P < 1x10-6)
- Differential missingness between collections (P < 1x10-7)