High-density genotyping study involving 5,850 individuals with systemic sclerosis (SSc) and 9,401 unrelated, healthy controls of European ancestry using the Illumina ImmunoChip platform. A total of 126,270 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 implemented in IMPUTE2 with the use of the 1000 Genomes Phase 3 reference panel. Association at genome-wide significance (P < 5x10-8) was observed for 3 novel loci, as well as validating previously reported SSc risk loci (including the HLA region).
- Inferred ethnicity by principal-component analysis
- Call rate ≤ 95%
- Deviation from Hardy-Weinberg equilibrium in controls (P < 1x10-5)
GDXHsS00034 meets the following criteria: