A meta-analysis of SLE was carried out. Firstly a multi-cohort GWAS was conducted for 4,036 cases and 6,959 controls resulting in 644,674 markers typed on both HumanOmni1-Quad and HumanOmni2.5 genotyping platforms. This identified 25 loci of which three were novel. The results from this meta-analysis were combined with an additional cohort of 1,165 cases and 2,107 controls, which validated the original loci identified. Loci which achieved significance (P<2.5 x 10-5 for potential novel loci and P<1x10-4 for previously reported loci) were included in a replication step in 6,925 cases and 2,018 controls . Finally a post replication analysis was carried out using all available datasets, on a custom chip, this uncovered an additional 18 loci. All association analyses were performed using SNPTEST. The final Meta analysis was imputed to 1000 genomes using SHAPEIT to prephase the data and IMPUTE (v2.2.3) to impute.
- Individual missingness > 3%.
- Identity by descent (IBD > 0.125).
- Population structure.
- SNP missingness > 3%
- MAF < 0.2 %
GDXHsS00047 meets the following criteria: