In discovery phase genotyping was carried out using immunochip platform on 14,498 Multiple sclerosis cases and 24,091 controls of european ancestry. Data was QC'ed and then analysed using PLINK by 11-country strata, based on ascertation. A replication phase was carried out using 14,802 cases and 26,703, controls genotyped in previous GWAS studies, leveraging imputation of phase 1a 1000 genomes data (BEAGLE). In total after combining discovery and replication phases in a meta-anlysis, 48 novel susceptibility variants were discovered in 45 discrete loci.
- Reported gender and genotyping gender mismatch
- Call rate < 95 %
- Heterozygosity > 3 SD from mean
- Excessive identity by descent.
- Population outliers identified through PCA analysis
- Mendelian error within family
- Call rate < 98%
- HWE deviation p <= 1 x 10-5
- Differential missingness between cases and controls
- Monomophic SNPs
GDXHsS00030 meets the following criteria: