2,861 primary billiary cirrhosis cases from UK PBC Consortium and 8,514 UK controls were genotyped using iSelect Illumina Infinium array (ImmunoChip), optiCall was used to call variants. Imputation, in order to include additional genotypes was carried out using data from 1000 genomes project and computed using IMPUTE2. Association statistics were calculated using PLINK v1.07. In total 16 known (including MHC) and three novel loci were reported (P < 5 x 10-8).
SNPs with the following properties were excluded from analysis.
- HWE P < 1 x 10-6.
- MAF < 0.1.
- Call rate > 98% or call rate between case/control significanly different (P < 10-5).
Samples with the following properties were excluded from analysis
- < 98% call rate
- heterozygosity > 3 s.d. from the mean.
- For samples with IBD > 18.75% sample with lower call rate removed.
- Non-european ancestry.
GDXHsS00020 meets the following criteria: