GDXHsS00032
Immunochip
Overview
Fine mapping was performed on Immunochip platform, in 3789 cases with Primary sclerosing cholangitis (PSC) and 25079 controls of European ancestry across 130422 markers. PLINK (version 1.07) was used to calculate genotype call rate and heterozygosity call rate. Aberrant (clustering algorithm) was used to identify outlying samples. Principal-component analysis (PCA) was performed using SMARTPCA (Eigenstrat). Imputation was performed using IMPUTE2 with the 1000 Genomes Project Phase 1 reference panel. Association analysis was performed using a linear mixed model as implemented in MMM. This study reported 12 non-HLA genome-wide significant (P < 5 x 10-8) loci, out of which 9 are novel.
Study Paper
Study Type
Case-Control Study
Samples
| Group | Phenotype | Population | Cases | Controls | Families | Trios |
|---|---|---|---|---|---|---|
| Discovery | PSC | 3789 | 25079 | - | - |
Exclusion Criteria
Samples:
Initially SNPs with call rate < 80% were removed, followed by removing samples that have
- Missingness/heterozygosity outliers
- Ancestry outliers
- Duplicates (identity by descent ≥ 0.9)
SNP:
- Deviation from Hardy-Weinberg equilibrium (P < 10-5)
- Differential missingness between cases and controls (P < 10-5)
- Call rate < 98%
- Minor allele frequency < 0.1%
- Poor signal intensity clusters