Computational protocol: Fine Mapping and Functional Analysis of the Multiple Sclerosis Risk Gene CD6

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Protocol publication

[…] The data obtained was analyzed using PLINK software (version 1.07) http://pngu.mgh.harvard.edu/purcell/plink/. Hardy-Weinberg equilibrium (HWE) test was performed to check for deviances among the control population. The strength of association was assessed via the odds ratio (OR) values in the individual datasets. The Cochran-Mantel-Haenszel (CMH) test was done on the replication and combined datasets to test for association after stratification. A test of heterogeneity (Breslow-Daystest) was performed on the replication and combined datasets to identify any heterogeneity. Haplotype analysis for the original sample set was performed using the Haploview software (version 4.2) , and the sliding window analysis and Max-T permutation P values were calculated using PLINK. […]

Pipeline specifications

Software tools PLINK, Haploview
Application GWAS
Organisms Homo sapiens
Diseases Multiple Sclerosis