Computational protocol: Evaluation of Genetic Association of the INK4 Locus with Primary Open Angle Glaucoma in East Indian Population

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Protocol publication

[…] Power calculations were done for ‘A' allele of rs1063192 which is the most replicated SNP in different reported studies by Genetic power calculator software (http://pngu.mgh.harvard.edu/~purcell/gpc/).The relative risk was kept constant as 1.8 (for homozygous genotype) and 1.2 (for heterozygous genotype) as reported by Fan B.J. et al () and allele frequency of respective populations were taken as parameters. Chi-square test of association was performed using PLINK software. The regional plots were generated by an online available Locus Zoom tool (http://csg.sph.umich.edu/locuszoom/). LD calculations and haplotype association were performed using haploview software version 4. […]

Pipeline specifications

Software tools PLINK, LocusZoom, Haploview
Application GWAS
Organisms Homo sapiens
Diseases Neoplasms