Computational protocol: Novel common variants and susceptible haplotype for exfoliation glaucoma specific to Asian population

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Protocol publication

[…] In order to manage and analyze all of the genotype data, our in-house Genoika Server System was used. The Genoika Server System comes with PLINK, R program with some packages, EIGENSTRAT, and Haploview (see URLs for the details of each software) built in, and all of the analyses were performed by use of this system. In addition, Microsoft Office Excel 2003 (Microsoft Corporation, Redmond, Washington, USA) was used for preparing the data sets and statistical analysis. The frequency of alleles in the case and control samples was compared by use of the basic allele test. The odds ratio (OR) and the upper and lower limit of the 95% confidence interval (CI) of each SNP were calculated for the allele possessing a higher frequency in the case samples than in the control samples. The HWE was evaluated by use of the chi-square test. A regional plot in was drawn by use of LocusZoom ver. 1.1 (see URLs) genetic analysis software. Q-Q plots were generated by ranking the observed values from minimum to maximum and plotting them against their expected chi-square values using the “snpStats” package ver. 1.10.0 in the R program (see URLs). [...] PLINK software v1.07, http://pngu.mgh.harvard.edu/~purcell/plink/; EIGENSTRAT software v3.0, http://genetics.med.harvard.edu/reich/Reich_Lab/Welcome.html; MACH ver. 1.0.16 and mach2dat ver. 1.1.9 softwares, http://www.sph.umich.edu/csg/abecasis/MACH/index.html; Haploview v4.2, http://www.broadinstitute.org/scientific-community/science/programs/medical-and-population-genetics/haploview/haploview; LocusZoom version 1.1, http://csg.sph.umich.edu/locuszoom/. R programs, http://www.r-project.org/; SIFT dbSNP DB (build 132), http://sift.jcvi.org/; PolyPhen-2 version 2.2.2 r398, http://genetics.bwh.harvard.edu/pph2/. […]

Pipeline specifications

Software tools PLINK, Haploview, LocusZoom, snpStats, SIFT, PolyPhen
Databases dbSNP
Applications Population genetic analysis, GWAS
Organisms Homo sapiens
Diseases Exfoliation Syndrome