Computational protocol: Interaction of genetic markers associated with serum alkaline phosphatase levels in the Japanese population

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[…] Genome-wide genotype data from 2,994 healthy Japanese subjects were obtained from the Japan PGx Data Science Consortium (http://www.jpdsc.org/english/) database. The Japanese subjects recruited in this study all had parents and grandparents who were also Japanese. The inclusion criteria for the subjects were as follows: (1) over 20 years of age at the time of informed consent; (2) healthy Japanese adult residing in Japan; and (3) received adequate explanations of the purpose and contents of the study, volunteered of their own will and gave a written consent to participate in the study. The exclusion criteria were as follows: (1) persons with cardiovascular disease, kidney disease, liver disease or some other condition considered to render them ineligible for the study; (2) those with a blood relative within the third degree of kinship who had already participated in the study; (3) past participants in the study; and (4) persons whom the principal investigators judged to be ineligible to participate. Informed consent was obtained from all subjects for the use of their DNA for association studies, and the ethical committee of Japan PGx Data Science Consortium approved the DNA sampling study. The characteristics of the study population are shown in .The genotype data included 2,379, 855 SNPs analyzed using an Illumina HumanOmni 2.5–8 platform (San Diego, CA, USA). For quality control, SNPs with call rates of <99%, minor allele frequencies (MAFs) of <0.01, and Hardy–Weinberg equilibrium values of <5.0×10−8 (Fisher’s exact test) were excluded from the GWAS. [...] The population structure was evaluated by principal component analysis using the software package EIGENSTRAT 3.0 (Harvard Medical School, Boston, MA, USA), and the GWAS was performed with PLINK 1.07 (http://pngu.mgh.harvard.edu/~purcell/plink/). A quantile–quantile plot (Q-Q plot) was generated using R 2.15.2 (http://cran.r-project.org/index.html). The Manhattan plot of −log10 P was depicted, and linkage disequilibrium (LD) analysis was performed using Haploview (http://www.broadinstitute.org/scientific-community/science/programs/medical-and-population-genetics/haploview/haploview). The regional plot was generated with ggplot2 (http://ggplot2.org/) or LocusZoom. The pre-phasing, imputation and association analyses of the imputed genotypes were performed with MaCH, Minimac and mach2qtl (http://www.sph.umich.edu/csg/abecasis/MACH/download/), respectively. […]

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