Computational protocol: Association between Low Density Lipoprotein Receptor-Related Protein 2 Gene Polymorphisms and Bone Mineral Density Variation in Chinese Population

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Protocol publication

[…] Haplotypes were constructed from the population genotypic data by the algorithm of Stephens using Phase program version 2.0.2. The significance level for LD between the LRP2 gene markers was assessed according to the observed haplotype and allelic frequencies using Haploview version 3.2. The Lewontin's D' and LD coefficient r2 between all pairs of biallelic loci were examined. [...] Genotype frequencies were tested against Hardy-Weinberg equilibrium by the χ2 test to estimate the population homogeneity of the study subjects. To ensure unrelated individual samples, only genotype data from the 1460 parents of the nuclear families were used in the statistical analysis .The quantitative transmission disequilibrium test (QTDT) program, available at `http://www.sph.umich.edu/csg/abecasis/QTDT/, was used to determine population stratification, total family association and within-family association between SNPs and haplotypes and the BMD phenotypes in female- and male-offspring families separately. This method , , extends the trio-based TDT to quantitative trait data and uses genotypic data from available sibling and parents. Sex was not used as a covariate during analysis because only healthy sons or daughters were recruited in the study families and the effects of the parental phenotypes were already excluded.One-way ANOVA and general linear model-ANOVA (GLM-ANOVA) were also employed to test the association between genotypes and peak BMD in 330 unrelated adult daughters and 400 unrelated adult sons from the studied nuclear families. Statistical analyses were performed using the SPSS package, version 17.0 (SPSS, Chicago, IL, USA).In all above-mentioned statistical analyses, BMD values were previously adjusted by age, height and weight as covariates. P<0.05 was considered significant for all analyses. […]

Pipeline specifications

Software tools Haploview, QTDT
Application GWAS
Organisms Mus musculus
Diseases Bone Diseases, Vitamin D Deficiency
Chemicals Vitamin D