Computational protocol: CRP Genotypes Predict Increased Risk to Co-Present with Low Vitamin D and Elevated CRP in a Group of Healthy Black South African Women

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Protocol publication

[…] As previously mentioned, 25(OH)D concentrations were available for 660 randomly selected women. Only individuals for whom 25(OH)D concentrations, CRP concentrations, CRP genetic data, and all anthropometric markers were available were included in our statistical analyses (n = 534). Furthermore, women with 25(OH)D or natural log-transformed (ln)CRP concentrations greater than 5 standard deviations were excluded as outliers. The final number of participants was 505. Statistical analyses were conducted in R [].Numeric variables were visually inspected for normality as well as measures of skewness. Non-parametric variables (CRP) were log-transformed, yet still reported as median and interquartile ranges. Women were grouped as two phenotypes: the case phenotype including individuals with deficient/insufficient 25(OH)D (<75 nmol/L) and elevated CRP (>3 mg/L), and a control phenotype consisting of the remaining volunteers. Pairwise comparisons using the Wilcoxon ranked-sum test were performed to identify significant differences in stratified continuous variables. Comparative tables were created with the compare Groups library in R [] using non-parametric methods. Spearman correlations were used for testing associations between numeric variables. Multivariate linear models predicting lnCRP concentrations from continuous 25(OH)D values were constructed using backward step-wise linear regressions and evaluated based on the Akaike Information Criterion (AIC). Adherence to Hardy–Weinberg equilibrium (HWE) was tested by a chi-squared (χ2) test using SNPassoc, and linkage disequilibrium (LD) was calculated using the LDheatmap library of the R package.Variables identified in regression analyses were evaluated for co-linearity. Possible environment–SNPs interaction was determined using SNPassoc [] while including covariates obtained from the linear regression model. To determine whether CRP SNPs influence vitamin D status, 25(OH)D was used as the dependent variable. To evaluate the risk associated with certain CRP SNPs to present with the phenotype of low 25(OH)D combined with elevated CRP concentrations, the case and control phenotypes were entered as dependent variables.Where applicable, p-values were adjusted using the methods suggested by Bonferroni. Significance was defined as an α level of 0.05. […]

Pipeline specifications

Software tools SNPassoc, LDheatmap
Application GWAS
Organisms Homo sapiens
Diseases Adrenal Insufficiency, Cardiovascular Diseases, Vitamin D Deficiency
Chemicals Vitamin D