Computational protocol: Polymorphisms in CaSR and CLDN14 Genes Associated with Increased Risk of Kidney Stone Disease in Patients from the Eastern Part of India

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Protocol publication

[…] Allelic and genotypic associations of each SNP were tested by using chi-squared or Fisher exact test where appropriate. Hardy-Weinberg equilibrium of each SNP in the case and control individuals were also examined using a χ2 test. To calculate any statistically significant difference of continuous independent variables like age, serum calcium within the control and patient groups, we used Student t-test. Mann-Whitney U test was used to analyze non-parametric variables. All tests were done using Graphpad Instat software (Graphpad Instat software, San Diego, CA) and SNPassoc version 1.8‐1 software (Catalan Institute of Oncoloy, Barcelona, Spain). The odds ratio and 95% confidential intervals were also calculated using the same software. Linkage disequilibrium (LD) pattern of SNPs in three genes was analyzed using Haploview 4.2. A Bonferroni correction was applied to multiple testing. Power was estimated using genetic power calculator [].The combined effect of the four SNPs on the risk of KSD was determined through allele dosage analysis by categorizing the subjects based on the number of “effective” risk alleles. We computed the “effective” number of risk alleles harbored by each individual using a weighted score: k∑i=1kWiRi∑i=1kWi Where, k is the number of SNPs, Ri is the number of risk alleles at the ith locus and Wi is the logarithm of the odds Ratio (OR) of the risk allele at the ith locus, i = 1,2,…, k. The analysis included only those individuals in whom genotypes at all four SNPs were available. Since the effect sizes (defined by the SNP-specific ORs) were not uniform, the allele dosage score of an individual was computed by the weighted mean of the proportion of risk alleles at the four SNPs (i.e., two for two risk alleles, one for one risk allele, and 0 for no risk allele) with weights as the relative log ORs of different SNPs. The “effective” number of risk alleles was obtained as the allele dosage score multiplied by 4 (number of SNPs). Considering subjects with two or fewer numbers of “effective” risk alleles as the reference group, ORs and P values for every unit increase in the number of “effective” risk alleles were calculated. […]

Pipeline specifications

Software tools SNPassoc, Haploview
Application GWAS
Organisms Homo sapiens
Diseases Kidney Diseases
Chemicals Calcium, Vitamin D