Computational protocol: Interaction between allelic variations in vitamin D receptor and retinoid X receptor genes on metabolic traits

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Protocol publication

[…] Tag SNPs for VDR and RXRG genes were chosen using the genotype data from the International HapMap collected in individuals of Northern and Western European ancestry (CEU) (HapMap data release 24/ phase II Nov08, on NCBI B36 assembly, dbSNP b126). The Haploview software V3.3 ( http://www.broadinstitute.org/haploview/haploview-downloads) was used to assess the linkage disequilibrium (LD) structure between SNPs []. Tagger software was used to select tag SNPs with the ‘pairwise tagging only’ option and an r2 threshold of >0.8 (±10 kb upstream and downstream of the genes). In the tag SNP selection, we force included the functional SNPs (VDR SNPs: rs731236 and rs2228570; RXRG SNPs: rs2134095) previously studied [-] before running tagger. There were 30 VDR and 31 RXRG tag SNPs; however, after applying the quality control criteria [call rate >99% for genotyped SNPs, average genotype probability across all individuals in the sample >90% for imputed SNPs and minor allele frequency >5%], there were only 22 VDR and 23 RXRG tag SNPs. [...] For NFBC, genomic DNA was extracted from whole blood using standard methods. All DNA samples for the Illumina Infinium 370cnvDuo array were prepared for genotyping by the Broad Institute Biological Sample Repository (BSP). The 1000 Genome imputation was carried out for the NFBC66 samples using IMPUTE2. […]

Pipeline specifications

Software tools Haploview, Tagger, IMPUTE
Databases dbSNP
Application GWAS
Chemicals Cholesterol, Nitroprusside, Triglycerides, Vitamin D