Computational protocol: Associations between microRNA binding site SNPs in FGFs and FGFRs and the risk of non-syndromic orofacial cleft

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Protocol publication

[…] Common SNPs (minor allele frequency, MAF ≥ 5%) of 18 FGFs (FGF1–FGF10 and FGF16–FGF23) and 4 FGFRs (FGFR1-FGFR4) of Homo sapiens in Chinese Han population based on the dbSNP database ( and HapMap Project database ( were screened from gene regions (including ± 2kb). Then, in silico bioinformatics predictions from the SNPinfo Web Server ( and mirSNP ( were collectively applied to select the miRNA binding site SNPs. Linkage disequilibrium (LD) analysis with an r2 threshold of 0.80 was applied to filter these SNPs. Finally, ten SNPs were analyzed in our study. The characteristic information of the final identified SNPs as well as their corresponding potential binding miRNAs are listed in . [...] Pairwise linkage disequilibrium (LD) was computed as r2 for all SNPs by the Haploview program. Student’s t test was employed for continuous values. The gender distribution between cases and controls was evaluated with a two-sided Chi-square test, and the HWE among the controls was calculated using a goodness-of-fit Chi-square test. All results were two-sided. P < 0.05 was considered statistically significant. All tests were performed with version 9.1 of the SAS® software (SAS Institute Inc., Cary, NC, USA).The association between the SNPs and the risk of NSOC and subgroups was measured by the odds ratio (OR) and 95% confidence interval (95% CI). Four kinds of genetic models were adopted. In , if T is the variant of interest (the mutant allele), and C is the dominant allele, a 2 by 2 table and an unconditional logistic regression with one degree of freedom could be used to determine statistical significance of allele frequencies under the assumption of an allelic comparison. A heterozygous comparison presented the comparison of CT genotypes with CC genotypes. Likewise, comparison of CC with TT genotypes was assumed as homozygous comparison. Scores of 0, 1, and 2 assigned to genotype CC, CT, and TT respectively and ORs calculated by unconditional logistic regression model was a test for association between the variant allele and the disease named as additive model. […]

Pipeline specifications

Software tools SNPinfo, Haploview
Databases dbSNP MirSNP
Application GWAS
Organisms Homo sapiens