Computational protocol: Rs7206790 and rs11644943 in FTO Gene Are Associated with Risk of Obesity in Chinese School-Age Population

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Protocol publication

[…] Genomic DNA was extracted from the peripheral blood samples using the TOYOBO MagExtractor Genomic DNA Purification Kit (Toyobo, Osaka, Japan) following the manufacturer's protocol. A comprehensive SNP selection strategy was applied to select candidate SNPs in FTO . We selected candidates by tagging SNPs using a targeted approach ranging from 3 kb upstream to 3 kb downstream of FTO, including the extensively studied rs9939609 . SNPs were selected using a targeted tagging approach using the East Asians (CHB, CHD, JPT plus Asia) HapMap phase II database based on a pair-wise r2 of ≥0.8 among all common SNPs with a minor allele frequency(MAF) of ≥0.05. The FastSNP and SNP Function Predication softwares were used to predict the potential biological functions. Functional SNP changes includes nonsense mutations, mis-sense mutations, synonymous mutations, splicing regulation, transcription factor binding sites, enhancers, and microRNA sites; a total of 24 SNPs were selected in this study (), of which 23 were predicated to affect intron enhancement and one to affect the promoter/regulatory region. None of the candidate SNPs was in not in LD with known obesity-associated SNP (rs9939609, rs1421085, rs8057044 and rs8050136). Genotyping of the candidate SNPs was performed using SNPScan at Gene-sky Biotechnology Co. Ltd. Shanghai. In total, 499 cases and 489 controls were successfully genotyped. Repeated control samples were included in every genotyping plate with a concordance of more than 99%. [...] Quantitative variables with normal distributions were expressed as means ± standard deviations (SD), and those with non-normal distributed variables were expressed as medians (inter-quartile range). Categorical variables were expressed as frequencies (percentages). Hardy–Weinberg equilibrium testing for each SNP in the control group was performed with the Pearson's chi-square test using the PLINK software (version 1.0.7) . Statistical significance between case and controls was examined by two independent variable t-test for normally distributed variables or by Kruskal-Wallis tests for non-normally distributed ones. The Pearson's chi-square test was used to compare differences between categorical variables. Multivariate logistic or linear regression was used to analyze the associations between FTO genetic variants and obesity or obesity-related traits adjusted for potential confounders such as age, gender and location. HaploView and R for Windows 2.14.0 were used for Haplotype analysis of the 24 SNPs. The false discovery rate (FDR) approach was used to correct for multiple comparisons, using the PLINK software (version 1.0.7). The genetic risk score (GRS) was calculated as the sum of the number of risk alleles and the dose-response association was tested by the chi-square test for trend. All statistical analyses were performed using the SPSS statistical software for Windows, version 16.0 (SPSS Institute Inc., Chicago, Illinois). A P-value of <0.05 was considered statistically significant. […]

Pipeline specifications

Software tools FastSNP, PLINK, Haploview, SPSS
Applications Miscellaneous, GWAS
Organisms Homo sapiens