Computational protocol: FTO Genetic Variation and Association With Obesity in West Africans and African Americans

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Protocol publication

[…] The study included two sets of participants: 1) 968 unrelated African Americans (estimated African ancestry 0.78 ± 0.11) enrolled from the Washington, D.C., metropolitan area in the U.S. as part of the Howard University Family Study, and 2) 517 unrelated West Africans enrolled as control subjects as part of the Africa-America Diabetes Mellitus (AADM) Study. After obtaining written informed consent, participants underwent an interview followed by a physical examination during which weight, height, and WC were measured using standard methods. BMI was computed as weight (measured in kilograms) divided by the square of the height (measured in meters). Body composition was estimated using bioelectric impedance analysis with validated population-specific equations as previously described (). PFM was calculated as (fat mass/weight)*100. DNA was extracted from buffy coats using PureGene kits (Gentra).Based on the International HapMap Project (HapMap) YRI data, tag single nucleotide polymorphisms (SNPs) at a pairwise r2 >0.8 and with a minor allele frequency (MAF) ≥0.02 were selected for genotyping. The resulting 273 SNPs were genotyped as part of a custom Illumina panel using the Illumina GoldenGate Assay. Of the 273 SNPs, 264 were successfully genotyped, giving a locus success rate of 96.7%. The genotype call rate was 99.32%. The concordance rate for blind duplicates was 99.98%. Two SNPs deviated significantly (P < 0.001) from Hardy-Weinberg equilibrium and were excluded from further analysis, leaving 262 SNPs.MAFs were computed and LD visualized using Haploview (). Association with obesity traits was tested under an additive model with adjustment for age and sex using PLINK version 1.06. Potential population stratification was accounted for in each sample by adjusting for the first principal component derived from a set of 142 ancestry-informative SNPs genotyped in the African American subjects and by adjusting for ethnic group among the West African subjects. Each sample was analyzed separately. Then, combined analysis was done using a meta-analysis technique that computes weighted statistics for association and tests for heterogeneity, implemented in METAL (Meta Analysis Helper, available through the University of Michigan). Previous European studies have estimated that the FTO variant explains ∼1% of the phenotypic variance in BMI (–). The present study has ∼88% power (for the African American sample) and ∼63% power (for West African sample) to explain ∼1% of the variance in BMI for a SNP with an MAF of at least 0.05 at a two-tailed α level of 0.05.Given the strong prior information about the role of FTO variation in obesity, we considered our evaluation of the association between intron 1 SNPs and obesity a replication study; thus, nominal P values ≤0.05 were considered significant. For SNPs in the rest of the gene, tests of associations could be considered discovery rather than replication for which a Bonferroni-corrected P value threshold of 0.0002 (0.05/209 SNPs) would be significant. […]

Pipeline specifications

Software tools Haploview, PLINK, METAL
Databases International HapMap Project
Application GWAS