Association of FTO and IRX3 genetic variants to obesity risk in north India

Abstract

Background: Obesity is an increasingly important health problem worldwide as well as in developing countries like India. Recent genetic studies suggest that obesity associated FTO and IRX3 are functionally linked and many effects due to genetic variants in FTO gene act through IRX3.

Aim: To evaluate the association of FTO and IRX3 genetic variants towards obesity risk.

Subjects and methods: North Indian individuals categorised as non-obese (BMI < 30 kg/m²) and obese (BMI ≥ 30 kg/m²) were selected. FTO rs8050136, rs1421085, rs9939609, rs17817449 and IRX3 rs3751723 were genotyped by means of validated Taqman® allelic discrimination to evaluate their association with obesity by means of single locus logistic regression by SPSS ver. 19 and multi-locus linkage and haplotype analysis by SNPStats and gene–gene interaction with Generalised Multifactor Dimensionality Reduction (GMDR) ver.6.

Results: In single locus analysis, FTO rs8050136 CA (p = 0.0001; OR (95% CI) = 2.4 (1.7–3.4) and AA (p = 0.0001; OR (95% CI) = 3.1 (1.9–5.2); FTO rs1421085 TA (p = 0.0001; OR (95% CI) = 2.1 (1.4–3.0) and AA (p = 0.0001; OR (95% CI) = 3.0 (1.8–5.0); FTO rs9939609 TC (p = 0.0001; OR (95% CI) = 2.1 (1.5–3.1) and CC (p = 0.0001; OR (95% CI) = 4.2 (2.5–7.3) along with TG (p = 0.001; OR (95% CI) = 2.1 (1.3–3.2) and GG (p = 0.021; OR (95% CI) = 3.8 (1.2–11.8) genotypes of FTO rs17817449 with GT (p = 0.0001; OR (95% CI) = 2.1 (1.5–3.1) and TT (p = 0.012; OR (95% CI) = 3.3 (1.8–3.6) genotypes of IRX3 rs3751723 were significantly associated with obesity. In multi-locus analysis, SNPs of FTO and IRX3 were in strong linkage disequilibrium and in haplotype and GMDR analysis the SNPs were significantly associated with obesity risk (p < 0.05).

Conclusion: This is the first study to reveal that genetic variants of both FTO and IRX3 genes are in high linkage disequilibrium (LD) and are associated with obesity risk in North Indians.

• Linkage disequilibrium
• haplotypes
• generalised multifactor dimensionality reduction

Acknowledgements

The authors acknowledge all the participants of the study and the Department of Biotechnology (DBT), New Delhi, India for its financial assistance to carry out the research work [SAN No 102/IFD/SAN/PR-2015/2010–2011 dated 9 December 2010].

Declaration of interest

The authors report no conflicts of interest. The authors alone are responsible for the content and writing of the paper.