Common variant within the FTO gene, rs9939609, obesity and type 2 diabetes in population of Karachi, Pakistan.

Aim: To determine the effect of genetic variants within the FTO gene (rs9939609) on obesity related traits and type 2 diabetes in South Asian population of Karachi, Pakistan.

Methods: A case-control study was conducted at Baqai Institute of Diabetology and Endocrinology (BIDE), Baqai Medical University situated in Karachi. A total of 296 patients with known type 2 diabetes and 198 controls aged greater than and equal to 45 years were recruited. The Anthropometric, clinical and biochemical data was collected on a structured questionnaire. Single nucleotide polymorphism (SNP) in FTO gene was identified by Amplification Refractory Mutation System-Polymerase Chain Reaction (ARMS-PCR). Association between the single nucleotide polymorphism and categorical variables such as type 2 diabetes and obesity category was tested through logistic regression analysis.

Results: We observed a strong association of the minor allele A at rs9939609 with type 2 diabetes. Significant difference was observed in frequency of FTO genotype when diabetic subjects were compared with controls in co dominant, dominant and recessive models. This association remained significant even after adjusting for body mass index (BMI) and for waist circumference. The frequency of homozygous risk Alleles (AA) was found to be higher in obese & overweight (≥ 23 kg/m(2)) and females with central obesity in our study population. The association of FTO variant with BMI and central obesity does not reach to statistical significance.

Conclusion: In the study population of South Asian ancestry, variants of the FTO gene predispose to type 2 diabetes, but not entirely through their effect on BMI.