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Background Polycystic ovary syndrome (PCOS) is among the most common complex genetic endocrinopathy, and its etiology and pathophysiology remain controversial.  FTO  is a large highly polymorphic gene and was coined as the first locus associated with adiposity. The association of the intronic variant  FTO  rs9939609 or  FTO  rs1421085 with PCOS has been controversial and unclear, mainly due to ethnic differences among populations. The present study aims to investigate the association of FTO rs9939609 or FTO rs1421085 polymorphisms with PCOS in Saudi Arabian women. Results A total of 98 PCOS patients and 99 healthy females were included in this study. PCR and genotyping (TaqMan®SNP Genotyping Assay) were employed. For  FTO  rs9939609, the genotype  TA  and the recessive model ( TA  +  AA ) in PCOS patients were significantly different compared with control subjects ( p  = 0.008 and  p  = 0.007, respectively). The allele frequency of the  FTO  rs9939609 gene variant was associated significantly ( p  = 0.027) with PCOS, suggesting that the A allele is a risk factor for PCOS susceptibility. However, for the  FTO  rs1421085 variant, the genotype and allele distributions did not differ significantly between PCOS patients and controls ( p  &gt; 0.05). Conclusions This is the first report to study the association of  FTO  rs9939609 and  FTO  rs1421085 with PCOS in Saudi women. Results suggest that the  FTO  rs9939609 gene variant could be a genetic predisposing factor for PCOS Saudi women.

Association of FTO gene variants rs9939609 and rs1421085 with polycystic ovary syndrome