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ObjectiveTo evaluate HIF2α polymorphisms and glucose metabolism in a group of women with polycystic ovary syndrome (PCOS) or unexplained infertility (UI).PatientsThe infertile group (n=148) consisted of 96 women with PCOS, 52 women with UI, and176 women without infertility as a healthy control group.InterventionWe genotyped 29 single nucleotide polymorphisms (SNPs) of HIF2α by using matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS)-based genotyping technology. The genetic associations were analyzed statistically.Main outcome measuresAllele frequency, genotype distribution and haplotype analyze of the HIF2α polymorphisms were performed. Body mass index (BMI), waist circumference, uric acid (UA), high-sensitivity C-reactive protein (hsCRP), lipids, glucose and insulin tolerance - were also measured.ResultsInfertile women with PCOS had a higherBMI and waist circumference, elevated hsCRP and uric acid (UA) levels, impaired glucose tolerance, and increased levels of plasma insulin compared to UI patients and healthy women. SNP analysis of HIF2α revealed that the allele and genotype frequencies of rs4953361 were significantly associated with infertile women with PCOS. Haplotype analysis of the HIF2α polymorphism identified haplotypes TGG and TGA as being associated with infertile women with PCOS. Women with the AA genotype of rs4953361 had a significantly higher BMI and post load plasma glucose and insulin levels than those of women with the GG genotype.ConclusionInfertile women with PCOS more commonly have metabolic disturbances than those with UI. This is the first study to report an association between HIF2α polymorphisms (rs4953361) and the risk of infertile women with PCOS, not UI, in Han Chinese population. These results require replication in larger populations.In this observational study, we did not report the results of a health care intervention on human participants. The study was approved by the Human Research Ethics Committee of the First Affiliated Hospital of Chongqing Medical University. Clinical data and peripheral blood samples were collected only after explaining the objectives of the study and obtaining a signed informed consent form.