Genome-wide association study for SNPs associated with PCOS in human patients

Abstract

This study investigated the possible association between single nucleotide polymorphism (SNP) sites on a genome wide level and the presence of polycystic ovary syndrome (PCOS) in a local population. Patients treated for PCOS in the outpatient clinic of the reproductive medicine center of Changzhou Maternal and Child Health Care Hospital (affiliated to Nanjing Medical University) from January of 2010 to December 2012 were selected. Female patients affected by infertility due to simple oviduct reasons or male factors, during the same period, were enrolled for the control group. A genome-wide association study was performed. Specific experimental steps included extraction of the total human DNA and optimization of PCR amplification of target genes; flight mass spectrometry for genotyping; and statistical analyses of sequencing results. By primary selection and secondary verification at two stages in the experiment, three SNP sites were found to contain significantly different allele frequencies between the patient and control groups (P<0.05): rs346795081 on THADA, rs346803513 on DENND1A and rs346999236 on TOX3. The average expression levels at the three discovered SNPs sites were significantly different between the patient and the control groups, indicating their correlation with PCOS, and the possible role of their corresponding genes on the pathogenesis of the disease.

Keywords: genetics; genome-wide association study; polycystic ovary syndrome.

Figure 1.

DNA electrophoresis of whole DNA and PCR amplicons. (A) Total genome samples of control group subjects showing successful DNA extraction. (B) PCR amplification, patient group samples, after optimization of conditions, the electrophoretic bands are clear and conform to the expected sizes. M, size marker.

Figure 2.

Plot of allelic distribution by time-of-flight mass spectrometry. The triangles indicate homozygous genes. The squares indicate heterozygous genes. The circles indicate unknown types.

Figure 3.

Difference in expression level averages at 10 SNP sites between the patient and control groups. *Significant difference between trait and control groups. SNPs, single nucleotide polymorphisms.

Figure 4.

Allele frequency of four SNP sites between the patient and the control groups. *Significant differences between groups. SNPs, single nucleotide polymorphisms.