eQTL Mapping of Mid-Secretory Phase Endometrial Cells

We performed an unbiased genome-wide expression quantitative trait locus (eQTL) mapping study to identify common regulatory (expression) single nucleotide polymorphisms (eSNPs) in mid-secretory endometrium, corresponding to the luteal phase of the ovarian cycle. Biopsies were collected from 58 women with two or more early pregnancy losses and 53 of these samples passed all quality control. RNA was extracted from endometrial biopsies and DNA was extracted for sequencing from blood. Gene expression data can be found at NCBI GEO Series GSE77688.]]>
This study included fifty-eight women who were undergoing clinical evaluation for recurrent pregnancy loss at the University of Chicago. These women underwent endometrial biopsies as part of the clinical evaluation. From the endometrial biopsies we collected gene expression data and from a blood draw DNA was collected. The women in the study were between the ages of 26 and 43 years and had at least two previous pregnancy losses before10 weeks gestation. Of the original fifty-eight women, fifty-two (90%) were of European ancestry, two (3%) were of Asian ancestry, and four (7%) were of African ancestry. DNA were genotyped with the Affymetrix Axiom Genome-Wide CEU 1 Array at the UCSF Genomics Core Facility. After quality control which included the removal of 4,922 SNPs with <95% genotype call rates, 503 SNPs with Hardy-Weinberg P-values ≤0.001, 336 non-autosomal SNPs, and 252,872 SNPs with minor allele frequencies <0.10, there were 370,008 SNPs remaining. Five women were excluding due to failed quality control of gene expression data and two women were excluded due to low call rates during genotyping. The remaining 53 subjects with both high quality expression and genotype data (49 European ancestry, 2 Asian ancestry, 2 African American ancestry) had SNP call rates >97%]]>