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ID

45816

Description

Principal Investigator: Carole Ober, PhD, University of Chicago, Chicago, IL, USA MeSH: Fertility,Infertility, Female,Time-to-Pregnancy https://www.ncbi.nlm.nih.gov/projects/gap/cgi-bin/study.cgi?study_id=phs001146 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.

Link

dbGaP study = phs001146

Keywords

Versions (1)
  1. 6/29/23 6/29/23 - Simon Heim
Copyright Holder

Carole Ober, PhD, University of Chicago, Chicago, IL, USA

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June 29, 2023

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Creative Commons BY 4.0
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    dbGaP phs001146 eQTL Mapping of Mid-Secretory Phase Endometrial Cells

    English

    Eligibility Criteria

    5 forms  
    1. StudyEvent: SEV1
      1. Eligibility Criteria
      2. Subject ID and consent group of participants in mid-secretory endometrium, corresponding to the luteal phase of the ovarian cycle and involved in the "Expression Quantitative Trait Locus Mapping Studies in Mid-Secretory Phase Endometrial Cells Identifies HLA-F and TAP2 as Fecundability-Associated Genes" project.
      3. Subject ID, sample ID, and sample use variable obtained from participants in mid-secretory endometrium, corresponding to the luteal phase of the ovarian cycle and involved in the "Expression Quantitative Trait Locus Mapping Studies in Mid-Secretory Phase Endometrial Cells Identifies HLA-F and TAP2 as Fecundability-Associated Genes" project.
      4. Subject ID, age, BMI, race, number of previous miscarriages at time of endometrial biopsy, and time of year of endometrial biopsy of participants in mid-secretory endometrium, corresponding to the luteal phase of the ovarian cycle and involved in the "Expression Quantitative Trait Locus Mapping Studies in Mid-Secretory Phase Endometrial Cells Identifies HLA-F and TAP2 as Fecundability-Associated Genes" project.
      5. Sample ID, genotyping center, body site where sample was obtained, analyte type, and tumor status of samples obtained from participants in mid-secretory endometrium, corresponding to the luteal phase of the ovarian cycle and involved in the "Expression Quantitative Trait Locus Mapping Studies in Mid-Secretory Phase Endometrial Cells Identifies HLA-F and TAP2 as Fecundability-Associated Genes" project.
    Inclusion and exclusion criteria
    Description

    Inclusion and exclusion criteria

    Alias
    UMLS CUI [1,1]
    C1512693
    UMLS CUI [1,2]
    C0680251
    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.
    Description

    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.

    Data type

    boolean

    Alias
    UMLS CUI [1,1]
    C0947630
    UMLS CUI [1,2]
    C1512693
    UMLS CUI [1,3]
    C0043210
    UMLS CUI [1,4]
    C4084924
    UMLS CUI [1,5]
    C2921106
    UMLS CUI [2,1]
    C1510477
    UMLS CUI [2,2]
    C0017262
    UMLS CUI [2,3]
    C0190979
    UMLS CUI [2,4]
    C0012854
    UMLS CUI [3,1]
    C0001779
    UMLS CUI [3,2]
    C0687675
    UMLS CUI [3,3]
    C0032979
    UMLS CUI [4,1]
    C1257905
    UMLS CUI [4,2]
    C1257906
    UMLS CUI [4,3]
    C1257891
    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%
    Description

    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%

    Data type

    boolean

    Alias
    UMLS CUI [1,1]
    C0012854
    UMLS CUI [1,2]
    C1285573
    UMLS CUI [1,3]
    C4085938
    UMLS CUI [1,4]
    C5239481
    UMLS CUI [1,5]
    C1707515
    UMLS CUI [2,1]
    C0034378
    UMLS CUI [2,2]
    C0752046
    UMLS CUI [2,3]
    C1881032
    UMLS CUI [2,4]
    C0017270
    UMLS CUI [3,1]
    C0043210
    UMLS CUI [3,2]
    C2828389
    UMLS CUI [3,3]
    C0034378
    UMLS CUI [3,4]
    C5200924
    UMLS CUI [3,5]
    C0017262
    UMLS CUI [4,1]
    C1257905
    UMLS CUI [4,2]
    C1257906
    UMLS CUI [4,3]
    C4540921
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    Similar models

    Eligibility Criteria

    5 forms
    1. StudyEvent: SEV1
      1. Eligibility Criteria
      2. Subject ID and consent group of participants in mid-secretory endometrium, corresponding to the luteal phase of the ovarian cycle and involved in the "Expression Quantitative Trait Locus Mapping Studies in Mid-Secretory Phase Endometrial Cells Identifies HLA-F and TAP2 as Fecundability-Associated Genes" project.
      3. Subject ID, sample ID, and sample use variable obtained from participants in mid-secretory endometrium, corresponding to the luteal phase of the ovarian cycle and involved in the "Expression Quantitative Trait Locus Mapping Studies in Mid-Secretory Phase Endometrial Cells Identifies HLA-F and TAP2 as Fecundability-Associated Genes" project.
      4. Subject ID, age, BMI, race, number of previous miscarriages at time of endometrial biopsy, and time of year of endometrial biopsy of participants in mid-secretory endometrium, corresponding to the luteal phase of the ovarian cycle and involved in the "Expression Quantitative Trait Locus Mapping Studies in Mid-Secretory Phase Endometrial Cells Identifies HLA-F and TAP2 as Fecundability-Associated Genes" project.
      5. Sample ID, genotyping center, body site where sample was obtained, analyte type, and tumor status of samples obtained from participants in mid-secretory endometrium, corresponding to the luteal phase of the ovarian cycle and involved in the "Expression Quantitative Trait Locus Mapping Studies in Mid-Secretory Phase Endometrial Cells Identifies HLA-F and TAP2 as Fecundability-Associated Genes" project.
    Name
    Type
    Description | Question | Decode (Coded Value)
    Data type
    Alias
    Item Group
    Inclusion and exclusion criteria
    C1512693 (UMLS CUI [1,1])
    C0680251 (UMLS CUI [1,2])
    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.
    Item
    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.
    boolean
    C0947630 (UMLS CUI [1,1])
    C1512693 (UMLS CUI [1,2])
    C0043210 (UMLS CUI [1,3])
    C4084924 (UMLS CUI [1,4])
    C2921106 (UMLS CUI [1,5])
    C1510477 (UMLS CUI [2,1])
    C0017262 (UMLS CUI [2,2])
    C0190979 (UMLS CUI [2,3])
    C0012854 (UMLS CUI [2,4])
    C0001779 (UMLS CUI [3,1])
    C0687675 (UMLS CUI [3,2])
    C0032979 (UMLS CUI [3,3])
    C1257905 (UMLS CUI [4,1])
    C1257906 (UMLS CUI [4,2])
    C1257891 (UMLS CUI [4,3])
    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%
    Item
    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%
    boolean
    C0012854 (UMLS CUI [1,1])
    C1285573 (UMLS CUI [1,2])
    C4085938 (UMLS CUI [1,3])
    C5239481 (UMLS CUI [1,4])
    C1707515 (UMLS CUI [1,5])
    C0034378 (UMLS CUI [2,1])
    C0752046 (UMLS CUI [2,2])
    C1881032 (UMLS CUI [2,3])
    C0017270 (UMLS CUI [2,4])
    C0043210 (UMLS CUI [3,1])
    C2828389 (UMLS CUI [3,2])
    C0034378 (UMLS CUI [3,3])
    C5200924 (UMLS CUI [3,4])
    C0017262 (UMLS CUI [3,5])
    C1257905 (UMLS CUI [4,1])
    C1257906 (UMLS CUI [4,2])
    C4540921 (UMLS CUI [4,3])
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