ID
45406
Beschrijving
Principal Investigator: Susan E. Clare, MD, PhD, Indiana University School of Medicine, Indianapolis, IN, USA MeSH: Menstrual Cycle,Breast https://www.ncbi.nlm.nih.gov/projects/gap/cgi-bin/study.cgi?study_id=phs000644 The Susan G. Komen for the Cure® Tissue Bank at the IU Simon Cancer Center [www.komentissuebank.iu.edu] (KTB) was established expressly for the prospective collection of normal, healthy breast tissue from volunteer donors. Blood is also obtained from donors at the time of donation and is processed for serum, plasma and peripheral blood leukocyte DNA. Specimens are annotated and data includes age, race, ethnicity, personal health history, family cancer history, medication usage at the time of donation, and breast cancer risk factors. Premenopausal donors to the KTB were identified by a query of the Bank's database. Hematoxylin and eosin stained sections of the formalin-fixed paraffin-embedded tissue of the identified donors were reviewed and tissue was graded on the basis of the abundance of epithelium within the section. Only tissue containing abundant epithelium was considered for this study. Based on dates, the specimens of nine women in the follicular phase of the menstrual cycle and five in the luteal phase were chosen. Six donors using hormonal contraception at the time of donation were also included. Whole blood obtained from 19 of the 20 donors at the time of tissue donation was available and it was processed for serum. Estradiol, estriol, luteinizing hormone and progesterone concentrations were determined by the Indiana University Health Pathology Laboratory using a Beckman Unicel DxI 800 Immunoassay System. The phase of the menstrual cycle was verified by serum progesterone concentration. The epithelium of these 20 specimens was microdissected from multiple 8 micron frozen tissue sections. Total RNA extracted from the tissue was subsequently depleted of rRNA via locked nucleic acid probes. This enabled profiling of both poly-A and non-poly-A RNA species. Barcoded cDNA libraries from the 20 normal breast epithelia were prepared and sequenced on an Applied Biosystems (AB) SOLiD3 or SOLiD 4 platform. RNA-seq reads for each sample were then mapped to the human genome (hg19) using the LifeScope software version 2.5.1 (Life Technologies, Foster City, CA) and BAM (Binary Alignment/Map) files generated. Read counts for each gene were derived from the output BAM files using the RefSeq database (UCSC Genome Brower) as the gene model.
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- 19-11-22 19-11-22 - Simon Heim
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Susan E. Clare, MD, PhD, Indiana University School of Medicine, Indianapolis, IN, USA
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19 november 2022
DOI
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Creative Commons BY 4.0
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dbGaP phs000644 The Effect of the Menstrual Cycle on the Normal Human Breast
Eligibility Criteria
- StudyEvent: SEV1
- Eligibility Criteria
- This data table contains subject IDs, consent group information, subject aliases, and affection status.
- This data table contains mapping of study subject IDs to sample IDs and sample aliases. Samples are the final preps submitted for genotyping, sequencing, and/or expression data. For example, if one patient (subject ID) gave one sample, and that sample was processed differently to generate 2 sequencing runs, there would be two rows, both using the same subject ID, but having 2 unique sample IDs. The data table also includes sample use.
- This subject phenotype table includes measurements of race, height, weight, age of donor, and first degree relatives diagnosed with breast cancer. Specifically relating to the menstrual cycle, variables were collected for the day of the first menstrual cycle, phase of the menstrual cycle, hormone levels (n=4 variables; estradiol, estriol, progesterone, and luteinizing hormone), and use of hormonal contraception and type.
- This sample attributes table includes body site where sample was extracted, analyte type, histological type, tumor status, genotyping and sequencing centers, manufacturer and kit information (n=7 variables; laser capture, RNA measurement, ribosomal depletion, library prep, and sequencing platform), RNA total, concentration, volume, and mass, sequencing chemistry and read length.
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Eligibility Criteria
- StudyEvent: SEV1
- Eligibility Criteria
- This data table contains subject IDs, consent group information, subject aliases, and affection status.
- This data table contains mapping of study subject IDs to sample IDs and sample aliases. Samples are the final preps submitted for genotyping, sequencing, and/or expression data. For example, if one patient (subject ID) gave one sample, and that sample was processed differently to generate 2 sequencing runs, there would be two rows, both using the same subject ID, but having 2 unique sample IDs. The data table also includes sample use.
- This subject phenotype table includes measurements of race, height, weight, age of donor, and first degree relatives diagnosed with breast cancer. Specifically relating to the menstrual cycle, variables were collected for the day of the first menstrual cycle, phase of the menstrual cycle, hormone levels (n=4 variables; estradiol, estriol, progesterone, and luteinizing hormone), and use of hormonal contraception and type.
- This sample attributes table includes body site where sample was extracted, analyte type, histological type, tumor status, genotyping and sequencing centers, manufacturer and kit information (n=7 variables; laser capture, RNA measurement, ribosomal depletion, library prep, and sequencing platform), RNA total, concentration, volume, and mass, sequencing chemistry and read length.
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