ID
45054
Description
Principal Investigator: Peter W. Laird, PhD, University of Southern California, Los Angeles, CA, USA MeSH: Colorectal Carcinomas https://www.ncbi.nlm.nih.gov/projects/gap/cgi-bin/study.cgi?study_id=phs000385 DNA methylation, together with chromatin modifications, constitute the epigenome that functions to regulate gene expression and genome integrity. DNA methylation alterations are ubiquitous in human cancers, as many genes acquire DNA methylation in a cancer-specific manner. DNA methylation at these sites in the genome of cancer cells not only serves as a marker for tumor identification, but together with gene mutation and gene expression data, can also be used to describe subsets of tumors of the same organ source. We have previously shown distinct human colorectal cancer subtypes based on DNA methylation differences. Correlating these DNA methylation differences with clinical co-variates will serve to further understand how these distinct subtypes are generated. We have collected 100 colorectal tumor tissues (for which clinical information is known) and have obtained (unprotected) genome-wide DNA methylation and chromatin modification information for each sample for the purposes of identifying and classifying unique tumor subtypes of colorectal cancers. In addition, we have determined mutations of key genes relevant to colorectal cancer as well as gene expression profiles. We will use the clinical data for each de-identified sample to correlate with the DNA methylation, mutation and gene expression information so as to understand the driving forces behind these distinct colorectal subtypes. We have selected the most promising tumors for whole-genome bisulfite sequencing using next-generation sequencing technology to obtain complete maps of colon cancer methylomes. Researchers will be unable to identify the subjects because the samples and associated information have been de-identified and anonymized by the tissue source site. In addition, upon receipt by the USC Epigenome Center, we have assigned new random identifiers for each sample. The data generated using these new codes are not traceable to the patient identity.
Link
https://www.ncbi.nlm.nih.gov/projects/gap/cgi-bin/study.cgi?study_id=phs000385
Keywords
Versions (2)
- 8/4/22 8/4/22 - Simon Heim
- 10/12/22 10/12/22 - Adrian Schulz
Copyright Holder
Peter W. Laird, PhD, University of Southern California, Los Angeles, CA, USA
Uploaded on
August 4, 2022
DOI
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License
Creative Commons BY 4.0
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dbGaP phs000385 Epigenetic Profiling of Human Colorectal Cancer
Eligibility Criteria
- StudyEvent: SEV1
- Eligibility Criteria
- Subject ID, consent group, subject source ID, and affection status of participants with colorectal cancer and involved in the "Epigenetic Profiling of Human Colorectal Cancer" project.
- Sample ID, subject ID, and sample source of participants with colorectal cancer and involved in the "Epigenetic Profiling of Human Colorectal Cancer" project.
- Subject ID, sex, age, primary tumor(s) location, and treatment of participants with colorectal cancer and involved in the "Epigenetic Profiling of Human Colorectal Cancer" project.
- Sample ID, analyte type, histological type of samples, somatic mutation in tumor tissue, metastases, tumor grade and stage, methods of sample collection, and pathological characteristics of tumors obtained from participants with colorectal cancer and involved in the "Epigenetic Profiling of Human Colorectal Cancer" project.
- Sample ID and GEO accession ID associated with DNA methylation of tumor and adjusted normal tissue obtained from participants involved in the "Epigenetic Profiling of Human Colorectal Cancer" project.
Similar models
Eligibility Criteria
- StudyEvent: SEV1
- Eligibility Criteria
- Subject ID, consent group, subject source ID, and affection status of participants with colorectal cancer and involved in the "Epigenetic Profiling of Human Colorectal Cancer" project.
- Sample ID, subject ID, and sample source of participants with colorectal cancer and involved in the "Epigenetic Profiling of Human Colorectal Cancer" project.
- Subject ID, sex, age, primary tumor(s) location, and treatment of participants with colorectal cancer and involved in the "Epigenetic Profiling of Human Colorectal Cancer" project.
- Sample ID, analyte type, histological type of samples, somatic mutation in tumor tissue, metastases, tumor grade and stage, methods of sample collection, and pathological characteristics of tumors obtained from participants with colorectal cancer and involved in the "Epigenetic Profiling of Human Colorectal Cancer" project.
- Sample ID and GEO accession ID associated with DNA methylation of tumor and adjusted normal tissue obtained from participants involved in the "Epigenetic Profiling of Human Colorectal Cancer" project.
C2708733 (UMLS CUI [1,2])