Ethical, Legal and Social Issues (ELSI)
Inclusion: TCGA utilizes a strict set of criteria for inclusion into the study due to the rigorous and comprehensive nature of the work being performed. Tumor samples and matched source of germline DNA are curated and processed by the Biospecimen Core Resource, a centralized site that reviews sample data and processes all samples to ensure consistent pathology assessment and generation of molecular analytes (DNA and RNA).
TCGA is focusing on primary untreated tumors that were snap frozen upon collection. All tumors must have a matched normal sample from the same patient. In many cases, the matched normal is a sample of the patient's blood.
Once at the BCR, all samples are subjected to a quality control protocol before they are accepted for full analysis into the TCGA pipeline. Each sample is reviewed by a pathologist to confirm the diagnosis and that the sample meets inclusion criteria. Specifically, TCGA requires that samples contain at least 60% tumor nuclei and have less than 20% necrotic tissue. Once the sample passes the pathology review, nucleic acids are isolated and genotyping is performed so that each tumor sample is properly associated with the correct normal tissue. An important goal in establishing this central resource is to ensure that molecular analytes (i.e. DNA and RNA) extracted from tissue samples are of consistent and high quality. Next, these analytes, undergo a molecular quality control process and then are distributed to TCGA Cancer Genome Characterization Centers and Genome Sequencing Centers for genomic analysis.
All samples in TCGA have been collected and utilized following strict policies and guidelines for the protection of human subjects, informed consent and IRB review of protocols.
Confidentiality: Usage of Open Access data has been deemed safe for general usage with minimal risk to patients. Restricted Access data could be used to potentially re-identify a given patient and so needs special requirements to access.
Considerations for external resources utilized: N/A
Human Subjects
REGULATORY
OTHER CONSIDERATIONS
- REB/IRB approval for data collection?: Generally, for these studies all patients have provided informed consent but see dbGaP for more details
- Sample were collected from patients in the following countries:
- N/A
- Known ELS issues introduced by preprocessing: N/A
- Known problematic proxies: N/A
- Was a data protection impact analysis performed?: N/A
| Collected Sensitive Data Fields | ||
|---|---|---|
| Field Name | Definition | Distribution |
| gender | Text designations that identify gender. Gender is described as the assemblage of properties that distinguish people on the basis of their societal roles. [Explanatory Comment 1: Identification of gender is based upon self-report and may come from a form, questionnaire, interview, etc.] |  |
| race | An arbitrary classification of a taxonomic group that is a division of a species. It usually arises as a consequence of geographical isolation within a species and is characterized by shared heredity, physical attributes and behavior, and in the case of humans, by common history, nationality, or geographic distribution. The provided values are based on the categories defined by the U.S. Office of Management and Business and used by the U.S. Census Bureau. |  |
| ethnicity | An individual's self-described social and cultural grouping, specifically whether an individual describes themselves as Hispanic or Latino. The provided values are based on the categories defined by the U.S. Office of Management and Business and used by the U.S. Census Bureau. |  |
| age_at_diagnosis | Age at the time of diagnosis expressed in number of days since birth. |  |
| submitter_id | All submitted IDs can potentially contain identifiable information | |
Intentionality of sensitive human attribute collection: N/A
LICENSING
- IP / Terms of Use:
- Raw data available from the Genomic Data Commons with access granted through dbGaP and adherence to their policies
- Third party intellectual property considerations:
- N/A
- Export controls or other regulations impacting dataset access/download or storage:
- N/A