Biospecimen (patient sample information):
biospecimen_aliquot A list of sample aliquots that were shipped by the BCR to TCGA characterization centers. An aliquot is sub-division of an analyte.
biospecimen_analyte A list of patient sample analytes that were isolated from sample portions. Each analyte is sub-divided into aliquots for shipment to the TCGA genome characterization centers.
biospecimen_diagnostic_slides A list of diagnostic images available for the patient sample, representing sections of the diagnostic block.
biospecimen_portion A list of patient samples subjected to histopathological validation prior to being processed into DNA and RNA analytes. A portion is a sub-division of a sample.
biospecimen_protocol The specific protocol used by the BCRs to process a particular sample portion into an analyte.
biospecimen_shipment_portion Information regarding sample shipments to TCGA characterization centers. This information is provided by the BCR after shipping the samples.
biospecimen_slide A list of histopathological slide images available for the patient sample, representing sections of sample portions.
Clinical (patient information):
clinical_drug Available drug treatment information for the patient regarding the treatment of the tumor event submitted to TCGA.
clinical_follow_up Available follow-up data for the patient collected at time points after enrollment. Some deceased patients with older enrollment form versions might have follow-up forms completed at the time of enrollment in order to ensure all data elements were captured. (Please see below note regarding follow-up data files.)
clinical_nte Available new tumor event information for the patient, including recurrences, metastasis, and new primaries. This information is submitted by the Tissue Source Site on the enrollment form or on subsequent follow-up forms.
clinical_follow_up_nte Available new tumor event information for the patient, including recurrences, metastasis, and new primaries. This information is derived from subsequent follow-up forms.
clinical_patient Available clinical information for the patient.
clinical_radiation Available radiation treatment information for the patient regarding the treatment of the tumor event submitted to TCGA.
Other useful information:
Field descriptions Descriptions of the clinical data elements can be obtained at: https://gdc-docs.nci.nih.gov/Data_Dictionary/viewer/.
Indexed vs XML data For more information about the difference between indexed data and the XML data, please read this section in the TCGAbiolinks vignette.