The work of the BCR includes the following important functions:
- Serving as the interface between the TCGA program and the different Tissue Source Site collecting tumor and matched normal controls
- Ensuring and verifying that TCGA human subjects protections and guidelines are adhered to and that all regulations are followed at each Tissue Source Site
- Including use of language consistent with the TCGA informed consent documents
- Examining of all biospecimens to ensure they meet rigorous standards for each tumor type (including percent necrosis and percent tumor nuclei)
- Reviewing of pathology to ensure accurate diagnosis and inclusion in TCGA
- Collecting clinical information for each sample and applying standardized terminology, definitions and formats that are caBIG compliant
- Extracting and distributing DNA and RNA from samples to each of the genomic characterization and sequencing centers
Interaction with Other Centers
After samples are collected from a Tissue Source Site, a BCR ensures sample quality through a [TCGAM:Pathology Review] before extracting molecular analytes: DNA or RNA, which are in turn analysed for quality1
Analytes are aliquoted and assigned aliquot barcodes by the BCR before they are sent to the other centers.
The BCR sends the following samples and data as indicated below:
|1||For more information on analyte preparation, watch The Role of Tumor Samples video.|
Data Submissions to the DCC
- Participant information
- Biospecimen data
- Clinical pathology data
- Corresponding TCGA barcodes (across all biospecimen data levels)
- Tissue slide images
Data Archive Format
Clinical and biospecimen data are represented in two file types, XML and a tab-delimited text file type called biotab which present the same data structure in different ways. Both are open access data. They enable the collection of a series of barcodes corresponding to participants that fit within the clinical data types of interest.
Each XML file contains data for a single participant; each biotab file contains data for multiple participants.
Either type of file can be used to extract and aggregate aliquot barcodes associated with participants' clinical data. Once relevant sample or aliquot barcodes and data have been parsed from the available XML or biotab file, samples can be aggregated according to clinical data elements of interest. The aggregated barcodes can then be mapped to the relevant data (see TCGA barcode).