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A Biospecimen Core Resource (BCR) is a TCGA center where samples are carefully catalogued, processed, quality-checked and stored along with participant clinical information.

Contents of this page

Overview

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 quality

{footnote}For more information on analyte preparation, watch [The Role of Tumor Samples|http://cancergenome.nih.gov/newsevents/multimedialibrary/videos/tumorsamples] video.{footnote}

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:

{display-footnotes:reset=true}

Data Submissions to the DCC

Center

Data Type

File Extension

Level

BCR

Clinical data

.xml

1

BCR

Biospecimen data

.xml

1

BCRClinical Biotab.txt2
BCRBiospecimen Biotab.txt2

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).

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