TCGA Barcode

Source: https://docs.gdc.cancer.gov/Encyclopedia/pages/TCGA_Barcode/

Description

The TCGA barcode is the primary identifier of biospecimen data within the TCGA project. A copy of the content formerly found at https://wiki.nci.nih.gov/display/TCGA/TCGA+barcode can be found below.

Overview

Historically, the BCR received participant samples and their associated metadata from TSSs. The BCR then assigned human-readable IDs, referred to as TCGA barcodes, representing the metadata of the participants and their samples. TCGA barcodes were used to tie together data that spans the TCGA network, since the IDs uniquely identify a set of results for a particular sample produced by a particular data-generating center (i.e. GCC, GSC or GDAC). The constitutive parts of this barcode provided metadata values for a sample.

Currently the BCR is assigning both a TCGA barcode and a UUID to samples. The UUID is the primary identifier. For more information on the ID transition, see UUIDs.

Creating Barcodes

All TCGA barcodes are created by the BCR. The following figure illustrates how a sample is processed and assigned a TCGA barcode at each step. Starting from the Tissue Source Site (TSS) and the participant (who donated a tissue sample to the TSS), the barcodes TCGA-02 and TCGA-02-0001 are assigned respectively. The sample itself is also assigned a barcode: TCGA-02-0001-01. The sample is split into vials (e.g. TCGA-02-0001-01B) which are divided into portions (e.g. TCGA-02-0001-01B-02). Analytes (e.g. TCGA-02-0001-01B-02D) are extracted from each portion and distributed across one or more plates (e.g. TCGA-02-0001-01B-02D-0182), where each well is identified as an aliquot (e.g. TCGA-02-0001-01B-02D-0182-06). These plates are sent to GCCs or GSCs for characterization and sequencing. FIX this below

Creating Barcodes

Reading Barcodes

A TCGA barcode is composed of a collection of identifiers. Each specifically identifies a TCGA data element. Refer to the following figure for an illustration of how metadata identifiers comprise a barcode. An aliquot barcode, an example of which shows in the illustration, contains the highest number of identifiers.

Reading Barcodes

Label	Identifier for	Value	Value Description	Possible Values
Analyte	Molecular type of analyte for analysis	D	The analyte is a DNA sample	See Code Tables Report
Plate	Order of plate in a sequence of 96-well plates	182	The 182nd plate	4-digit alphanumeric value
Portion	Order of portion in a sequence of 100 - 120 mg sample portions	1	The first portion of the sample	01-99
Vial	Order of sample in a sequence of samples	C	The third vial	A to Z
Project	Project name	TCGA	TCGA project	TCGA
Sample	Sample type	1	A solid tumor	Tumor types range from 01 - 09, normal types from 10 - 19 and control samples from 20 - 29. See Code Tables Report for a complete list of sample codes
Center	Sequencing or characterization center that will receive the aliquot for analysis	1	The Broad Institute GCC	See Code Tables Report
Participant	Study participant	1	The first participant from MD Anderson for GBM study	Any alpha-numeric value
TSS	Tissue source site	2	GBM (brain tumor) sample from MD Anderson	See Code Tables Report

Barcode Types

Barcodes can also be visualized hierarchically, with TSS barcodes at the top of the tree and aliquot barcodes at the bottom. A parent barcode prefixes any of its descendent barcodes, reflecting the derivation of one biospecimen type from another. For example, samples are collected from a participant and so the corresponding sample barcodes contain the participant barcode from which they were derived.

Barcode Hierarchy

Using the aliquot barcode example from the figure in Reading Barcodes, the following table displays a possible set of related barcodes at each level of the hierarchy:

Level	Bacode	Comment
Analyte	TCGA-02-0001-01C-01D	Analytes of W and X both refer to analytes derived from whole genome amplification
Drug	TCGA-02-0001-C1	Drug ID is 'C','D','H','I' or 'T' followed by a number
Examination	TCGA-02-0001-E3124	Examination ID is 'E' followed by a number
Participant	TCGA-02-0001	--
Portion	TCGA-02-0001-01C-01	--
Radiation	TCGA-02-0001-R2	Radiation ID is 'R' followed by a number
Sample	TCGA-02-0001-01	--
Shipped Portion	TCGA-CM-5341-01A-21-1933-20	Used in the platform of MDA_RPPA_CORE only
Slide	TCGA-02-0001-01C-01-TS1	Tissue slide ID can be 'TS' ('Top Slide'), 'BS' ('Bottom Slide') or 'MS' ('Middle slide'), followed by a number or letter to indicate slide order
Surgery	TCGA-02-0001-S145	Surgery ID is 'S' followed by a number
TSS	TCGA-02	--