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Links added, tables rearranged, minor edit #328

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Links added, tables rearranged, minor edit #328

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20 changes: 11 additions & 9 deletions docs/Encyclopedia/pages/TCGA_Barcode.md
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Expand Up @@ -21,15 +21,15 @@ A TCGA barcode is composed of a collection of identifiers. Each specifically ide

| 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 |
| TSS | Tissue source site | 02 | GBM (brain tumor) sample from MD Anderson | See the list of [Tissue Source Site Codes](https://gdc.cancer.gov/resources-tcga-users/tcga-code-tables/tissue-source-site-codes) |
| Participant | Study participant | 0001 | The first participant from MD Anderson for GBM study | Any alpha-numeric value |
| Sample | Sample type | 01 | A solid tumor | See [Sample Type Codes](https://gdc.cancer.gov/resources-tcga-users/tcga-code-tables/sample-type-codes) |
| Vial | Order of sample in a sequence of samples | C | The third vial | A to Z |
| Portion | Order of portion in a sequence of 100 - 120 mg sample portions | 01 | The first portion of the sample | 01-99 |
| Analyte | Molecular type of analyte for analysis | D | The analyte is a DNA sample | See the table of [Portion / Analyte Codes](https://gdc.cancer.gov/resources-tcga-users/tcga-code-tables/portion-analyte-codes)|
| Plate | Order of plate in a sequence of 96-well plates | 0182 | The 182nd plate | 4-digit alphanumeric value |
| Center | Sequencing or characterization center that will receive the aliquot for analysis | 01 | The Broad Institute GCC | See the table of [Center Codes](https://gdc.cancer.gov/resources-tcga-users/tcga-code-tables/center-codes) |

### Barcode Types ###

Expand All @@ -40,6 +40,7 @@ Barcodes can also be visualized hierarchically, with TSS barcodes at the top of
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 |
|---|---|---|
| Aliquot | TCGA-02-0001-01C-01D-0182-01 | -- |
| 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 |
Expand All @@ -49,12 +50,13 @@ Using the aliquot barcode example from the figure in Reading Barcodes, the follo
| 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 |
| Slide | TCGA-02-0001-01C-01-TS1 | Tissue slide ID can be 'TS' (Top Slide), 'BS' (Bottom Slide), 'MS' (Middle slide), or 'DX' (Diagnostic 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 | -- |

## References ##
1. [PDF from original TCGA wiki page](images/TCGA-TCGAbarcode-080518-1750-4378.pdf)
2. [TCGA Code Tabels](https://gdc.cancer.gov/resources-tcga-users/tcga-code-tables)


Categories: General