Skip Navigation
NIH | National Cancer Institute | NCI Wiki   New Account Help Tips
Page tree
Skip to end of metadata
Go to start of metadata

BCRs generate images of tissue slides that are used for pathology QC. A slide barcode is a unique identifier for each slide. The fields in the barcode are based on the tissue sample, and the position within the sample where the tissue slice for the slide was taken.

Synopsis

Slides are taken from tissue on the edges of tumor portions (see the following figure, Tumor Portions and Slides).

Each slide is assigned a unique identifier (SlideBarCode) that consists of the Portion Barcode , appended with a field of two letters indicating whether the slide is the TopSlide (TS) or the Bottom Slide(BS) of the portion, and a single character equivalent of the Portion (either '1' or 'A' for the Portion of '01', and either  '2' or 'B' for the Portion of '02', etc).

Example:
Portion barcode: TCGA-08-0245-11A-01
Slide barcode: TCGA-08-0245-11A-01-TS1

Note, however that there are situations where a portion and its corresponding slide have different portions fields in their barcodes.

  • When a slide represents the region between two portions, the slide can be described either as representing the bottom of its portion, or representing the top of its neighbor portion.  Thus a slide field of BS1 (BottomSlide of Portion 1) would be equivalent to a slide field of TS2 (TopSlide of Portion 2).
    Example:
    Portion barcode: TCGA-C4-A0EZ-01A-02
    Slide barcode: TCGA-C4-A0EZ-01A-01-BS1
  • When a barcode represents a sub-portion, the Portion field will no longer match the original Portion field.
    Example:
    Portion barcode: TCGA-08-0245-11A-01
    SubPortion barcode: TCGA-08-0245-11A-13
    Slide barcode: TCGA-08-0245-11A-01-TS1

Tumor Portions and Slides

illustration of slide portion and legend

Additional Example

See the additional figure showing the derivation of slide barcodes at the bottom of this topic.

Specification

A slide barcode must have a valid leading portion barcode:

TCGA-\w{2}-\w{4}-\d{2}[A-Z]-\d{2}

Note that there is no analyte character at the end: e.g., TCGA-08-0245-11A-01, and not TCGA-08-0245-11A-01A

The final field should have the form

(T|M|B)S[0-9A-Z]

Based on the Synopsis, the final character should be consistent, but not necessarily the portion number. For example:

Portion

Final Character

1

'1' or 'A'

2

'2' or 'B'

3

'3' or 'C'

Examples of barcode and slide barcodes

Consistent or not

PortionBarcode

Slide Barcode

Consistent

TCGA-08-0245-11A-01

TCGA-08-0245-11A-01-BS1

Consistent

TCGA-08-0245-11A-13

TCGA-08-0245-11A-02-TS2

Consistent

TCGA-08-0245-11A-01

TCGA-08-0245-11A-02-TS2

Consistent

TCGA-08-0245-11A-02

TCGA-08-0245-11A-02-TS3

Consistent

TCGA-08-0245-11A-02

TCGA-08-0245-11A-03-TS3

Inconsistent

TCGA-08-0245-11A-01

TCGA-08-0245-11A-02-TS3

Example of Slide Barcode Derivation

The following figure provides an example of slide barcode derivation.

  • The bottom left slide barcode (green) represents the top slide of portion 1
  • The bottom center slide barcode (green) represents the bottom slide of portion 1
  • The bottom right slide barcode (green) represents the bottom slide of portion 2

illustration of slide barcode derivation, described in text

  • No labels