Changes between Initial Version and Version 1 of Ticket #771


Ignore:
Timestamp:
Nov 10, 2015, 1:59:02 PM (6 years ago)
Author:
Nicklas Nordborg
Comment:

Renamed the RepresentativeSpecimen annotation to YellowLabel.

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  • Ticket #771 – Description

    initial v1  
    1 A new annotation named `RepresentativeSpecimen` (Boolean, TRUE/FALSE) for samples of subtype Specimen.
     1A new annotation named `YellowLabel` for samples of subtype Specimen. It should be a string enum with one allowed value: `yellow` (more values may be defined in the future).
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    3 At some point, one of the available labels on the pathology referral form will be colored yellow (the yellow label). The idea is that the pathologist should use the yellow label to mark a tube that contains a representative specimen (tissue sample), i.e. the biopsy that the pathologist consider as representative of the breast cancer. When registered, a specimen with the yellow label should be annotated as `RepresentativeSpecimen = TRUE`. The idea is that the pathologist will highlight a biopsy as `RepresentativeSpecimen` (using the yellow label) to indicate that it is suitable for further analysis with respect to clinically relevant end-points. That is, a yellow label is the pathologists way of ‘requesting’ a clinical report or at least indicating that a report generated for the specimen should be relevant for the breast cancer.
     3At some point, one of the available labels on the pathology referral form will be colored yellow (the yellow label).
     4
     5When registered, a specimen with the yellow label should be annotated as `YellowLabel = yellow`. The idea is that the pathologist will highlight a biopsy (using the yellow label) to indicate that it is suitable for further analysis with respect to clinically relevant end-points. That is, a yellow label is the pathologists way of ‘requesting’ a clinical report or at least indicating that a report generated for the specimen should be relevant for the breast cancer.
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    57The pathologist will still have the possibility to collect additional tissue samples (specimen) in separate RNAlater tubes marked with individual labels (not yellow). The instructions to the pathologist will go so far as to specify that if it’s deemed that a representative specimen cannot be collected the yellow label should not be used at all. In such a senario, the pathologist will still have the possibility to collect a non-representative specimen, e.g., a node-metastasis or a piece of tumor adjacent tissue or tumor tissue that the pathologists simply does not deem as representative.
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    7 ?? Once we start with referrals forms containing yellow labels all samples registered with regular labels (not yellow) should be annotated as `RepresentativeSpecimen = FALSE`.
     9Samples registered with regular labels (not yellow) should be not be annotated.
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    9 Samples that are already registered will not be ‘retro’ annotated using `RepresentativeSpecimen`.
     11Samples that are already registered will not be ‘retro’ annotated.
    1012
    1113This ticket may be divided into subtickets:
    1214
    13  * Changes in specimen registration for marking the `RepresentativeSpecimen` tube
    14  * Gui changes in other wizard to highlight the `RepresentativeSpecimen`
    15  * Track and report `RepresentativeSpecimen` separately
     15 * Changes in specimen registration for marking the `YellowLabel` tube
     16 * Gui changes in other wizard to highlight the `YellowLabel`
     17 * Track and report `YellowLabel` separately
    1618
    1719