Changes between Initial Version and Version 1 of Ticket #771
- Timestamp:
- Nov 10, 2015, 1:59:02 PM (8 years ago)
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Ticket #771 – Description
initial v1 1 A new annotation named ` RepresentativeSpecimen` (Boolean, TRUE/FALSE) for samples of subtype Specimen.1 A 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). 2 2 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. 3 At some point, one of the available labels on the pathology referral form will be colored yellow (the yellow label). 4 5 When 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. 4 6 5 7 The 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. 6 8 7 ?? Once we start with referrals forms containing yellow labels all samples registered with regular labels (not yellow) should be annotated as `RepresentativeSpecimen = FALSE`.9 Samples registered with regular labels (not yellow) should be not be annotated. 8 10 9 Samples that are already registered will not be ‘retro’ annotated using `RepresentativeSpecimen`.11 Samples that are already registered will not be ‘retro’ annotated. 10 12 11 13 This ticket may be divided into subtickets: 12 14 13 * Changes in specimen registration for marking the ` RepresentativeSpecimen` tube14 * Gui changes in other wizard to highlight the ` RepresentativeSpecimen`15 * Track and report ` RepresentativeSpecimen` separately15 * 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 16 18 17 19
