New sample annotation (LinkedSpecimen) to highlight prior specimen

[Nicklas Nordborg]

The current SCANB BASE model permit a patient to have up to 2 cases (Left and Right laterality). A case can have any number of specimen (samples). Specimen are annotated with (among other) BiopsyType. Annotation BiopsyType is an enumeration with options: SpecimenCoreBiopsy2nd, SpecimenFineNeedleAspiration, SpecimenCoreBiopsy, SpecimenSurgery.

The main purpose of LinkedSpecimen is to highlight that the parent case (or patient) have a prior specimen of BiopsyType SpecimenCoreBiopsy or SpecimenCoreBiopsy2nd. This is of importance since the presence of a prior core biopsy indicate that the patient has undergone preoperative systemic treatment or have a prior diagnosis. Specimen that are collected after systemic treatment or after prior diagnosis are not representative biopsies from primary breast cancer. Annotation LinkedSpecimen will also highlight prior samples of type Specimen or NoSpecimen in the absence of core biopsies.

LinkedBiopsy should be an enumeration with the following options and multiplicity 1:

• IpsilateralCoreBiopsy
• ContralateralCoreBiopsy
• IpsilateralSample
• ContralateralSample

When a new specimen is associated with a case LinkedSpecimen should automatically be set using the following rules.

1. if the case have one or more prior (create date) specimen of BiopsyType SpecimenCoreBiopsy or SpecimenCoreBiopsy2nd => IpsilateralCoreBiopsy

2. if the patient have another case (other laterality) and this case have one or more prior (create date) specimen of BiopsyType SpecimenCoreBiopsy or SpecimenCoreBiopsy2nd => ContralateralCoreBiopsy

3. if the case have one or more prior (create date) samples of Type Specimen or NoSpecimen => IpsilateralSample

4. if the patient have another case (other laterality) and this case have one or more prior (create date) samples of Type Specimen or NoSpecimen => ContralateralSample

When a new sample is registered and the creation date is earlier than other samples for the same case or patient the user should be notified to this fact and prompted to manually check whether LinkedSpecimen should be set (manually) for any of the present samples.

Existing specimen need to manually curated.

[Nicklas Nordborg]

On the meeting today we discussed potential problems with this annotation. The main issue is that not all information may be known at the time of registration. This may make it difficult to know if a sample is before or after another sample and even if we make an educated guess it may turn out to be incorrect. In some cases dates, etc. may be modified using the regular BASE interface and not via a Reggie wizard. This may cause already set annotations to become incorrect.

We decided to investigate if it would be better to have a wizard that can go through all items in the database, check their relationship, and then update the annotation. This wizard must still be able to handle the cases with missing information (it should not set the annotation on any sample?).

[Nicklas Nordborg]

(In [3394]) Fixes #772: New sample annotation (LinkedSpecimen) to highlight prior specimen