Clinical/Tumor module¶
The following table shows the recommendations from the PDX-MI manuscript.
| Field | Rec | Description | Example | PDXNet |
|---|---|---|---|---|
| Submitter Tumor ID | E | Tissue ID | TUM-123 | Unique ID |
| Primary Tumor Tissue | E | Primary Tumor Tissue | breast | UBERON code |
| Primary, Met, Recurrence | E | Disease Progression | Recurrence | enumeration |
| Specimen Tumor Tissue | E | Sampled Tissue | breast | UBERON code |
| Tissue Histology | D | Histologic Diagnosis | invasive ductal carcinoma | NCIT code |
| Tumor Grade | D | Tumor Grade | grade 3 | AJCC Grade |
| Stage; T N M | D | Tumor Stage | AJCC TNM Stages | |
| Diagnostic Markers | D | Clinical BioMarkers | ER+, PR+, HER2+; | |
| Treatment Naive Patient | D | yes/no | enumeration | |
| Tumor Sample Type | D | Collection Procedure | biopsy | enumeration |
| Subline of | Subline of model | PDX-123 | Model Identifier | |
| Subline reason | Why a subline | Lost Cisplatin Resist. | String |
1. Submitter Tumor ID Display as CenterID:TumorID to act as a primary key. If not provided, patient ID can be used. Tumor 123 from JAX would be shown on the PDXNet website as JAX:TUM-123
2. Primary tumor tissue The tissue of the primary tumor. For now, the simulation shows a random UBERON code for an anatomical entity. We will use the uberon cross-species anatomy ontology [8] that is developed by Monarch Initiative (M. Haendel, C. Mungall).
3. Primary, metastasis,recurrence Is the specimen tissue from the primary tumor, a metastasis or a recurrance For now, we are using PDXNet entities, but we should use the NCIT terms for these items. This would allow users to enter a more specific NCIT term such as Distant metastasis (C18206), which is a child of Metastasis (C19151)
4. Specimen tumor tissue Tissue from which the specimen was collected. Same as Primary tissue if the tumor is not metastatic. Uberon as above. TODO For melanoma do we want to capture specimen location?
5. Tissue histology This is the pathologist’s diagnosis and may often represent a refinement of the clinical diagnosis given in the Patient/Clinical module. Should use the same terminology as diagnosis, but represent the pathologist’s findings.
6. Tumor Grade For now we are using PDXNet codes, but we will switch to the NCIT subhierarchy, although I think they may need some TLC. We will work with NCIT to revise these terms as a part of Monarch’s ongoing collaboration with NCIT.
7. Disease Stage; classification T3N2M1; TNM or Non applicable (example blood cancer) Should follow Tumor Grade; classification standard Use AJCC. This will be seperated into pT,pN,PM and stage
8. Specific markers (diagnostic linked) Clinically relevant bio markers. Pairs of Marker:Status where status can be “positive”, “negative”, a percent value, or a variant and optional platform Most of the assays such as IHC are covered by the NCIT under the subhierarchy “Laboratory Procedure”. That NCIT subhierachy also includes items for Receptor status (e.g., HER2/Neu positive), and these will be linked to external representations of genes/proteins by the Monarch collaboration.
9. Treatment naive patient? yes/no (enumeration) Yes means patient has never had neoadjuvant treatment. per TCGA
10. Original tumor sample type The process used to collect the sample. biopsy, surgical sample, punch NCIT has a subhierarchy of terms for biopsy and biopsy locations, that will be linked to uberon etc by the Monarch collaboration. Some terms appear to be missing, e.g., “ascites fluid”, but will be added to NCIT as needed for PDXNet.
11. Subline of If this model is created as a subline of an existing model indicate which model it is a subline of.
12. Subline reason We may need to create our own mini-terminology to describe the reasons for using a subline