Model creation module¶
The following table shows the recommendations from the PDX-MI manuscript.
| Field | Rec | Description | Example | PDXNet |
|---|---|---|---|---|
| Submitter PDX ID | E | Unique ID for the PDX Model | PDX#123 | CenterID:PatientID |
| Passage | E | Tissue Passsage. P0 tissue is from PT | P1 | create PDXNet classes? |
| Mouse strain | E | Name of strain used for engraftment | NOD.Cg-Prkdc<scid> Il2rg<tm1Wj>l/SzJ | create PDXNet classes? |
| Mouse source | E | Institution supplying strain | The Jackson Laboratory | create PDXNet classes? |
| Mouse sex | D | Sex of mouse used for engaftment | Male | |
| Mouse immune system humanised? | E | yes/no | ||
| Type of humanisation | E | CD34+hematopoietic stem cell-engrafted | ||
| Engraftment Procedure | D | suspension | ? | |
| Engraftment Method | D | ? | ||
| Engraftment Site | D | right flank | ? | |
| Mouse treatment for engraftment | D | estrogen treatment | ? | |
| Engraftment rate | D | 80% | literal | |
| Engraftment time | D | 8 weeks | literal |
1. Submitter PDX ID. This field is analogous to PatientID. We display as CenterID:PDXID and keep an internal ID that will not be shown externally to act as a primary key. For instance, PDX 123 from JAX would be shown on the PDXNet website as JAX:PDX-123
2. Passage. We neet to have a standard for this. Suggesting that P0 would indicate engrafted tissue is from the patient. P1 tissue comes from P0. P2 from P1 etc.
3. Mouse Strain. We will allow strains to be denoted according to the MGI guidelines.
4. Mouse Source. Institution providing the strain. An enumeration.
5 Mouse Sex.
6. Strain Immune System Humanised? Yes or No
7. Type of Humanisation. Description of humanisation method.
8. Engraftmet Procedure. Enumeration (TODO Need input: list of all the methods and whether any vocabulary exists?)
9. Engraftment Method. Enumeration (TODO Need input: list of all the methods and whether any vocabulary exists?)
10. Engraftment Site. Subcutaenous, Mammary Fat Pad, Orthotopic, etc. Where the tissue is engrafted to the mouse.
11. Mouse Treatment for Engraftment. estrogen treatment Enumeration (TODO Need input: list of all the methods and whether any vocabulary exists?)
12. Engraftment Rate. 80%. Would it be better to state “n of m” rather than a percentage? TODO Use percent or N of M?
13. Engraftment Time. 8 weeks Number of weeks/days PDMR uses “Estimated days from implant to 500 mm3” Both Rate and Time would benefit from noting if tissue was cryopreserved. Should this be captured as a field?