icgc-argo / argo-dictionary

Development of the ARGO Data Dictionary
https://docs.icgc-argo.org/dictionary
GNU Affero General Public License v3.0
2 stars 1 forks source link

Add "Cannot be assessed" to stage_group controlled terminology and validation script #316

Closed hknahal closed 3 years ago

hknahal commented 3 years ago

According to AJCC Guidelines 8th Ed. (page 9), if TX or NX categories are used, such cases usually cannot be assigned a stage group. In such a case, the data submitter will be allowed to submit "Cannot be assessed" for the stage_group field. However, there are exceptions according to the guidelines as follows:

Exceptions:

Stage may be assigned when the TNM stage group results in  Any T or Any N with M1, which includes TX or NX. These  are classified as Stage IV. Examples include:  
- TX NX M1, or  
- TX N3 M1.  

Stage may be assigned when the TNM stage group results  in Any T or Any N with M0, which includes TX or  NX. Examples include:  
- TX N1 M0 Stage III in melanoma clinical stage 
- T4 NX M0 Stage III in pancreas

Amin, Mahul B.; Gress, Donna M.; Meyer Vega, Laura R.; Edge, Stephen B.. AJCC Cancer Staging Manual, Eighth Edition (p. 9). American College of Surgeons. Kindle Edition. 

In order to ensure the "Cannot be assessed" value is being submitted corrected, a validation script will need to implemented which will check the value of clinical/pathological_t_category and clinical/pathological_n_category.

akachru-github commented 3 years ago
hknahal commented 3 years ago

Tested in QA using dictionary version 111.3

rosibaj commented 3 years ago

Dictionary released Sept 02, 11:45