I am using ATLAS to make a new cohort for malignant melanoma. I want to create a cohort with only stage III/IV melanoma patients. I was not able to find codes for the concept set for staging information. Would appreciate any help on how to find cancer staging information on ATLAS.
Hi @skim338
All the attributes of a tumor such as stage, grade, metastasis, lymph nodes, margins, etc., are Cancer Modifiers, which are post-coordinated concepts in the MEASUREMENT table and linked to the corresponding CONDITION_OCCURRENCE record. These concepts are represented in the Cancer Modifier vocabulary.
For your specific case, you can use the following concepts for staging:
These concepts correspond to all grouped stage III and IV, irrespective of the AJCC version and whether the stage is clinical or pathological.
Additionally, you should create concept sets (using Cancer Modifier vocabulary, class: staging/grading) for different T (Tumor), N (Node), and M (Metastasis) values corresponding to clinical or pathological stage III and IV melanoma. You will then combine these concept sets with the appropriate logic in your cohort definition to accurately capture the desired stage of melanoma.