Cancer Modifier. Staging and Grading

Cancer Modifier: Staging/Grading Concept Class

Overview

The Staging/Grading Concept Class was designed as part of the Cancer Modifier Vocabulary and was primarily developed to represent facts of staging related parameters and grading attributes of each cancer.

We grouped the concepts into the class based on their common logic nature: the entities similar to each other because they are approximations / derivations from other more precise and frequently captured as narratives parameters(grouped by their collinearity): number, size, invasion depth, cell appearance and histoarchitecture, cellularity .

Also, the class has concepts to reflect the staging parameters as narratives. Concept_class entities may be used to capture the response to treatment.

Sources

The source data came from the same repositories as described in Cancer Modifier general chapter.

Transformation

The procedures for transforming Concepts from the source to the OMOP Standard Vocabularies can be found on the OHDSI GitHub.

Concept Names

Concept names are constructed as combinations of several data attributes retrieved by source name parising with deduplication and alignment through look-up tables.

The examples are listed below

Concept Name	Attribute1 (staging system	Attribute2 (system version)	Attribute2 (prefix)	Attribute3 (aka suffix∓postfix)	Attribute4 (staging parameter)
AJCC/UICC 6th clinical T2a Category	AJCC/UICC	6th	clinical	T2a	Category
CHOI: complete response	CHOI				complete response
Pathological Gleason Score 4+3	Gleason		Pathological	4+3	Score

Concept Code

Staging/Grading concept codes are built in the same fashion as thier names.

In general, they atomic attributes of ocnept codes are concatenated by ‘-’ symbol to delineate every meaningful “particle” of the name. The ‘_’ symbol is used to separate the version of the staging system.

Concept Code	Attribute1 (staging system	Attribute2 (system version)	Attribute2 (prefix)	Attribute3 (aka suffix∓postfix)	Attribute4 (staging parameter)
c-6th_AJCC/UICC-T2a	AJCC/UICC	6th	c	T2a
CHOI-CR	CHOI				CR
p-Gleason-Score-4+3	Gleason		p	4+3	Score

Standard Concepts

Mostly all of the concepts within the concept class are standard and valid entities.

Domains

The class-specific entities belong to the Measurement domain as was predefined by Oncology WG perspective.

Concept Relationships

Hierarchy

Cancer Modifier Staging/Grading Concepts are aligned in hierarchical structure according to step-wise loss of an attribute and/or within a suffix-prefix level.

Hierarchical type	Concept-Relationship-Concept	Concept Name	Attribute1 (staging system	Attribute2 (system version)	Attribute2 (prefix)	Attribute3 (aka suffix∓postfix)	Attribute4 (staging parameter)
Suffix∓postfix fluctuation	Concept 1	AJCC/UICC 6th clinical T2a Category	AJCC/UICC	6th	clinical	T2a	Category
	Relationship	Is a
	Concept 2	AJCC/UICC 6th clinical T2 Category	AJCC/UICC	6th	clinical	T2	Category
Attribute loss	Concept 1	AJCC/UICC 6th clinical T2a Category	AJCC/UICC	6th	clinical	T2a	Category
	Relationship	Is a
	Concept 3	AJCC/UICC clinical T2a Category	AJCC/UICC		clinical	T2a	Category

Instructions for ETL

1. Stages should be used as comprehensive and self-sufficient concept (by default no need to add any type of value)
2. Concepts designed to trigger the Extent Episode and Dynamic Episode

a) Episodes can not be defined by the Stage only for the entire cancer population. E.g. “4a stage in patient with tonsillar HPV-positive cancer is not the same as 4 stage Melanoma (4th stage is not always Metastatic)”

b) More general rule may be applied only for TNM descriptors and may look like

i) N≥1 ⇒Invasive Disease

ii) M≥1 ⇒Metastatic Disease

c) Upstaging and Downstaging (the increment/reduction of numeric value of staging parameter) may be used to define the Progression Episode or Remission episode, respectively. This particular case should be treated with caution with high compliance to study protocol, as definition of specific disease extent episodes may vary from one protocol to other.