New concepts for Cancer modifier vocabulary

[mechyserra]

We are currently working on a retrospective oncology research project with several hospitals in Europe. In an initial phase, all the information filled in eCRFs will be saved within each hospital using OMOP-CDM. We were able to find standard concepts for almost every entry, but we've encountered the need to include additional concepts for some isolated missing terms. As most of the concepts we need to include are already defined according to international guidelines we wanted to know if it would be possible to include them within the cancer modifier vocabulary and Athena. The list of concepts we aim to include is the following:

• Extramural vascular invasion (imaging finding)
• Distance from the anorectal junction (imaging finding)
• Mesorectal fascia invasion (imaging finding)
• External anal sphincter invasion (imaging finding)
• Internal anal sphincter invasion (imaging finding)
• Breast lesion biopsy reporting categories: B1 normal tissue
• Breast lesion biopsy reporting categories: B2 benign lesion
• Breast lesion biopsy reporting categories: B3 lesion of uncertain malignant potential
• Breast lesion biopsy reporting categories: B4 suspicious
• Breast lesion biopsy reporting categories: B5 malignant
• Breast cancer triple-negative subtypes: Basal-like 1
• Breast cancer triple-negative subtypes: Basal-like 2
• Breast cancer triple-negative subtypes: Immunomodulatory
• Breast cancer triple-negative subtypes: Mesenchymal like
• Breast cancer triple-negative subtypes: Mesenchymal stem-like
• Breast cancer triple-negative subtypes: Luminal androgen receptor
• Breast cancer recurrence at the site of the primary cancer
• Breast cancer ipsilateral recurrence at a site different from that of the primary tumor
• Breast cancer contralateral recurrence
• Prostate Imaging Reporting & Data System category 1
• Prostate Imaging Reporting & Data System category 2
• Prostate Imaging Reporting & Data System category 3
• Prostate Imaging Reporting & Data System category 4
• Prostate Imaging Reporting & Data System category 5

Thank you in advance for your help.

Mercedes

[mik-ohdsi]

@mechyserra , thanks for bringing this to our attention. @cgreich should be interested to see. What would be helpful is to see the sources for each of these concepts to put them in context.

[mik-ohdsi]

Hi @mechyserra , have you been successful in digging up more material that would support your case?

[mechyserra]

Hi @mik-ohdsi. I am sorry for the delay in my response. I've worked on this material and shared everything with project leaders on this issue. The project team is meeting within the next weeks to revise this material with the pertinent group of experts before submitting it.

[mechyserra]

Hi @mik-ohdsi, Thank you so much for guiding us on the process to request the inclusion of new terms. Sorry our answer took a little bit longer than expected, I wanted to be sure to have the pertinent revision by the clinical experts. On behalf of Chaimeleon project (https://chaimeleon.eu/project/), please find attached a pdf document summarizing the terms we would like to be evaluated for inclusion along with there use cases and pertinent sources. Thank you once again, Mercedes

Oncology_Vocabulary_extension_ChaimeleonWG.pdf

[mik-ohdsi]

hi @mechyserra - thanks for the feedback! @cgreich and @vladkorsik , could you take a look and assess the attached list?

[cgreich]

@mechyserra:

We probably need a little more thought how to incorporate this:

• Breast lesion biopsy reporting categories: B1 is a flavor of null (OMOP only states pathological conditions). The B2-B5 are roughly equivalent to the ICD-O-3 behavior codes:
  • /0 Benign
  • /1 Uncertain whether benign or malignant
  • /2 Carcinoma in situ
  • /3 Malignant, primary site We may have to map them over, if you think there is a good use case.
• Breast cancer triple-negative subtypes: These would have to be added to the histological patterns as they exceed what ICD-O-3 has for breast cancer morphologies.
• Breast cancer recurrence location: We only have topography of a tumor lesion, whether it is recurrent or not, or metastasis. In your case, you would just add a new ICD-O-3 for the new location.
• Prostate Imaging Reporting & Data System V2 (PI-RADS v2): this is hard-core imaging content. We have not yet standardized that. Do you have a analytical use case for that that goes beyond image processing?
• Rectal cancer imaging findings: We do have invasion of rectal cancer into the surrounding organs and tissues. Do you think we need to add some of these?

[MeliHenry]

Hi @vladkorsik do we have any update on the cancer modifiers?

[vladkorsik]

Hi @vladkorsik do we have any update on the cancer modifiers?

Hello the answer is pretty simple.

From march2023 OncoWG and Odysseus vocabulary team

a)implemented: 1) Staging/grading hierarchy 2) mapping update to new Staging/Grading targets(community helps a lot) 3) new concepts based on pre-simposium request 4) source refactoring for genomic vocabularies

b)put in development 1) Lymph nodes class refactoring (likely to be a part of spring release) 2) HemOnc vocabulary maintenance (will be released during nearest vocabulary update) 3) new genomic vocabulary (will be released during nearest vocabulary update)

c) we are going to 1) analyze and crystalyze ideas on other cancer modifier classes of specific interest ( as invasion/extension https://github.com/OHDSI/Vocabulary-v5.0/issues/718#issue-1454596214) 2) Adopt NAACCR mappings to metastasis provided by @rtmill https://github.com/OHDSI/Vocabulary-v5.0/issues/740#issue-1513156712