Breast cancer Rx Treatment concept "number of fractions" mapping

[CHE (Cordelia He)]

Hi All,
I am trying to map a clinical oncology report into the OMOP CDM5.4, and I am stuck in finding an appropriate standard OMOP concept ID for each of the following four terms on my screenshot here:

And here is my mapping through Usagi and Athena.
Rx_Athena_Mapping.xlsx (14.2 KB)

This Radiation Treatment report is for DCIS breast cancer oncology treatment.
I am not satisfied with my mapping because “brachytherapy” is a type of internal radiotherapy whereas “boost radiation” is a type of external beam radiotherapy. I wonder if there is a better way to differentiate the “number of radiation dose fractions” from the “number of boost dose fractions”. Many thanks for your help.

[Polina_Talapova]

Hello @CHE!

Please, see below one of the possible ways how to map your source codes (taking into account Usagi results presented in the spreadsheet):

#	source_code	target_concept_id	target_concept_name	comment
1	Total radiation dose (cGy)	40483776	Total radiation dose delivered	alternative_id - 46236014 (LOINC)
2	# of fractions planned	4037631	Number of fractions
3	# of fractions received	35918481	Phase I Number of Fractions
4	Boost	3031539	Boost radiation treatment modality Radiation treatment
5	Total boost dose (cGy)	40484226	Total boost radiation dose delivered	alternative_id - 3032272 (LOINC)
6	# of fractions planned (boost)	4161287	Prescribed fractions - teletherapy	synonym for teletherapy - external beam radiation therapy
7	# of fractions received (boost)	35918561	Phase II Number of Fractions	usually boost dose is used after the I Phase of radiotherapy

Not ideal, but workable anyhow.

[CHE (Cordelia He)]

Dearest Polina,
You are so quick in response and thank you so so much for your help
I agree with you that it is not ideal and I have 3 concerns:

1. I have googled the term “teletherapy”. It is a treatment method for mental health, not for breast cancer treatment. Moreover, in my hospital, radiation oncology treatment options include: “IMRT”, “Brachytherapy”, “SBRT or SABR”, "Stereotactic radiosurgery, and a combination of surgery and chemotherapy treatment. I haven’t seen any “teletherapy” in all my clinical data at all. For this reason, I hesitate to map “teletherapy” into my use case
2. I am not sure if the Phase I, Phase II, and Phase III Number of Fractions are applicable to the specific context of my use case here in Toronto, Canada.
3. The “number of fractions” fields are extracted from Elekta’s MOSAIQ Oncology Management System. The values were initially automatically calculated. “The Number of Fractions field is automatically calculated. For example, if the Rx Dose is 5040 with a Fractional Dose of 180, the Number of Fractions shows 28. This indicates that, to deliver the prescribed dose, the patient needs 28 treatment sessions. The calendar view on the right side of the fractionation phase field shows 28FxPattern?, indicating that the fractionation pattern has not been added.”(MOSAIQ Version 2.0 User’s Guide, 2010, page 88) Our end users, however, only required the calculated values of the “number of fractions” in the sessions of “radiation treatment” and “boost radiation treatment”.

Still, I really appreciate your help, Polina I will combine my own mapping with yours, and probably dig into MOSAIQ UI to see how the data was manually captured, and then discuss it with my data specialists and my software engineer to see if we can find the best solution.

In my use case, clinical data are extracted from five different database systems based on a customized user specification. Therefore, I need to look into different angles and directions so that I can recommend various options for my database development team to consider.

Once again, thank you so much for your great help, Polina! It is really a blessing for me to work with the excellent OHDSI community.

[Polina_Talapova]

Dear @CHE,
Always welcome! Thank you for your kind words and let me add details (which might be somehow helpful).

@CHE

I have googled the term “teletherapy”. It is a treatment method for mental health, not for breast cancer treatment.

Teletherapy is a homonym or multiple-meaning word. According to our case, it refers to external beam radiotherapy that you mentioned in the 1st message. Please, see the links below:
https://www.sciencedirect.com/topics/medicine-and-dentistry/teletherapy
https://browser.ihtsdotools.org/?perspective=full&conceptId1=33195004&edition=MAIN/2021-07-31&release=&languages=en

@CHE

I am not sure if the Phase I, Phase II, and Phase III Number of Fractions are applicable to the specific context of my use case here in Toronto, Canada.

One of the OMOP features is that, in some cases (!), you can put into existing Standard concepts the meaning that your study needs. However, there is another way. Your developers can make these concepts locally Standard as described here.

@CHE

For example, if the Rx Dose is 5040 with a Fractional Dose of 180, the Number of Fractions shows 28.

The concept of ‘4161287 Prescribed fractions - teletherapy’ is of the Observation domain, which allows storing any digit value in the field of value_as_number in the Observation table. However, if you need something less granular (without “teletherapy”), you have to create a custom Standard concept for this case as well.