FHIR Chat · tumor-normal testing · Orders and Observation WG

Stream: Orders and Observation WG

Topic: tumor-normal testing

Patrick Werner (Mar 09 2020 at 16:11):

In the CG WG the representation of (tumor-normal tests)[https://www.cegat.de/en/diagnostics/tumor-diagnostics/#comparison] are currently discussed. This tests consists of two specimen: tumor and normal tissue/blood; and compares the found variants to determine if a variant is somatic or germline.

Patrick Werner (Mar 09 2020 at 16:14):

Representing in FHIR this would lead to three observations. For which we got pushback from implementers as this would triple the Observation count of a genomic report which is already quite high.
Another issue is, that current paper based reports (https://drive.google.com/file/d/1y4E5lzsxLJ644kHpR7fTYN-xoGgPQVmt/view?usp=sharing) are not containing the explicit findings of the two base observations. But are representing the test of the tumor. Only germline/somatic is added through comparison with the normal test.

Patrick Werner (Mar 09 2020 at 16:16):

Thats why we came up with the idea of an complex Extension on Observation.specimen which would allow to link to the second specimen (normal tissue) with a typed qualifier for normal tissue, tumor tissue, maternal tissue .......

Patrick Werner (Mar 09 2020 at 16:17):

Now we are asking O&O feedback about this idea.

Rob Hausam (Mar 09 2020 at 16:44):

@Patrick Werner Do you have examples of how this looks (or how you think it would look) in FHIR? I don't see any reference to a definition or example of the complex extension, but it seems like there might be some alternatives.