Updated analysis: embryonal subtyping to use pathology diagnosis

[jharenza]

What analysis module should be updated and why?

https://github.com/AlexsLemonade/OpenPBTA-analysis/tree/master/analyses/molecular-subtyping-embryonal

What changes need to be made? Please provide enough detail for another participant to make the update.

Currently, this module uses broad_histology to search for the subset of samples to be subtyped. However, with the rework of rules to determine broad_histology post integrated_diagnosis (#748), we should rework this module to search for samples using pathology_diagnosis and the new field for free text pathology diagnosis, which will be present in `pbta-histologies.tsv in #732.

What input data should be used? Which data were used in the version being updated?

pbta-histologies.tsv from V17 instead of from V16

When do you expect the revised analysis will be completed?

unsure

Who will complete the updated analysis?

unsure

[cbethell]

I can work on this issue this sprint!

[jharenza]

Hi @cbethell and @jaclyn-taroni! After consulting with Cassie Kline, the below list should be used in embryonal subtyping:

pathology_diagnosis
Neuroblastoma (see note)
Supratentorial or Spinal Cord PNET

pathology_free_text_diagnosis
embryonal tumor with multilayer rosettes, ros (who grade iv)
embryonal tumor, nos, congenital type
ependymoblastoma
medullooepithelioma

NOTE:

• It looks like we may have to update the CNS NBL logic to ensure we are capturing only CNS Neuroblastomas and not peripheral NBL. For instance, if pathology_diagnosis == CNS Neuroblastoma & primary_site != Other locations NOS & pathology_free_text_diagnosis does not contain "peripheral", then we can consider them as CNS region NBLs and they can proceed to subtyping. The two tumors we currently have subtypes as CNS NB-FOXR2 fit this, but if any are added in the future, we will want to be sure that we aren't subtyping NBLs that are non-CNS.