Updated analysis: molecular subtyping pathology - Craniopharyngioma

[jharenza]

What analysis module should be updated and why?

As outlined in #967, we would like to integrate some of the information in pathology_free_text diagnosis to the integrated_diagnosis or harmonized_diagnosis. For this ticket, we will further subtype Craniopharyngioma samples which may have been annotated as "To be classified" since they lacked canonical mutations which subtype the samples. In addition, for adamantinomatous craniopharyngioma, the b-catenin SNV is not present in 100% of these samples. Ref:

In our cohort of ACP specimens from 117 patients we found CTNNB1 mutations in 89 cases (76.1%).

Below are the samples which were not able to be classified by molecular-subtyping-CRANIO, but which

> v18 %>%
+   filter(pathology_diagnosis == "Craniopharyngioma") %>%
+   filter(grepl("adam", pathology_free_text_diagnosis) & molecular_subtype == "CRANIO, To be classified") %>%
+   select(sample_id, pathology_free_text_diagnosis, molecular_subtype)%>%
+   distinct()
# A tibble: 2 x 3
  sample_id pathology_free_text_diagnosis                         molecular_subtype       
  <chr>     <chr>                                                 <chr>                   
1 7316-3891 adamantinomatous craniopharyngioma                    CRANIO, To be classified
2 7316-1795 craniopharyngioma, adamantinomatous type, who grade i CRANIO, To be classified

I checked both of these pathology reports and indeed, the samples were described as Adamantinomatous, therefore, I think we can update these by specific sample, rather than rules, since they have been confirmed, into integrated_diagnosis and molecular_subtype.

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

Add to the above samples:

broad_histology	short_histology	harmonized_diagnosis	molecular_subtype
Tumors of sellar region	Craniopharyngioma	Adamantinomatous craniopharyngioma	CRANIO, ADAM

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

pbta-histologies.tsv

When do you expect the revised analysis will be completed?

this week

Who will complete the updated analysis?

@kgaonkar6 or @jharenza