v21 release: minor histology file update

[jharenza]

What data file(s) does this issue pertain to?

histologies.tsv

What release are you using?

v20

• The cancer_group column has ganglioglioma samples annotated as either GNG or Ganglioglioma, which separates them for plotting and will be fixed with a quick release.

> v20 %>%
+   filter(cancer_group == "GNG" | cancer_group == "Ganglioglioma") %>%
+   select(cancer_group) %>%
+   table()
.
Ganglioglioma           GNG 
            2            93 

• Substitute "/" with space and ";" with dash in cancer_groups

• add molecular_subtype based integrated_diagnosis for GNT,SEGA,GNG samples using pathology_free_text_diagnosis based subtyping

• Update [pathology_diagnosis_Other_harmonized_dx_rules.tsv](pathology_dx\ and\ pathology_free_text_diagnosis\ to\ broad_histology\ for\ subtyping\ module\ -\ other_diagnosis_rules.tsv )

• Updated analysis: Add pathology_diagnosis == Subependymal Giant Cell Astrocytoma (SEGA) to LGAT #1154

• Update broad/short histology matching in base histologies file #1155

Put a link to the relevant section of the OpenPBTA-manuscript here.

NA

Put your question or report your issue here.

NA

@kgaonkar6 will work on this

[kgaonkar6]

Additionally,
cancer_groups which currently have "/" will be updated to space so that while using the term for plots the "/" does not denote the subfolder.

Example:

Previous	Update
High-grade glioma/astrocytoma	High-grade glioma astrocytoma
Low-grade glioma/astrocytoma	Low-grade glioma astrocytoma

And cancer_group with ";" will be updated "-"

Example

Previous	Update
Metastatic secondary tumors;Neuroblastoma	Metastatic secondary tumors-Neuroblastoma
Germinoma;Teratoma	Germinoma-Teratoma

[kgaonkar6]

Closing with v21 release in #1157