Updated analysis: molecular subtyping LGAT: remove non LGG tumors

[jharenza]

What analysis module should be updated and why?

molecular subtyping LGAT - after review of pathology_free_text_diagnosis contents with Cassie Kline, it was decided that we should remove a few samples from the LGAT module, as they belong within the broad_histology of neuronal and mixed neuronal-glial tumors

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

Remove the following samples with keywords in pathology_free_text_diagnosis from the LGAT subtyping module

pathology_diagnosis	subtyping module	pathology_free_text_diagnosis	broad_histology
Low-grade glioma/astrocytoma (WHO grade I/II)	NA, remove from LGAT module	contains "desmoplastic infantile astrocytoma"	Neuronal and mixed neuronal-glial tumor
Low-grade glioma/astrocytoma (WHO grade I/II)	NA, remove from LGAT module	diffuse leptomeningeal glioneuronal tumor	Neuronal and mixed neuronal-glial tumor
Low-grade glioma/astrocytoma (WHO grade I/II)	NA, remove from LGAT module	contains "glioneuronal"	Neuronal and mixed neuronal-glial tumor
Low-grade glioma/astrocytoma (WHO grade I/II)	NA, remove from LGAT module	rosette forming glioneuronal tumor	Neuronal and mixed neuronal-glial tumor

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

[jaclyn-taroni]

I'm assigning myself to this, as I assigned myself to #996 and they are related.

[jaclyn-taroni]

@jharenza what should I do in this case, where these samples would be included because pathology_diagnosis == "Ganglioglioma" but also excluded because pathology_free_text_diagnosis contains "glioneuronal"

# A tibble: 2 x 5
  Kids_First_Biospecimen_ID sample_id experimental_strategy pathology_diagnosis pathology_free_text_diagnosis                     
  <chr>                     <chr>     <chr>                 <chr>               <chr>                                             
1 BS_7N0B2CY1               7316-1985 RNA-Seq               Ganglioglioma       low grade glial-glioneuronal lesion. ganglioglioma
2 BS_B6KCJF2B               7316-1985 WGS                   Ganglioglioma       low grade glial-glioneuronal lesion. ganglioglioma

Steps to reproduce

library(tidyverse)
histologies_df <- readr::read_tsv(file.path("data", "pbta-histologies-base.tsv"))

histologies_df %>%
  filter(str_detect(str_to_lower(pathology_free_text_diagnosis), "glioneuronal"),
         str_detect(str_to_lower(pathology_diagnosis), "ganglioglioma")) %>%
  select(Kids_First_Biospecimen_ID,
         sample_id,
         experimental_strategy,
         pathology_diagnosis,
         pathology_free_text_diagnosis)

[jharenza]

For these cases, even though Ganglioglioma are glial-neuronal tumors, Cassie Kline had asked us to subtype them with the LGGs, but as a part of that subtyping, when we add the short_histology, they should be Ganglioglioma instead of LGAT, and should have Ganglioglioma as the prefix for integrated_diagnosis - I may have to check the latter.

[jaclyn-taroni]

So when a sample has pathology_diagnosis == "Ganglioglioma", it should be included in LGG subtyping even if pathology_free_text_diagnosis contains "glioneuronal." Did I follow that correctly?

[jharenza]

yes