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update path subtyping #949

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update path subtyping #949

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4b2f239
update path subtyping
Feb 23, 2021
e40d30a
Update README.md
Feb 23, 2021
e5f0983
remove HGG BRAF subtyping from script 03
Feb 25, 2021
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15 changes: 10 additions & 5 deletions analyses/molecular-subtyping-pathology/01-compile-subtyping-results.Rmd
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Original file line number Diff line number Diff line change
Expand Up @@ -204,11 +204,16 @@ hgg_results_df <- bind_exp_strategies(hgg_results_df) %>%
Notes),
by = "Kids_First_Biospecimen_ID") %>%
mutate(integrated_diagnosis = case_when(molecular_subtype == "DMG, H3 K28"~ "Diffuse midline glioma, H3 K28-mutant",
molecular_subtype == "DMG, H3 K28, BRAF V600E"~ "Diffuse midline glioma, H3 K28-mutant, BRAF V600E",
molecular_subtype == "BRAF V600E"~ "High-grade glioma/astrocytoma, BRAF V600E",
Comment on lines -207 to -208
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Are these being removed because they don't occur any more in the data set? Or is there a scientific reason to remove these conditions (they will never occur)?

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BRAF was removed from HGG subtyping in #807 due to scientific reasons.

molecular_subtype == "DMG, H3 K28, TP53 activated"~ "Diffuse midline glioma, H3 K28-mutant",
molecular_subtype == "DMG, H3 K28, TP53 loss"~ "Diffuse midline glioma, H3 K28-mutant",
molecular_subtype == "HGG, H3 G35" ~ "High-grade glioma/astrocytoma, H3 G35-mutant",
molecular_subtype == "HGG, H3 G35, TP53 loss" ~ "High-grade glioma/astrocytoma, H3 G35-mutant",
molecular_subtype == "HGG, H3 wildtype" ~ "High-grade glioma/astrocytoma, H3 wildtype",
molecular_subtype == "HGG, H3 wildtype, TP53 activated" ~ "High-grade glioma/astrocytoma, H3 wildtype",
molecular_subtype == "HGG, H3 wildtype, TP53 loss" ~ "High-grade glioma/astrocytoma, H3 wildtype",
molecular_subtype == "HGG, IDH"~ "High-grade glioma/astrocytoma, IDH-mutant",
molecular_subtype == "HGG, IDH, TP53 loss"~ "High-grade glioma/astrocytoma, IDH-mutant",
molecular_subtype == "HGG, IDH, TP53 activated"~ "High-grade glioma/astrocytoma, IDH-mutant",
TRUE~ NA_character_),
broad_histology = "Diffuse astrocytic and oligodendroglial tumor",
short_histology = "HGAT",
Expand Down Expand Up @@ -250,9 +255,9 @@ epn_results_df <- bind_exp_strategies(epn_results_df) %>%
by = "Kids_First_Biospecimen_ID") %>%
mutate(molecular_subtype = subgroup) %>%
mutate(molecular_subtype = if_else(is.na(molecular_subtype), "EPN, To be classified", molecular_subtype),
integrated_diagnosis = case_when(molecular_subtype == "PT_EPN_A" ~ "Posterior Fossa Ependymoma, Type A",
molecular_subtype == "ST_EPN_RELA" ~ "Supratentorial Ependymoma, RELA fusion positive",
molecular_subtype == "ST_EPN_YAP1" ~ "Supratentorial Ependymoma, YAP1 fusion positive",
integrated_diagnosis = case_when(molecular_subtype == "EPN, PF A" ~ "Ependymoma, Posterior Fossa, Type A",
molecular_subtype == "EPN, ST RELA" ~ "Ependymoma, Supratentorial, RELA fusion positive",
molecular_subtype == "EPN, ST YAP1" ~ "Ependymoma, Supratentorial, YAP1 fusion positive",
TRUE~ NA_character_),
broad_histology = "Ependymal tumor",
short_histology = "Ependymoma",
Expand Down
141 changes: 64 additions & 77 deletions analyses/molecular-subtyping-pathology/01-compile-subtyping-results.nb.html
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103 changes: 42 additions & 61 deletions analyses/molecular-subtyping-pathology/02-incorporate-clinical-feedback.nb.html
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38 changes: 13 additions & 25 deletions analyses/molecular-subtyping-pathology/03-incorporate-pathology-feedback.Rmd
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Expand Up @@ -145,7 +145,7 @@ So we will revise the `molecular_subtype`, `integrated_diagnosis`, `short_histol
compiled_df <- compiled_df %>%
mutate(
integrated_diagnosis = case_when(
Kids_First_Participant_ID == "PT_7E3V3JFX" ~ "Ependymoma",
Kids_First_Participant_ID == "PT_7E3V3JFX" ~ "Ependymoma, H3 K28-mutant",
TRUE ~ integrated_diagnosis
),
short_histology = case_when(
Expand Down Expand Up @@ -203,7 +203,7 @@ There are no _BRAF_ fusions in `BS_H1XPVS9A`, so we are able to classify this sa
compiled_df <- compiled_df %>%
mutate(
integrated_diagnosis = case_when(
sample_id == "7316-1106" ~ "Low-grade glioma/astrocytoma",
sample_id == "7316-1106" ~ "Low-grade glioma/astrocytoma, BRAF V600E",
TRUE ~ integrated_diagnosis
),
short_histology = case_when(
Expand All @@ -225,29 +225,6 @@ compiled_df <- compiled_df %>%
)
```

### HGG BRAF V600E

We will be removing this from subtyping, so this can be left for now

The follow point comes from another issue [#627 (comment)](https://github.com/AlexsLemonade/OpenPBTA-analysis/issues/627#issuecomment-598789232):

> We have a standalone BRAF V600E subtype, but this is HGG only, and should be labeled as such (will create an update HGG analysis ticket).

```{r}
compiled_df %>%
filter(molecular_subtype == "BRAF V600E")
```

Now that we have addressed the one sample that should have been reclassified as LGG, we are able to update `molecular_subtype` to `HGG, BRAF V600E` for the remaining samples.

```{r}
compiled_df <- compiled_df %>%
mutate(molecular_subtype = case_when(
molecular_subtype == "BRAF V600E" ~ "HGG, BRAF V600E",
TRUE ~ molecular_subtype
))
```

### `PT_AQWDQW27`

> 2. `PT_AQWDQW27` specimen was consistent with meningioma, even though it has a hallmark EPN fusion, so pathology would also call this a rare meningioma with a _YAP1_ fusion.
Expand Down Expand Up @@ -549,6 +526,17 @@ compiled_df <- compiled_df %>%
)
```

###Check list of subtypes look as expected at this point in time
```{r}
# sort first
list_subtypes <- compiled_df %>%
filter(!grepl("To be classified", molecular_subtype)) %>%
select(integrated_diagnosis, molecular_subtype) %>%
distinct() %>%
arrange(integrated_diagnosis)
list_subtypes
```

### Write revised table to file

```{r}
Expand Down
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