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Update integrated dx for 3 samples based on pathology review #879

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Jan 5, 2021
Merged

Update integrated dx for 3 samples based on pathology review #879

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b282a71
add Notes, update int_dx for K28M update
kgaonkar6 Dec 23, 2020
53dbeea
add Notes to pathology updates
kgaonkar6 Dec 23, 2020
9e69daa
add Notes to pathology updates
kgaonkar6 Dec 23, 2020
3fd999b
run with v17 histology file
kgaonkar6 Dec 23, 2020
14070b7
Merge branch 'master' into update_pathology_dx
jashapiro Jan 4, 2021
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202 changes: 93 additions & 109 deletions analyses/molecular-subtyping-pathology/01-compile-subtyping-results.nb.html
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30 changes: 25 additions & 5 deletions analyses/molecular-subtyping-pathology/02-incorporate-clinical-feedback.Rmd
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Original file line number Diff line number Diff line change
Expand Up @@ -115,6 +115,9 @@ diff_subtype <- subtype %>% left_join(pnoc003_review,by=c("Kids_First_Participan
# checking for samples where clinically reviewed subtype is H3 K28M
# but molecular subtype is not DMG H3 K28
(grepl("K28M",.$`H3 Status`) & !grepl("DMG, H3 K28",molecular_subtype)) |
# checking for only RNA-Seq HGG samples where clinically reviewed subtype is H3 K28M
# but molecular subtype is HGG, To be classified
(grepl("K28M",.$`H3 Status`) & grepl("HGG, To be classified",molecular_subtype)) |
# checking for samples were clinical review was not found
grepl("no report",.$`H3 Status`) ) %>%
dplyr::select(Kids_First_Participant_ID,
Expand All @@ -141,9 +144,7 @@ diff_subtype %>%
```


Seems like 6 sample (WXS and matching RNA-Seq from PT_NK8A49X5, PT_QA9WJ679, PT_WGVEF96B) molecular subtype
need to be updated and Notes columns for these samples will be updated to capture this
information
Seems like for a subset of PNOC samples (WXS and matching RNA-Seq samples from PT_NK8A49X5, PT_QA9WJ679, PT_WGVEF96B) Notes,molecular_subtype and integrated_diagnosis will need to be updated to capture this information.

```{r}
subtype_clinical_review_df <- subtype %>%
Expand All @@ -165,20 +166,39 @@ subtype_clinical_review_df <- subtype %>%
# THEN the value in Notes will be updated to specify that the value is
# updated because of clinical review
~ paste(Notes,"Updated to DMG, H3 K28 from clinical review", sep=","),
# IF K28M in clinical review and molecular subtype is HGG, To be classified
(grepl("K28M",.$`H3 Status`) & grepl("HGG, To be classified",molecular_subtype))
# THEN the value in Notes which will be NA will need to be updated to
# specify that the it's DMG K28M from clinical review
~ paste("Updated to DMG, H3 K28 from clinical review", sep=","),
# IF clinical review and molecular subtype match OR
# no clinical review is provided then keep values from Notes
TRUE ~ Notes
),
integrated_diagnosis = case_when(
# IF we have K28M in clinical review and molecular subtype if not DMG K28M
(grepl("K28M",.$`H3 Status`) & !grepl("DMG, H3 K28",molecular_subtype))
# THEN the value in integrated_diagnosis will be updated to specify that the value is
# updated because of clinical review
~ "Diffuse midline glioma, H3 K28-mutant",
# IF clinical review and molecular subtype match OR
# no clinical review is provided then keep values from Notes
TRUE ~ integrated_diagnosis
),
molecular_subtype = case_when(
# Don't think we would need to ever change from K28 to H3 wildtype
# since there would be evidence for K28 from snv data for the sample
#(grepl("H3 WT",.$`H3 Status`) & !grepl("HGG",molecular_subtype)) ~
# gsub("DMG, H3 K28","HGG, H3 wildtype",molecular_subtype),
#
# IF we have K28M in clinical review and molecular subtype if not DMG K28M
(grepl("K28M",.$`H3 Status`) & !grepl("DMG, H3 K28",molecular_subtype)) ~
# IF we have K28M in clinical review and molecular subtype is "HGG, H3 wildtype"
(grepl("K28M",.$`H3 Status`) & grepl("HGG, H3 wildtype",molecular_subtype)) ~
# THEN the value in molecular subtype will be updated
gsub("HGG, H3 wildtype","DMG, H3 K28",molecular_subtype),
# IF we have K28M in clinical review and molecular subtype is "HGG, To be classified"
(grepl("K28M",.$`H3 Status`) & grepl("HGG, To be classified",molecular_subtype)) ~
# THEN the value in molecular subtype will be updated
gsub("HGG, To be classified","DMG, H3 K28",molecular_subtype),
# IF clinical review and molecular subtype match OR
# no clinical review is provided then keep values from molecular subtype
TRUE ~ molecular_subtype
Expand Down
245 changes: 128 additions & 117 deletions analyses/molecular-subtyping-pathology/02-incorporate-clinical-feedback.nb.html
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31 changes: 29 additions & 2 deletions analyses/molecular-subtyping-pathology/03-incorporate-pathology-feedback.Rmd
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Original file line number Diff line number Diff line change
Expand Up @@ -155,6 +155,10 @@ compiled_df <- compiled_df %>%
molecular_subtype = case_when(
Kids_First_Participant_ID == "PT_7E3V3JFX" ~ "EPN, H3 K28",
TRUE ~ molecular_subtype
),
Notes = case_when(
Kids_First_Participant_ID == "PT_7E3V3JFX" ~ "Updated via OpenPBTA subtyping",
TRUE ~ Notes
)
)
```
Expand Down Expand Up @@ -279,7 +283,10 @@ compiled_df <- compiled_df %>%
short_histology= case_when(sample_id == "7316-272"~"ETMR",
TRUE ~ short_histology),
integrated_diagnosis = case_when(sample_id == "7316-272"~"Embryonal tumor with multilayer rosettes, C19MC-altered",
TRUE ~ integrated_diagnosis)
TRUE ~ integrated_diagnosis),
Notes = case_when(sample_id == "7316-272" ~ "Updated via OpenPBTA subtyping",
TRUE ~ Notes
)
) %>%
unique()
```
Expand Down Expand Up @@ -316,6 +323,10 @@ compiled_df <- compiled_df %>%
molecular_subtype = case_when(
sample_id == "7316-1102" ~ "DMG, H3 K28",
TRUE ~ molecular_subtype
),
Notes = case_when(
sample_id == "7316-1102" ~ "Updated via OpenPBTA subtyping",
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I don't quite understand why it looks like there's recoding by individual samples -- it would probably be good to look into a more systematic way to do this, but that should be in a different PR, not now.

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This notebook is designed to handle individual cases based on feedback from pathologists / clinical expertise. I think it's possible that coding for individual cases with lots of context is more clear.

TRUE ~ Notes
)
)
```
Expand Down Expand Up @@ -345,6 +356,10 @@ compiled_df <- compiled_df %>%
molecular_subtype = case_when(
sample_id == "7316-765" ~ "CNS HGNET-MN1",
TRUE ~ molecular_subtype
),
Notes = case_when(
sample_id == "7316-765" ~ "Updated via OpenPBTA subtyping",
TRUE ~ Notes
)
)
```
Expand Down Expand Up @@ -374,6 +389,10 @@ compiled_df <- compiled_df %>%
molecular_subtype = case_when(
sample_id == "7316-158" ~ "HGG, H3 G35",
TRUE ~ molecular_subtype
),
Notes = case_when(
sample_id == "7316-158" ~ "Updated via OpenPBTA subtyping",
TRUE ~ Notes
)
)
```
Expand Down Expand Up @@ -412,7 +431,8 @@ compiled_df <- compiled_df %>%
sample_id == "7316-229" ~ "EWS",
TRUE ~ molecular_subtype
),
Notes = case_when(sample_id == "7316-229" ~ "Updated via OpenPBTA subtyping",
Notes = case_when(
sample_id == "7316-229" ~ "Updated via OpenPBTA subtyping",
TRUE ~ Notes
)
)
Expand Down Expand Up @@ -451,6 +471,10 @@ compiled_df <- compiled_df %>%
molecular_subtype = case_when(
sample_id == "7316-238" ~ "ETMR, C19MC-altered",
TRUE ~ molecular_subtype
),
Notes = case_when(
sample_id == "7316-238" ~ "Updated via OpenPBTA subtyping",
TRUE ~ Notes
)
)
```
Expand Down Expand Up @@ -480,6 +504,9 @@ compiled_df <- compiled_df %>%
molecular_subtype = case_when(
sample_id == "7316-1105" ~ "HGG, H3 G35",
TRUE ~ molecular_subtype
),
Notes = case_when(sample_id == "7316-1105" ~ "Updated via OpenPBTA subtyping",
TRUE ~ Notes
)
)
```
Expand Down
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