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

* add Notes, update int_dx for K28M update * add Notes to pathology updates * add Notes to pathology updates * run with v17 histology file Co-authored-by: jashapiro <josh.shapiro@ccdatalab.org>
AlexsLemonade · Jan 5, 2021 · 57e947a · 57e947a
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commit 57e947a
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diff --git a/analyses/molecular-subtyping-pathology/01-compile-subtyping-results.nb.html b/analyses/molecular-subtyping-pathology/01-compile-subtyping-results.nb.html
diff --git a/analyses/molecular-subtyping-pathology/02-incorporate-clinical-feedback.Rmd b/analyses/molecular-subtyping-pathology/02-incorporate-clinical-feedback.Rmd
@@ -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,
@@ -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 %>%
@@ -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

diff --git a/analyses/molecular-subtyping-pathology/02-incorporate-clinical-feedback.nb.html b/analyses/molecular-subtyping-pathology/02-incorporate-clinical-feedback.nb.html
diff --git a/analyses/molecular-subtyping-pathology/03-incorporate-pathology-feedback.Rmd b/analyses/molecular-subtyping-pathology/03-incorporate-pathology-feedback.Rmd
@@ -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
     )
   )
 ```
@@ -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()
 ```
@@ -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",
+      TRUE ~ Notes
     )
   )
 ```
@@ -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
     )
   )
 ```
@@ -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
     )
   )
 ```
@@ -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
     )
   )
@@ -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
     )
   )
 ```
@@ -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
     )
   )
 ```