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Update HGG subtyping (4/11) #108

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Update HGG subtyping (4/11) #108

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komalsrathi
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@komalsrathi komalsrathi commented Jun 20, 2024 •
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Created this branch off of update-nf1-score branch.

Comparison of base and annotated histologies file:

base_file <- read_tsv("data/Hope-GBM-histologies-base.tsv")
annotated_file <- read_tsv("analyses/molecular-subtyping-HGG/results/Hope-GBM-histologies.tsv")

# new samples
annotated_file %>%
  filter(sample_id %in% c("7316-3000", "7316-1106")) %>%
  dplyr::select(sample_id, Kids_First_Biospecimen_ID, experimental_strategy, cancer_group, cancer_group_short, molecular_subtype)

  sample_id Kids_First_Biospecimen_ID experimental_strategy cancer_group                  cancer_group_short molecular_subtype
  <chr>     <chr>                     <chr>                 <chr>                         <chr>              <chr>            
1 7316-1106 BS_96QPQX80               Methylation           Pleomorphic xanthoastrocytoma NA                 PXA              
2 7316-1106 BS_9XHV04WE               WGS                   NA                            NA                 NA               
3 7316-1106 BS_H1XPVS9A               RNA-Seq               Pleomorphic xanthoastrocytoma NA                 PXA              
4 7316-1106 BS_J4E9SW51               WGS                   Pleomorphic xanthoastrocytoma NA                 PXA              
5 7316-3000 BS_0TCRV9AC               WGS                   NA                            NA                 NA               
6 7316-3000 BS_ABZ3BK38               WGS                   High-grade glioma             HGG                HGG, H3 wildtype 
7 7316-3000 BS_JRYJGYC4               RNA-Seq               High-grade glioma             HGG                HGG, H3 wildtype 
8 7316-3000 BS_Z0KPQPN2               Methylation           NA                            NA                 NA

Wanted to ask what needs to be done for the PXAs?

@komalsrathi komalsrathi self-assigned this Jun 20, 2024
@komalsrathi komalsrathi changed the base branch from master to update-nf1-score July 15, 2024 17:40
@komalsrathi komalsrathi changed the title Update HGG subtyping Update HGG subtyping (4/11) Jul 15, 2024
@jharenza jharenza requested a review from naqvia August 16, 2024 16:58
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Wanted to ask what needs to be done for the PXAs?

can you make these cancer_group_short == HGG?

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Added the condition cancer_group_short is HGG where molecular_subtype is PXA.

naqvia
naqvia requested changes Aug 19, 2024
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Made a suggestion. Seemed like the intended file was not being saved properly.

analyses/molecular-subtyping-HGG/03-molecular-subtype-integrate.R Outdated Show resolved Hide resolved
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Actually there is one more thing I am realizing with running on docker - I am getting a warning with data.table::fread which is reading large files incorrectly. This is because the default /tmp folder does not have enough space. I will update the fread calls to use scratch directory as temp directory and rerun again.

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FYI - This is the warning I was getting and seems to be only on docker. This was causing file reading to be interrupted way before and the output was incorrect.

Avoidable 14.461 seconds. This file is very unusual: it ends abruptly without a final newline, and also its size is a multiple of 4096 bytes. Please properly end the last row with a newline using for example 'echo >> file' to avoid this  time to copy.

This was fixed by changing the tmpdir parameter to scratch dir (default was /tmp).

Also, I checked even with the same version of data.table and R, I don't get this on my local machine.

@komalsrathi komalsrathi linked an issue Aug 20, 2024 that may be closed by this pull request
Move Pleomorphic xanthoastrocytoma into cancer_group_short HGG #86
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jharenza
jharenza reviewed Aug 20, 2024
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one comment about the dockerfile

Dockerfile
Comment on lines +1 to 3
FROM --platform=linux/amd64 rocker/tidyverse:4.4.0
LABEL maintainer = "Jo Lynne Rokita (rokita@chop.edu)"
WORKDIR /rocker-build/
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can you pull the master dockerfile into this PR, looks like some conflict here

jharenza
jharenza reviewed Aug 20, 2024
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analyses/molecular-subtyping-HGG/results/HGG_cleaned_mutation.tsv
@@ -76,7 +76,7 @@ PT_RSDTCFDA 7316-204 BS_SK4H5MJQ No No No No No No No No No No None No R132 or R
PT_S2BEPYQ0 7316-3000 BS_ABZ3BK38 No No No No No No No No No No None No R132 or R172 None No V600E
PT_SDPA6AAP 7316-624 BS_SMHNXC5G No No No No No No No No No No None No R132 or R172 None No V600E
PT_SYHB12RN 7316-194 BS_9DM8H1RX No No No No No No No No No No FGFR1 No R132 or R172 None No V600E
PT_T8V9ES93 7316-1106 BS_J4E9SW51 No No No No No No No No No No None No R132 or R172 None No V600E
PT_T8V9ES93 7316-1106 BS_J4E9SW51 No No No No No No No No No No BRAF No R132 or R172 None p.V600E
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noting this is expected.

jharenza
jharenza reviewed Aug 20, 2024
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analyses/molecular-subtyping-HGG/results/Hope_subtype.tsv
Comment on lines +186 to +190
PT_CB1DN0V8 BS_3J4X955P 7316-2241 HGG, H3 wildtype NA other
PT_CB1DN0V8 BS_84XCR9GG 7316-2241 HGG, H3 wildtype NA other
PT_CB1DN0V8 BS_N5VEQ8RH 7316-2241 HGG, H3 wildtype NA other
PT_CB1DN0V8 BS_TNVSRPSV_PHOS 7316-2241 HGG, H3 wildtype NA other
PT_CB1DN0V8 BS_TNVSRPSV_WCP 7316-2241 HGG, H3 wildtype NA other
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I think once this is rerun with changes from TP53 we should see TP53 come back here

jharenza
jharenza reviewed Aug 20, 2024
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analyses/molecular-subtyping-HGG/results/Hope_subtype.tsv
Comment on lines +255 to +258
PT_JNEV57VK BS_85Q5P8GF 7316-2594 DMG, H3 K28 NA other
PT_JNEV57VK BS_AMDGBEMH_PHOS 7316-2594 DMG, H3 K28 NA other
PT_JNEV57VK BS_AMDGBEMH_WCP 7316-2594 DMG, H3 K28 NA other
PT_JNEV57VK BS_VF5XWFXD 7316-2594 DMG, H3 K28 NA other
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similarly here

jharenza
jharenza reviewed Aug 20, 2024
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analyses/molecular-subtyping-HGG/results/Hope_subtype.tsv
Comment on lines +402 to +404
PT_T8V9ES93 BS_96QPQX80 7316-1106 PXA NA other
PT_T8V9ES93 BS_H1XPVS9A 7316-1106 PXA NA other
PT_T8V9ES93 BS_J4E9SW51 7316-1106 PXA NA other
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correct

jharenza
jharenza reviewed Aug 20, 2024
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doc/release-notes.md
Comment on lines +3 to +9
## Current release (V3)
- release date: 2024-08-16
- Overview:
- Sequence sample:
- 87 RNA-seq
- 157 WGS
- 80 DNA methylation
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need to merge master and these will also go away

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Move Pleomorphic xanthoastrocytoma into cancer_group_short HGG
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@komalsrathi @jharenza @naqvia