The annotation of the panel **GRCC-SAFIR02** is incomplete. The file in `gene_panels` does not list the tested genes, and the file ` genomic_information.txt ` does not contain tested positions for this assay.
These are the genes and mutations reported in `data_mutations_extended.txt`:
```
hgvsg Chromosome Start_Position End_Position
Hugo_Symbol
FGFR4 NC_000005.9:g.176517832T>C 5 176517832 176517832
FLT1 NC_000013.10:g.29002014A>C 13 29002014 29002014
HRAS NC_000011.9:g.533874T>A 11 533874 533874
KRAS NC_000012.11:g.25398284C>A 12 25398284 25398284
NOTCH4 NC_000006.11:g.32188317C>T 6 32188317 32188317
NRAS NC_000001.10:g.115256528T>A 1 115256528 115256530
PIK3CA NC_000003.11:g.178936082G>A 3 178936082 178936082
PTPN11 NC_000012.11:g.112926888G>T 12 112926888 112926888
TP53 NC_000017.10:g.7578532A>T 17 7578532 7578532
TP53 NC_000017.10:g.7573976T>A 17 7573976 7573976
TSC2 NC_000016.9:g.2110761G>C 16 2110761 2110761
```
However, only 8 samples are reported as having been tested with that assay and having at least one of the above mutations. Therefore, maybe you might want to consider removing this assay from future releases.
Created by Henrik Seidel henrik.seidel Hi @henrik.seidel,
Doing some investigation, using the 15.0 release and the python client:
```
import pandas as pd
import synapseclient
syn = synapseclient.login()
genomic_info_entity = syn.get("syn53210444")
genomic_info_df = pd.read_csv(genomic_info_entity.path, sep="\t")
genes = genomic_info_df[genomic_info_df['SEQ_ASSAY_ID'] == "GRCC-SAFIR02"]['Hugo_Symbol'].unique()
# The following will return true
pd.Series(['FGFR4', 'FLT1' ,'HRAS', 'KRAS', 'NOTCH4', 'NRAS', 'PIK3CA', 'PTPN11', 'TP53', 'TSC2']).isin(genes).all()
```
We have a process internally where the site can define which genes they would like to leave out of the data_gene_panel.txt file, but they did use those regions. I'll follow up with more details soon - by the looks of it, these genes should be included in the data gene panel file, but is being left out on purpose as what the site submitted. Hi @henrik.seidel ,
Thanks for raising this, we are currently looking into this and will reach out to the site.
cc @ProjectGENIEAdmins
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