search

oncokb / oncokb-annotator

Annotates variants in MAF with OncoKB annotation.
GNU Affero General Public License v3.0
122 stars 61 forks source link

Oncokb gene symbol/behavior with gene aliases #203

Closed pintoa1-mskcc closed 10 months ago

pintoa1-mskcc commented 1 year ago

If I provide a gene symbol which is actually an alias to a known oncokb gene, will oncokb recognize the alias and annotate accordingly? Or would I need to provide the expected oncokb gene name to get the annotation?

zhx828 commented 1 year ago

If I provide a gene symbol which is actually an alias to a known oncokb gene, will oncokb recognize the alias and annotate accordingly? Or would I need to provide the expected oncokb gene name to get the annotation?

We recognize gene alias. For instance if you query BRAF1 V600E instead of BRAF V600E, you will get the same response. Some language in the summaries might need to be updated though, but I don't think it affects the data quality.

pintoa1-mskcc commented 1 year ago

This also applies for FusionAnnotator?

zhx828 commented 1 year ago

This also applies for FusionAnnotator?

yes

pintoa1-mskcc commented 1 year ago

I found a gene in my gtf file TRAC which matches TRA in gene cards and NCBI, however the gene aliases listed on oncokb/cancer_geneList do not include TRAC. Will this mean that my TRAC gene will not be annotated as an oncogene?

I am seeing that the genes in my gtf file that are not in the aliases of oncokb are primarily the T cell receptor loci (or IGH@, which is not in oncokb, but is a cancer gene)

Below are the oncokb accepted symbols that my gtf file is lacking a match in either aliases/name

"IGH" "IGK" "IGL" "TRA" "TRB" "TRD" "TRG" "RNF217-AS1"

zhx828 commented 1 year ago

I found a gene in my gtf file TRAC which matches TRA in gene cards and NCBI, however the gene aliases listed on oncokb/cancer_geneList do not include TRAC. Will this mean that my TRAC gene will not be annotated as an oncogene?

I am seeing that the genes in my gtf file that are not in the aliases of oncokb are primarily the T cell receptor loci (or IGH@, which is not in oncokb, but is a cancer gene)

Below are the oncokb accepted symbols that my gtf file is lacking a match in either aliases/name

"IGH" "IGK" "IGL" "TRA" "TRB" "TRD" "TRG" "RNF217-AS1"

Sorry about the late reply. We consider TRAC and TRA two different genes. In the HGNC gene list which is the one we use, they only associate one symbol with one gene. Therefore TRA is not associated as gene alias of TRAC