NTR: biallelic inactivation

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NTR: biallelic inactivation #548

Open ireneisdoomed opened 3 years ago

ireneisdoomed commented 3 years ago

What is this request referring to? biallelic inactivation

What is the name you would like SO to give the term? biallelic_inactivation

What is the definition that you would like for this term? An inactivating mutation that occurs on both alleles of a single gene.

Parent Term Please put this under feature_truncation (SO:0001906 )

Relevant Publications This term is used in the cancer biomarkers database from the Cancer Genome Interpreter (PMID: 29592813). We, at Open Targets, are curating this dataset to build pieces of evidence that establish the relationship between the tumors, the affected gene and the biomarker. Biallelic inactivation ("BIA") is one of the possible consequences of the variants.

We want to know if you think this term fits into any existing one or if it is sensible to create one for it. NCIT lists the term biallelic mutation (NCIT_C129829), it being less granular than the proposed one.

ireneisdoomed commented 3 years ago

I'd like to follow up on this ticket as I am not sure of the necessity of a new term in this case anymore. The fact that the variant occurs in both alleles rather points to how the variant is inherited than to a novel type of variant.

Please let me know if you have a different opinion, otherwise, feel free to close this NTR.

Many thanks.

egchristensen commented 3 years ago

Hello! Apologies for the delay. Thank you for your patience. If this term is commonly being used to annotate a sequence then we'll likely want to include it in the SO. Would you say that's still the case here?

egchristensen commented 3 years ago

Closing this issue for now. Please reopen this issue if you'd like to continue the conversation.

ireneisdoomed commented 3 years ago

Hi @egchr,

as I mentioned above, this type of alteration is used in the Cancer Biomarkers Database. There are a number of bibliographic references as well (https://www.nature.com/articles/s41431-018-0097-3), so I think it is worth creating the term in SO.

Many thanks.

egchristensen commented 2 years ago

A couple follow-up questions:

I'm wondering if the term 'biallelic_inactivation' might fit under 'loss_of_function_variant' (SO:0002054)? While the parent you proposed might work, I feel like this paper you cited focuses more on the affect the gene product had on the patients' phenotype as opposed to the structure of any affected gene product(s). Clearly these two ideas would be related, but I'm not sure. What you think? Are you aware of any research pertaining to the latter?
What do you think of this definition, "When inactivating variants occur on both alleles of a single gene."