ecc: introduces H3 K27M mutation characteristics #10
Conversation
claymcleod
requested review from
a team
and removed request for
claymcleod and
mcrusch
claymcleod
force-pushed
the
ecc/h3-k27m
branch
from
d6e1b19 to
4d26d55
Compare
| kind: binary | ||
| description: | ||
| "true": | ||
| summary: Here is a summary for the 'true' value. |
There was a problem hiding this comment.
This still needs to be filled out: how will the ECC be assigned, what will the permissible values be, and what do each of the permissible values mean.
There was a problem hiding this comment.
Thank you for your comments. However, I am not sure what the description of the binary feature refers to.
In my understanding, it could be one of two cases:
-
It describes the ECC, such as how we evaluate or confirm that ECC - criteria to define this ECC, for example:
descriptions:
"true":
summary: Confirm by Sanger sequencing.
"true":
summary: confirm by RNA seq. -
It describe the ontology characteristics, meaning it should be in the definition of an ontology, for example:
Ontology Class: Diffuse midline glioma, H3 K27-altered
ECC:
- identifier: ECC-MOLEC-00001
name: H3 K27M Mutation
appear: true
- identifier: ECC-MOPHL-00001
name: Vascular Proliferation
appear: false
...
Please let us know your ideas or examples if possible, and correct me if I misunderstood.
There was a problem hiding this comment.
H3 K27M refers to a specific mutation in the histone H3 protein, where lysine at position 27 is replaced by methionine.
This mutation is primarily associated with diffuse midline gliomas (DMGs), a category of highly aggressive brain tumors that predominantly affect children but can also occur in adults.
The mutation is linked to poor prognosis, with median overall survival ranging from 10.1 to 14.4 months post-diagnosis.PMC7739048, 38102230
@van-lamnguyen
A few things to add:
- I think we should describe if this variant is hg38 or hg19 and what it is in the alternative ref genome as this is important to note when classifying the biomarker.
- what is the Human Genome Variation Society (HGVS) nomenclature?
- This often occurs in the H3F3A (H3.3) or HIST1H3B/C (H3.1) genes.
- When this variant exists, what biological function is disrupted?
@Ssandor13 Thank you for your comments. The comments is all about detail of the variant. As I know that we have variant database, so is that possible if we have a field to add the ID of the variant from our database?. That will help us to easily get more information if needed and keep the content consistent. |
|
#10 (comment) The characteristic is having this variant specifically, so I think the content should be about the variant, if we can point out to other databases like OMIM or ClinVar that provide a details description, I think that is worth discussing internally with the team what the best practice is. I'd love to hear your thoughts on which direction we should take. |
This pull request adds or modifies an ECC.
ECC: H3 K27M Mutation
This is the first introduction of the ECC H3 K27M Mutation.
Close #8
Describe the changes you have implemented and link to any relevant issues.
Before submitting this PR, please make sure:
CHANGELOG.md(see"keep a changelog" for more information).