Entering edit mode
6.1 years ago
spanakorice
▴
10
Hello.
I would be interested to know if there are publicly available tools for generating gene panels based on HPO terms.
Something similar to PhenoXome ( https://phenoxome.chop.edu/phenoxome/index.jsp ) or XomeDxSlice ( https://www.genedx.com/xomedx-slice-tool/ ) but rather more uptodate.
For some reason Phenomizer or the HPO website give extensive and rather inappropriately large gene lists.
Thank you in advance.
Are you interested in finding commercial gene panels that best match your HPO terms, or in a list of genes that can be used for in-silico filtering (dynamic gene panels)?
Ideally I would like a tool to provide me dynamic gene panels based on my HPO terms. Usually I do not have access to bioinfomatic data but would wish to get some ideas and/or provide the gene panel to my colleagues for analysis.
Commercial gene panels are already available but often not exhaustive or uptodate.
Any idea? Thank you in advance.
Certainly, the most straightforward of doing this is to do full exome sequencing and then filter variants based on HPO-gene associations. Those associations are maintained by the HPO team and frequently updated: http://human-phenotype-ontology.github.io/downloads.html#genes. This is used within tools such as PhenoTips to provide dynamic HPO-based gene suggestions like you are asking about.
Anyone. Any idea? (20 characters)
For reference: You don't need to add an answer to bump a thread to main page. Just edit the original and hit save.
That said the reason you have not received anything so far is perhaps because not many are familiar with the two sites you have posted above. It would help to add some information about what those sites do and what you are looking to exactly get.