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Clinical-Genomics / scout

VCF visualization interface
https://clinical-genomics.github.io/scout
BSD 3-Clause "New" or "Revised" License
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Suggestion of added External Links for variants pages (Clinical SNV and INDELs). #4210

Open TJO-Lund opened 11 months ago

TJO-Lund commented 11 months ago

We (Lund) suggest two additional External Links for variants pages (Clinical SNV and INDELs).

  1. Decipher: Clinical-info page for genes e.g. https://www.deciphergenomics.org/gene/POLR3B/overview/clinical-info. Great to have - higher priority.
  2. MobiDetails: if possible linked to each missense-variant (https://mobidetails.iurc.montp.inserm.fr/MD/). Good to have - lower priority.
dnil commented 11 months ago

For the Decipher link, would you like to try to do something with the SV contained genes as well there? We could eg show links if there are only a few genes, show them only for the case default panel genes or whatnot. We could also just do the SNV links for now.

The MobiDetails looks like very cool beginnings, has attention to what is important, and actually has a defined API. But I will admit I get PhD project vibes from it. Not many variants yet, pages design feels temporary, instructions and docs are a bit difficult to find. Publications are a couple of years old. Do you know them? Have they secured stable funding and like a dev team to keep it running?

TJO-Lund commented 11 months ago

For Decipher we feel that a link to the main Gene page (for any SNV/INDEL in a gene) could help those who do the analysis (and reduce risk of missing important info from GeneRevies, ClinGen etc). An example is https://www.deciphergenomics.org/gene/UBE3A/overview/clinical-info (only the HGNC gene name differs in this address for different genes). For SVs, we mainly look at the "Genes" button after searching for e.g. a deleted segment https://www.deciphergenomics.org/search/genes?q=3%3A8968502-11698813 thus, we can by Clicking on the ClinGen-column (show all variants/protein coding genes etc) see if ClinGen has assessed any genes in the segment for Haploinsufficiency or Triplosensitivity. I am not sure I understood Daniels question above.

Regarding MobiDetails, I do not know about funding etc. and quite a few of the variants are perhaps added by us in Lund. What we do (and perhaps it could be automated?) is

  1. Go to the home-page https://mobidetails.iurc.montp.inserm.fr/MD/
  2. Enter variant info (Mane usually) e.g. NM_018082.6:c.701T>C
  3. Check info under e.g. Missense: with many prediction tools conveniently collected (including radar chart).