hanars
commented
10 hours ago Just an FYI that I added a feature request label because generally speaking from an engineering perspective bugs are things where something used to work and stopped working and you have to figure out why. This was actually never supported behavior, so the engineering work for this ticket is more similar to a feature request than a bug. However, I agree that to the end user this is very unexpected behavior so I do want us to prioritize it as a bug and not a nice-to-have feature so I have both labels applied
Describe the bug I'm trying to generate some Talos-mimicking searches, which use only a subset of the genes on the PanelApp Mendeliome list. The easiest way to generate this in the search interface is to select the Mendeliome list, then the dropdown for autosomal dominant mode of inheritance, and then I delete all the genes that are not in the Green panel. After customizing the list, I saved the search (named Talos DN/dominant in my account if that's helpful). When I select this search in a new case, however, the full Mendeliome list is shown in the Location options, rather than the subset of dominant genes on the Green panel that I wanted to include in my saved search.
I am able to get around this bug if I manually copy the subset of Mendeliome genes I want into the genes/intervals field without selecting a PanelApp gene list, but I'm creating a ticket anyway since I think this behavior could confuse others. A secondary issue is that I can't edit or delete any of the saved searches I created this way from my account (I presume because when I select the saved search from the dropdown it does not accurately reflect the search I saved but you would know better). Specifically for the purpose of automated reanalysis (Talos), it will be important for the search we use to be automatically updated to the most current list of dominant or recessive "green" mendeliome genes in PanelApp - not sure if the fix requested here would be required for that to be possible?
Link to page(s) where bug is occurring This search with the customized gene list should return 4 variants: https://seqr.broadinstitute.org/variant_search/results/ecbcff05bbd81e4d2d8ea03a903d7563?page=1&sort=gnomad_exomes
However if I refresh the case and select my Talos DN/dominant saved search again (which I saved with the gene list modified to just be the dominant genes on the green panel), I would get 12 variants because it searches the full Mendeliome list: https://seqr.broadinstitute.org/variant_search/results/8eb04e6754b9c89b14547e1e0da04316?page=1&sort=gnomad_exomes
Scope of the bug All projects. Same thing happens with any customization of the Mendeliome list (eg if I try to save only the recessive genes).
Screenshots Gene list I tried to save:
Gene list that appears when I reload the saved search: