Closed AliciaByrne closed 3 years ago
Hi Alicia,
When looking over the sample file you provided, I encountered the following concerns
Let me know what you think
Hi Hana
Thanks for your suggestions! I've responded to them below in the same order as you've raised them.
Thanks! :)
Re: your question on 4 "Would it be helpful to do this for 'previously tested genes' too in cases where there is a gene name listed?" I would say yes thats a good idea. If there isn't a gene for that field you could just start the line with a "-" (i.e. "- Panel" instead of just "Panel")
If you could create a new test file based on the changes discussed here and send it to me that would be really helpful. Slacking it to me the way you did the first one works fine
Sorry for the delay getting to this. Have just slacked you the new test file.
Also - we've decided to take out the free text phenotype information, as often times the clinicians will just copy and paste the autopsy report and there is sometimes identifying information. The majority of this information is captured in the HPO terms and diagnosis sections so we will not lose too much information by excluding it.
Hi, I'm sorry for the massive delay on this. As you may have realized, seqr no longer integrates directly with phenotips. Are these still data fields you would like to bulk upload directly to seqr?
Based on the new fields available in seqr now that we don't use phenotips, I think we should add the following fields as options for bulk upload. They should be added as optional to the EditHPOBulkForm
, and we should rename that form to something more descriptive (maybe "Edit Phenotypes")
Additional fields requested in https://github.com/broadinstitute/seqr/issues/1759 (this new field list includes everything previously required by this ticket)
Note: Case Review Status is a protected field so bulk updating it will happen in the main "update individual" form not the "update individual metadata" form
the "update individuals" bulk upload now supports all of these fields, including as json exported from a separate phenotips instance
Would be helpful to have bulk upload options for PhenoTips fields in addition to 'HPO Terms present' and 'HPO Terms absent'. Key fields of interest (for CMG_Scott projects) are: 'Candidate Genes', 'Previously Tested Genes', and 'Diagnosis' (as below). Would also be helpful to bulk upload 'maternal/paternal ethnicity' and 'consanguinity' (below) to cross-check with inferred results from sequencing.
Scott project data is exported from REDCap to an Excel file. Some fields (eg HPO terms) are currently split over multiple cells - we can condense these to single cell, comma separated. There is also a free-text phenotype entry field with additional info not necessarily matching to HPO term - unsure where this would best fit in Seqr.