nhs-ngs / gel2mdt Goto Github PK

Improve MDT export: Include NHS number, centre, clinician, tumour type, discussion and action in the export. Export the list in the same order as the main MDT table.

Requested by clinician in GOSH

Be able to sort cases in MDT (either manually drag/drop style or by sorting by tumour type/clinician/centre/priority).

• "Not started" when case first added.
• "Under review" when user assigned.
• "Awaiting MDT" when MDT status set to "Required"
• "Awaiting Validation" when any genes set to requires_validation, AND MDT status set to "Not Required" OR MDT status set to "Done".
• "Awaiting Reporting" when no genes require validation AND MDT status set to "Not Required" OR MDT status set to "Done".
• "Reported" once a report has been generated.
• "Completed" once a case becomes archived within CIP-API.

Be able to search or filter for cases with germline variants.

Allow users to archive old out of date interpretations of cases. These would be excluded from the main table

vep_util still runs merged whatever is specified in config for b38, which causes VEP to fail for 38s

When selecting cases for MDT include a look up for those with eg case status ‘awaiting MDT’ or MDT status ‘required’. Include more details on the cases so can assess if relevant to the MDT being created (eg tumour type/referral centre/comments)

A new page should be included which allows bulk assignment of cases to particular users. The main page should also allow display of cases by assigned user.

When editing discussion or action within MDT display patient name or identifier within the pop up box.

Need ability to add a comment to sample - not just to the patient. One patient may have multiple samples and currently writing in the comment box amends the same info in each sample. This feature is very important if multiple samples over a period of time are received and analysed which is highly likely for some cancer types.

It would be useful to display the sample ID on the main cases table so that you don't need to go into each case to work out which sample it relates to.

Would be useful to be able to see or link to other samples or analyses for the same patient when reviewing one set of results.

eg. be able to apply filters to main table to find cases ready to report and that also have specific MDT status such as not required.
This would help with dividing workload between people writing specific reports.

Include patient details/NHS number in the variants for validation table. Include whether the variant for validation is somatic or germline.

Only relevant here at gosh but request is for:

bulk download the outcome forms from an MDT

Asked to add a flag for urgent cases and then show as a filter for the main table

If you download a zipped release rather than cloning the repository it doesn't include the .git folder. This means that the build() function in gel2mdt_extras.py doesn't work as the subprocess command won't be able to access git log.

View edit_mdt is slow and need alternative. Perhaps allowing users to search cases instead of filtering all cases?

As well as negative cases, there should also be an option to generate positive technical reports with ability to choose which variants are included in this.

Test methodology should have the following sentence added: "Variants are classified using the ACMG/AMP guidelines (Richards et al., 2015 Genet Med) and confirmed using in-house Sanger sequencing.

Variant details should have a table of variants with the following columns:
Gene, Zygosity, Inheritance, HGVSc & HGCSp, Location (build), Classification, VEP Consequence.

When altering the validation status of multiple variants in the mdt_proband_view only a single variant (the first) has its status changed.

Gene validation should be more complex than True/False: once a variant is set for validation, it should also then have "validation outcomes" - pass or fail.

Prevent clinicians from starting mdt

Request from clinician: classification/ contribution to phenotype bit came before the discussion/ action box

Remove ability to easily and accidentally delete an MDT and all the information within it.

Users need to quickly pull out how many NPF cases have been reported

This causes confusion for CSs due to multiple versions of the same case

Genes to be validated should be split into rare disease and cancer genes

Users need to find a relative using some search function.

Could be implemented using DataTables

Genes can be assigned for validation at the ProbandVariant tab within the Proband view, but in the interest of time this should also be possible during the MDT view of variants.

Need to create a report template for GTAB

Export NHSno, Subtype, Gender in main table, not actually shown in table

If patient is discussed in multiple MDTs there needs to be a way to distinguish discussion and action points from each MDT.

Audit panel has the correct number of cases, but for the wrong categories:

e.g under review here has 133, but audit lists this as the number of validation

Add cancer clinical info the the proband view

Need to implement fix so that the correct status appears when users check cases assigned to them in the /profile view.

In the VEP section the URL for the location to see the list of repositories to download is missing.

The MDT functionality should be duplicated and renamed to GTAB to allow support for GTAB discussion and actions for cancer cases.