Add Clinical Validity Summary Matrix to GCI Summary page

[mrmin123]

A continuation of #1094. See this post for details.

This is now the ticket for adding the Clinical Validity Summary Matrix on the provisional curation page on the GCI, as defined above. This will involve:

• Displaying the data (rendered in a table or list-style, depending on timing)
• Adding a checkbox/dropdown to allow user to specify whether or not the 'Replication over time' field is True or False
• Adding or modifying an existing field to support the 'Valid Contradictory Evidence' field (may need furthering spec-ing out)
• Modifying the schema so these fields can be saved
• Update scripts for these fields, if applicable
• Ensuring that saved values for these fields can be properly retrieved, displayed, and edited by the user from the front-end

[selinad]

Per discussion, if easier, could check to see whether there is:

• Proband with "contradicts" selected
• Case-control with "contradicts" selected
• Experimental with "contradicts" selected

Would print this out:

Contradictory evidence:
Proband: (yes/no)
Case-control: (yes/no)
Experimental: (yes/no)

Instead of "Select" provisional clinical validity classification, use the term "Modify" and have "No Selection" be the default (mimic behavior of VCI).

[mrmin123]

note to self: "No Evidence" -> "No Selection"

[selinad]

@mrmin123 per curators, please round up if value is n.5 or higher and on the border between classifications. thx! - Selina

[selinad]

Hi @mrmin123 and @jimmyzhen -- re https://1184-mc-summary-table-fc2caf4-minchoi.demo.clinicalgenome.org/

It's looking fantastic! So far, the things I've checked have been great (much more to check). One quick thing that seems so trivial given all the hard work in this ticket -- could the "Yes" printout for Contradictory evidence? be in red? I think this would be super helpful and jolt the user into the fact that information exists there. There is a fair amount of text so it could get lost.

Love the timestamp.

Quick question -- will the button switch to "Generate New Summary" after their first Summary save?

Really amazing work - thanks @mrmin123 and @jimmyzhen. Will need to pound, but the replicated over time, the "contradictory" feedback, modifying classification all looking good thus far.

[selinad]

Two other small things

• change "Change Provisional Clinical Validity Classification" to "Modify..."
• where it says "Final Classification" it maybe should say "Current Provisional Classification," especially since it so nicely adjusts when the pull-down is changed - wow again! 👍

[jimmyzhen]

@mrmin123 I have submitted a PR for the schema changes and upgrade script: #1197

[wrightmw]

@mrmin123 and @jimmyzhen I've only just started pounding on this but I can already see this is great work guys. The functionality is great so far. You've achieved so much in such a short amount of time. Awesome!

[selinad]

HI @mrmin123 -- I forgot to say count a LOD score so went back to Family to answer that question yes and got an error on save (gives continually spinning wheel)

[mrmin123]

@selinad that'll probably need more information (values of fields) and probably a new ticket.

[selinad]

@mrmin123 could the checkbox for replicated over time be a bit larger?

[selinad]

thx @mrmin123 which value of fields do you need?

[mrmin123]

@selinad ideally all of them....

Screenshot of desired red text/modified text/larger checkbox

[mrmin123]

@selinad haven't been able to re-create the Family saving error... definitely another ticket if you can recreate.

This bug addressed in #1199

[selinad]

That's great -- thank you. Maybe a "?" after "Contradictory Evidence"...

[wrightmw]

@selinad
In the Curate Family Section, in the LOD score section if I go to estimate an autosomal dominant record but I have not entered the number of segregations in the Tested Individuals section, then it just tells me "Not enough information entered to calculate an estimated LOD score" but does not tell me why. In this case the curator simply needs to scroll up slightly and enter the number of segregations in the 'Number of segregations reported for this Family' field in the Tested Individuals section. Should we highlight the field in red when this happens? Or simply for now add text next to the 'Number of segregations reported for this Family' field...something along the lines of 'Number of segregations reported for this Family (required for dominant if estimating LOD score)'
@mrmin123 separate ticket?

[selinad]

thx @wrightmw it is not need to have, but @mrmin123 let us know if a text change would be quick to implement.

[mrmin123]

@wrightmw separate ticket.
Separate ticket created: #1200

[selinad]

@mrmin123 I know this is super picky -- the green to highlight the calculated classification reminds me a bit of "benign" -- could we have more neutral color. Maybe a light-ish blue? Not sure whether @wrightmw agrees or has suggestion (esp since he likes green). The blue would be more in keeping with colors on page (as long as different from section bars).

[selinad]

@mrmin123 should we just remove "Generate New Summary" button that is on Summary page? Maybe that's easier than changing text. If not, no worries. I feel it is a bit confusing there, though.

[wrightmw]

@selinad @mrmin123 If we change the color then I would opt for blue.

[selinad]

@mrmin123 the rounding up works great!

Should we add a note at bottom of table that things are rounded up? We could do next release...seeing it makes me realize it may look funny.

[wrightmw]

@selinad When I had a half point score it seemed counterintuitive to me that it rounds up when this is quite a conservative scoring system... so I think a message in a future release advising curators that half points are rounded up would be advisable.

[selinad]

This may be misleading:

If I "modify" to Strong even though at Strong:

If I select "No Selection" when Calculated = Strong

Preferable it would say:

Calculated Score
Provisional Classification

For both cases it would then be:
Calculated Score: 11.5 (Strong)
Provisional Classification: Strong

OR it would not say "No Selection" but print out the calculated classification since curator could have said it.

e.g.
Total Score: 11.5 (Strong)
Provisional Classification Strong

[selinad]

@mrmin123 if there is a score of "0" for Case-control, it should show count of 1, but shows "0" -- this may be the case for other evidence types -- will check.

[selinad]

@mrmin123 just realized that if I select "Contradicts" for Experimental, then get count of 1 (Expression) and score of "0" -- it should be "0" for count as well. At some point, we can be clearer that there was a contradictory piece of evidence there (maybe a count for contradicts)

p.s. this doesn't seem to be the case for probands...

[mrmin123]

@selinad

• I fixed the initial form not saving
• For the wording in the GDM header, that's outside the scope of this ticket so please create a new ticket. It might be best if @jimmyzhen works on this is in the same area as Change "Total" to "Calculated" in header for Classification #1206

[mrmin123]

@selinad instance has been updated to fix the initial form not saving (was not dependent on 0.5 score), and better counting of Contradicts and 0 score evidence.

[selinad]

@mrmin123 thanks!

• Initial form now saves...great!
• Contradicts does not count for Experimental now - great!
• 0 score counts now

Unfortunately, new bug re experimental...making new ticket ( #1209)

[selinad]

@mrmin123 this is fantastic! All worked as expected/specified. Super job!

Contradicts comes in correctly
Classification adjusts correctly
able to change with reason

Without replication over time

With replication over time

Modify classification

[wrightmw]

I concur. @mrmin123 you've done a fantastic job incorporating the Summary Matrix. It works perfectly and is bang on spec.

[kilodalton]

Included in last release (R9). Nice job and thanks for your hard work.