GenomeConnect Variation Tracker: Transition Excel-based functionality to Google-based Variation Tracker

[KelseaChang5]

Goal: Replace Excel-based reports with Google-sheet based reports fed by ClinVar ingest data for the following ClinVar GenomeConnect submitters:

• GenomeConnect; Clinical Genome Resource
• GenomeConnect - Invitae Patient Insights Network
• GenomeConnect - Brain Gene Registry
• GenomeConnect-Association for Creatine Deficiencies; Association for Creatine Deficiencies
• GenomeConnect - CFC International
• GenomeConnect - CureCADASIL
• GenomeConnect - GM1
• GenomeConnect - No Stomach For Cancer

SP Ticket Link: https://broadinstitute.atlassian.net/jira/software/projects/CGSP/boards/872?issueParent=468029&selectedIssue=CGSP-424

INFORMATION TO BE INCLUDED ON REPORT: (Collected by Kelsea and Larry, in discussion with Jules Savatt) 1. Variant classification from the GenomeConnect testing lab against previous classification submissions from the same lab (Invitae example: https://www.ncbi.nlm.nih.gov/clinvar/variation/1063220/?new_evidence=true) HIGH PRIORITY

• Display all variants from the testing lab. Within this list, flag all variants that are conflicting with this instance of GenomeConnect testing lab classification. Also note if they agree. [This equates to the LabConflicts and Lab Consensus tabs on the old report - can be combined here] Within this list of all variants, flag which ones are new additions
• Flag if no GTR OrgID is identified for the testing lab (the id is in the xml when available) [This equates to the LabNoOrgID tab on the old report]
• Flag if the testing lab has an OrgID but has no other SCVs on the variant in ClinVar [This equates to the LabNotSubmitted tab on the old report]

2. GC submissions against all other submissions NICE TO HAVE

• Display all ClinVar variants where the only submission is from GenomeConnect [This equates to the AllNovel tab on the old report]
• Display all ClinVar variants where there is a GenomeConnect submission [This equates to the AllSub tab on the old report] Include GCEP classification(s) here

3. Variant classification from the GenomeConnect testing lab against EP classifications HIGH PRIORITY

• Flag any variants in which the GenomeConnect testing lab classification conflicts with EP classification [This equates to the EPConflict tab on the old report]

Example of November 2021 GenomeConnect report pulled from code Tam wrote.

NOTE: (added 2/13/2024) combining the requrest for issue #61 to this epic since some of the items on that request got addressed during the early stages of this epic. All remaining items still need to be reviewed and converted into sub-issues here. To see the original #61 request go here.

Definition of Done: GenomeConnect team no longer needs to be sent Excel-based reports, can access all data that was available in Excel-based report through a Google sheet-based Variation Tracker with the ability to refresh the data to reflect a new ClinVar data release for the following submitters:

• GenomeConnect; Clinical Genome Resource
• GenomeConnect - Invitae Patient Insights Network
• GenomeConnect - Brain Gene Registry
• GenomeConnect-Association for Creatine Deficiencies; Association for Creatine Deficiencies
• GenomeConnect - CFC International
• GenomeConnect - CureCADASIL
• GenomeConnect - GM1
• GenomeConnect - No Stomach For Cancer

[jmsavatt]

1. GenomeConnect submissions in ClinVar all have "GenomeConnect" in the name. I have listed them below in case that is helpful:

• GenomeConnect; Clinical Genome Resource
• GenomeConnect - Invitae Patient Insights Network
• GenomeConnect - Simons Searchlight (HOLDING ON THIS REPORT)
• GenomeConnect - Brain Gene Registry
• GenomeConnect-Association for Creatine Deficiencies; Association for Creatine Deficiencies
• GenomeConnect - CFC International
• GenomeConnect - CureCADASIL
• GenomeConnect - GM1
• GenomeConnect - No Stomach For Cancer

2. Should we add additional submitters in the future, what will the process look like to have them added to the report? We expect to partner with additional registries, so could this be considered?

3. In addition to flagging new additions for the Variant classification from the GenomeConnect testing lab against previous classification submissions from the same lab report, would it be possible to add the date added?

4. For Variant classification from the GenomeConnect testing lab against EP classifications - could we also flag new additions and include the date added, if possible?

[larrybabb]

@jmsavatt re: above

1. thanks
2. If you can guarantee to stick with the naming approach that all will start with "GenomeConnect..." then I can automatically build this into the report so that you do not need a manual step to update a list. Otherwise we will have to discuss a solution whereby you maintain a list in a google sheet or db table somewhere. Maybe this is something the GPM system will handle eventually. We could as Danielle A.
3. yes
4. yes

[jmsavatt]

@larrybabb - retagging you in this thread

[dazzariti]

This ticket remains the highest priority, higher priority than https://github.com/clingen-data-model/clinvar-ingest-reports/issues/64

[dazzariti]

Assume all submitter orgs that are pulled into this report have "GenomeConnect" in the name

[dazzariti]

@dazzariti To convert this to an Epic and break down into individual issues

[dazzariti]

I have added the following from Jules' comment above to a new issue https://github.com/clingen-data-model/clinvar-ingest-reports/issues/61

Should we add additional submitters in the future, what will the process look like to have them added to the report? We expect to partner with additional registries, so could this be considered?

In addition to flagging new additions for the Variant classification from the GenomeConnect testing lab against previous classification submissions from the same lab report, would it be possible to add the date added?

For Variant classification from the GenomeConnect testing lab against EP classifications - could we also flag new additions and include the date added, if possible?

[larrybabb]

adding description info from #61 to this epic so that we have one place to go through and audit all the requests made over the past couple of years and assure nothing was missed.

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GenomeConnect Variation Tracker: Requested enhancements#61

Background: Once the Genome Connect Variation Trackers are available with the existing Excel-based functionality, the GenomeConnect team would like to request the following enhancements.

Note: Once (#62) is complete, @dazzariti will rereview these enhancement requests with Jules to see if anything has changed or been reprioritized

The report to be formatted as one sheet with all 8 registries, with a feature to select information pertaining to each individual registry GenomeConnect; Clinical Genome Resource GenomeConnect - Invitae Patient Insights Network GenomeConnect - Brain Gene Registry GenomeConnect-Association for Creatine Deficiencies; Association for Creatine Deficiencies GenomeConnect - CFC International GenomeConnect - CureCADASIL GenomeConnect - GM1 GenomeConnect - No Stomach For Cancer

Inheritance from submissions pulled into the report (Allele Origin) Add a column on Alert tab, "Date of first ClinVar data release when variant was flagged" - The intention of this request is to track how long the variant has been on GenomeConnect's radar Add a column on Alert tab for "Local ID" - this value is included in XML, adding this value makes it very helpful for the GenomeConnect team to map back to the participant with that variant In addition to flagging new additions for the Variant classification from the GenomeConnect testing lab against previous classification submissions from the same lab report, would it be possible to add the date added? For Variant classification from the GenomeConnect testing lab against EP classifications - could we also flag new additions and include the date added, if possible? Questions: Should we add additional submitters in the future, what will the process look like to have them added to the report? We expect to partner with additional registries, so could this be considered?

Definition of Done: All enhancements described above are available in the Google-sheet based Variation Tracker for the following GenomeConnect ClinVar submitters:

GenomeConnect; Clinical Genome Resource GenomeConnect - Invitae Patient Insights Network GenomeConnect - Brain Gene Registry GenomeConnect-Association for Creatine Deficiencies; Association for Creatine Deficiencies GenomeConnect - CFC International GenomeConnect - CureCADASIL GenomeConnect - GM1 GenomeConnect - No Stomach For Cancer

[dazzariti]

@larrybabb I removed the VUS report request https://github.com/clingen-data-model/clinvar-ingest-reports/issues/90 from this Epic - otherwise all the tickets related to transitioning away from Excel based reports is complete. The VUS report is separate issue so I think it makes sense to move it and close this Epic. Congrats!