GenomeConnect-Simons Searchlights specific LabConflicts tab

[toneillbroad]

Background: The goal of this ticket is to provide a Google sheet-based report for "GenomeConnect - Simons Searchlight" as requested by GenomeConnect team. There is no existing Excel-based report that offers the data requested below.

Definition of Done: GenomeConnect team can access all data requested below 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

Per communications with Danielle via Slack on 2020-12-10: ===== START ===== Hi Terry, I was wondering if we could request an additional ClinVar report for one of our GenomeConnect submitters, but slightly modified.

Here is the description of what Jules’ is looking for, but happy to get on the phone to clarify anything: This would be for submitter ” GenomeConnect – Simons Searchlight” and I have linked to the submitter page in case that is helpful - https://www.ncbi.nlm.nih.gov/clinvar/submitters/507786/. The Simons submissions are “Provider Interpretation” while our other submissions have been “Phenotyping Only.” As a result, the Simons submissions have both a classification from Simons and one from the reporting laboratory. Our “Phenotyping Only” submission only include the reporting laboratory classification from our participants’ reports. I imagine this could impact the reports. Ultimately, I think we are most interested in comparing the reporting laboratory’s current submission and the Simons’ classification. If we are able to compare the reporting lab classification that was submitted in the Simons to the lab’s current submission that also might be of interest.

Reading back over that, I will definitely need to get you more specification, I’ll work with Jules on modifying the current report criteria for this use case:

1. AllSubs: All ClinVar variants where there is a GenomeConnect submission.
2. AllNovel: All ClinVar variants where the only submission is from GenomeConnect.
3. LabConflicts: ClinVar variants where the GenomeConnect testing lab clinical significance [P] vs [LP] vs [VUS] vs [LB] vs [B] differs from the clinical lab with same name.
4. LabConsensus: ClinVar variants where the GenomeConnect testing lab clinical significance [P] vs [LP] vs [VUS] vs [LB] vs [B] is the same as that from the clinical lab with same name.
5. EPConflict: ClinVar variants where the GenomeConnect testing lab clinical significance [P/LP] vs [VUS] vs [LB/B] differs from an Expert Panel or Practice Guideline.
6. Outlier: ClinVar variants where the GenomeConnect testing lab clinical significance [P/LP] vs [VUS] vs [LB/B] differs from at least one 1-star or above (or clinical testing) submitter.
7. LabNotSubmitted: GenomeConnect SCVs where the testing lab has an OrgID but has NOT independently submitted an SCV on the variant.
8. LabNoOrgID: GenomeConnect SCVs where the testing lab was submitted without an OrgID.

Here is the request: NEW LabConflicts: ClinVar variants where the GenomeConnect – Simons Searchlight clinical significance [P] vs [LP] vs [VUS] vs [LB] vs [B] differs from the clinical lab with the same name as the GenomeConnect – Simons Searchlight testing lab. Example (https://www.ncbi.nlm.nih.gov/clinvar/variation/546371/): GenomeConnect – Simons Searchlight submission SCV001443471.1 GenomeConnect – Simons Searchlight Clinical Significance is Uncertain Significance GenomeConnect – Simons Searchlight Testing Lab is GeneDx GenomeConnect – Simons Searchlight Testing Lab Interpretation is Uncertain Significance The query is - Does GenomeConnect –Simons Searchlight clinical significance of Uncertain Significance differ from the clinical significance from the clinical lab submitter with the same name as the GenomeConnect - Simons Searchlight testing lab (GeneDx). In this example, no, GeneDx submission (SCV000780006.2) is also Uncertain Significance. ===== END =====

Per conversation with Danielle and Larry on 2021-01-05, Larry would like to learn more about the requirements from Jules to see if it is possible to handle the request via the DSP/ClinGen Represntation of ClinVar project.

Please note: The following statement was also included in this original ticket but that work is now part of https://app.zenhub.com/workspaces/genegraphdxclinvar-60340fb9898dae001107e94e/issues/gh/clingen-data-model/genomeconnect-report/5

In addition, we will need a report for the Invitae Patient Insights Network. The submitter name is “GenomeConnect – Invitae Patient Insights Network” and I have linked to the submitter page in case that is helpful https://www.ncbi.nlm.nih.gov/clinvar/submitters/508034/. These are phenotyping only” submissions, so the reports will mirror those we create for GenomeConnect and the other registries.

[dazzariti]

Discussed at August 31st Broad/Geisinger meeting - @larrybabb and @toneillbroad to work with Jules and Steven on an MVP for new ClinVar reporting system - Jules to be stakeholder for GenomeConnect reports

[dazzariti]

This topic is a lower priority than https://github.com/clingen-data-model/clinvar-ingest-reports/issues/62

[dazzariti]

@larrybabb This relates to the Simons Searchlight request we discussed with Jules and Caitlin today

[larrybabb]

This should be included as part of #84