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ClinGen Pathogenicity Calculator: Use case GLA Step-by-step instructions for the interactive exercise to be presented at the ClinGen Workshop at ASHG 2015. Workshop page: http://calculator.clinicalgenome.org/ashg-2015 Variant: NM_000169.2:c.639+919G>A Gene: GLA/Fabry Disease
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Pathogenicity Calculator and ACMG guidelines for variant interpretation
Previous presentation (Heidi Rehm) reviewed ACMG guidelines. ACMG guidelines provide:
Systematic categorization of evidence types and their strength Rules for making conclusions about pathogenicity based on the evidence
Rule application may be a tedious, sometimes error-prone process that may be hard to track and document and may involve personnel at various competence levels Pathogenicity Calculator eliminates error in rule application and provides tracking of evidence used to reach specific conclusions.
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BS1, BS2, BS3, BS4, BP4, BP1, BP7, BP3, BP2, BP6, BP5, PP1, PP2, PP3, PP4, PP5 PM2, PM5, PM4, PM1, PM6, PM3, PS1, PS2, PS3, PS4, PVS1
BS1-Supporting, BS2-Supporting PP1-Strong, PS1-Supporting
ACMG guidelines provide categorization of evidence and explicit rules for reaching conclusions about pathogenicity
ACMG Evidence Tags Upgrading/Downgrading Strength (Examples)
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Pathogenicity Evidence grid
Five cells contain one piece of evidence each in favor of pathogenicity. One may be inclined to assert the variant is pathogenic. However, the strongest assertion that can be reached using ACMG rules is “Likely Pathogenic”. Thus, application of rule-based reasoning is important when interpreting evidence.
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Step 1: Identify Allele Step 2: Launch the Calculator Step 3: Create evidence document and input evidence Step 4: Calculate conclusions and examine reasoning Step 5: Retrieve stored evidence and conclusions
Overview of Use Case 2
Allele: NM_000169.2:c.639+919G>A
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Allele: NM_000169.2:c.639+919G>A
Gene:GLA (alpha galactosidase)
Allele selected for curation in clinical sequencing and exploratory research (CSER)
Three groups curated the variant with PP1-Moderate,PS3, PS4,PVS1, PM4,PP1,PP5,
BP4,PP3 tags, leading to 3 different conclusions per ACMG Guidelines:
Pathogenic, Likely Pathogenic, Uncertain Significance
Consensus curation agreed on the following evidence tags for Fabry disease: PS4,
PVS1-Strong, PS3, PP1
In the present use case, these four evidence tags will be used for this allele to
calculate conclusion based on ACMG guidelines
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Step 1: Identify allele: Click on search
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Step 1: Identify allele: Click on HGVS
Click HGVS
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Step 1: Identify allele: The allele Search panel pops up
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Step 1: Identify allele: The allele search panel pops up. Search: NM_000169.2:c.639+919G>A
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Step 1: Identify allele: View search results
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Step 1: Identify allele: Inspect equivalent allele representations and confirm allele identity
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Step 2: Launch the calculator
Click on the calculator icon
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Learn more about gene/allele
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Step 2: Launch the calculator: Open the calculator tab
Because the evidence document is empty, the tab is not displayed Click on the red circle (with “-” sign) in “Toggle Evidence” row
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Step 3: Create evidence document and input evidence
The new evidence document that you will create now will be populated by evidence tags for this allele
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Step 3: Create evidence document and input evidence: Provide basic information
Provide information about condition and mode of inheritance
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Step 3: Create evidence document and input evidence
Click OK to notification
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Step 3: Create evidence document and input evidence: Turn PS4 tag on
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Step 3: Create evidence document and input evidence: Turn PS4 tag on
Click Add Tag
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Step 3: Create evidence document and input evidence: Turn PS4 tag on
1. Add “Tag PS4” in “Evidence Tag ID” column This must be any unique string of characters
1. Select one of the tags from the pull-down menu
2. Optional text explaining why the tag is turned on This text may help remind you why you turned the tag on when you revisit this allele in the future
1. Press the Update button 2. Press the Save Edits button in the
menu
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Step 3: Create evidence document and input evidence: Turn PVS1-Strong tag ON
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Step 3: Create evidence document and input evidence: Turn PVS1-Strong tag ON
See slide #21 for details
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Step 3: Create evidence document and input evidence: Turn PS3 tag ON
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Step 3: Create evidence document and input evidence: Turn PS3 tag ON
See slide #21 for details
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Step 3: Create evidence document and input evidence: Turn PS3 tag ON
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Step 3: Create evidence document and input evidence: Turn PS3 tag ON
See slide #21 for details
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Conclusion and Reasoning
The conclusion reached is “Pathogenic”. The rule that is satisfied is highlighted next to the conclusion. The rules that are not satisfied are also listed below but are not highlighted. For each rule that is not satisfied, the number of missing evidence items is listed. By clicking on the rule that is not satisfied, missing evidence items (grid columns) are highlighted, helping identify evidence tags that may lead to a conclusion.
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Step 5: Retrieve stored evidence and conclusions: Activate HGVS based search
Visit: Perform the HGVS search for the same allele: calculator.clinicalgenome.org/java-bin/clingenV2.0.jsp
Click Search
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Step 5: Retrieve stored evidence and conclusions: Activate HGVS based search
Click HGVS
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Step 5: Retrieve stored evidence and conclusions: Search for NM_000169.2:c.639+919G>A
Enter HGVS and Click Search
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Step 5: Retrieve stored evidence and conclusions: Launch the calculator to view evidence and conclusion
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Step 5: Retrieve stored evidence and conclusion
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Next: repeat exercise for the second variant
Search for: NM_001369.2:c.7468_7488del Turn the following evidence tags on: PM2, PM3, PM4 for Primary ciliary dyskinesia Use tag helper to locate the tags: http://calculator.clinicalgenome.org/site/cg-grid-guide Check the conclusion Examine the rules applied to reach the conclusion. Examine evidence that--if present--may lead to a different conclusion.
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Acknowledgments
Bioinformatics Research Laboratory at Baylor College of
Medicine
Ronak Patel
Piotr Pawliczek
Neethu Shah
Andrew Jackson
Ivenise Carrero
Sameer Paithankar
Aaron Baker
Matthew Roth
Xin Feng
Hailin Chen
Baylor College of Medicine
Sharon Plon
Rajarshi Ghosh
NIH/NHGRI U01 HG007436 NIH/NHGRI U01 HG007307