Clinical Significance (--> evidence level)

[crow1time]

Clinical Significance - current clinical significance does not adequately support the needs for somatic variant information.

• Current set of values defined by LOINC

• What needs to be added for Somatic Variants

  • http://cancergeneticslab.ca/guidelines/variants/
  • TIER I – VARIANTS OF STRONG CLINICAL SIGNIFICANCE; Variants are predictive of response or resistance in a specific tumour type to therapies approved by Health Canada or US FDA. Alternatively, these variants are predictive, prognostic or diagnostic biomarkers in the specific tumour type, based on well-powered studies with consensus from experts in the field and inclusion in professional guidelines. 
  • TIER II – VARIANTS OF POTENTIAL CLINICAL SIGNIFICANCE; Variants are predictive, prognostic or diagnostic biomarkers, based on convincing published evidence from smaller studies or case reports but without expert consensus. 
  • TIER IIIA –VARIANTS OF UNCERTAIN CLINICAL SIGNIFICANCE; Variants are known or presumed to alter normal gene function, however no convincing published evidence of a predictive, prognostic or diagnostic association was found or evidence is sufficiently conflicting that a conclusion cannot be reached. 
  • TIER IIIB – VARIANTS OF UNCERTAIN FUNCTION ; Variants are not observed at a significant allele frequency in population, pan-cancer or tumour-specific variant databases and their effect on normal gene function cannot be confidently predicted. No convincing published evidence of a predictive, prognostic or diagnostic association was found or evidence is sufficiently conflicting that a conclusion cannot be reached. 
  • TIER IV – BENIGN AND LIKELY BENIGN VARIANTS; Variants are known or presumed to not disrupt normal gene function, and/or are found at a significant allele frequency within the population.  [Tier IV variants are not routinely reported.] 
  • TIER I/II – VARIANTS OF STRONG OR POTENTIAL CLINICAL SIGNIFICANCE 

• Proposal

  • Make a submission to LOINC (can take years)
  • Define the coding system and include in the list Somatic clinical significance codes:
  • TIER 1 – VARIANTS OF STRONG CLINICAL SIGNIFICANCE 
  • TIER 2 – VARIANTS OF POTENTIAL CLINICAL SIGNIFICANCE
  • TIER 1/2 – VARIANTS OF STRONG OR POTENTIAL CLINICAL SIGNIFICANCE (extra compared to website suggestions)
  • TIER 3A –VARIANTS OF UNCERTAIN CLINICAL SIGNIFICANCE
  • TIER 3B – VARIANTS OF UNCERTAIN FUNCTION  
  • TIER 4 – BENIGN AND LIKELY BENIGN VARIANTS 

[crow1time]

I started the conversation with the Clinical Genomics Working Group regarding the addition of clinical significance based on the http://cancergeneticslab.ca/guidelines/variants/ (Tiers 1, 2, 3a, 3b, and 4).

The conversation started on Genomics Zulip with folks from the CGWG.

During the meeting on Mar 11th there was a discussion of how the CGWG has structured the GRIG to handle that information. They current expect it to be entered under the Diagnostic or Therapeutic Implication as an evidence-level, not a clinical significance. There was an asserted semantic delineation between clinical significance and evidence level and the two different answer lists that are being referenced. There was a request previously be the CGWG to create a LOINC answer list based on a similar set of tiers requested, http://loinc.org/93044-6. It is not an exact match for what you are seeking, but includes relevant narrative.

The suggested LOINC code for evidence-level references many of the similar lists that are used to inform the Cancer Genetics Lab BC list referenced above. None are an exact duplicate in addition to the fact that the LOINC answer list does not included the Levels or Tiers. However, the recommendation was that the evidence-level be used to capture what is being requested.

Here is an example from the GRIG using evidence level. It also includes examples of using ClinVAR and PharmGKB.

I believe the evidence level is open enough to be used for the evidence levels called out in http://cancergeneticslab.ca/guidelines/variants/.

If this doesn’t provide what is necessary to transmit the desired answer list please let me know. I believe there are additional options possible, but we will need to revisit them with the CGWG.

Notes from the Clinical Genomics Working Group session on March 11th. i. https://www.oncokb.org/levels#version=V2 CONFLATED SEMANTICS. Was tied to a previous ballot comment from Epic. Should confirm alignment with previous guidance. https://jira.hl7.org/browse/FHIR-33009 ii. Current concept: clinical-significance (DiagnosticImplication)

1. LOINC 53037-8
2. https://loinc.org/LL4034-6/
3. https://build.fhir.org/ig/HL7/genomics-reporting/StructureDefinition-diagnostic-implication.html#non-conflated-semantics

iii. Related concept: evidence-level (defined on Diagnostic and Therapeutic Implication)

1. https://loinc.org/93044-6 (only example lists exist)
2. Can be used to send AMP Tiers

iv. Could say more [in the GRIG narrative] about these specific lists and anticipated use cases (e.g., if you need to send AMP tiers, vs ACMG vs other lists) rather than just recommending folks not use them. v. Could also call out differential tables for concepts defined on abstract profiles.

[vitaliia-muzyka]

Does this recommendation mean that clinical-significance should be used only for Germline Variants, and evidence-level should be used for Somatic? If it is so, it would be good to call out about it in the Diagnostic Implication page. Can the coding system be defined to communicate AMP values + "strong or potential significance"?

[sirkyp]

@vitaliia-muzyka - I might suggest we focus the discussion and brainstorming in Zulip to get the broader CG community involved in the discussion?

https://chat.fhir.org/#narrow/stream/179197-genomics/topic/New.20Clinical.20Significance.20Somatic.20Answer.20List.20Addition

As a solution is proposed and worked out for the GRIG*, we can then come back here and see what that proposed solution means to the GenomeX community.

[crow1time]

Extended discussion related to this topic is occurring within the Clinical Genomics WG Zulip channel (aka genomics): https://chat.fhir.org/#narrow/stream/179197-genomics/topic/New.20Clinical.20Significance.20Somatic.20Answer.20List.20Addition

Please participate there and we will post the result here.