Specialization for somatic variant might not be necessary - 2018-May Genomics #56

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    • Type: Change Request
    • Resolution: Persuasive with Modification
    • Priority: Medium
    • Genomics Reporting (FHIR)
    • STU3
    • Clinical Genomics
    • (profiles) [deprecated]
    • 1.5.1
    • Hide

      Remove all current Implication profiles except abstract base, add 2 new profiles restructuring our current components and codes as Diagnostic Implication and Therapeutic Implication

       

      Genomic Implication Profile

      Extension: RelatedArtifact (0..*)

       

      derivedFrom (reference: Observation/Variant/Haplotype/Genotype) (1..*)

       

      Component: 93044-6 | Level of Evidence / “clinical validity” (0..1)
      Binding*:* LOINC Answer List LL5356-2 (preferred)

       

      Component: TBD code | prognosis (0..1)

      E.g. Better outcome, poorer outcome

      Binding*:* (unbound) (example)

       

       

      Diagnostic Implication Profile

      code: TBD code | Diagnostic implication

       

      Value 0..0

       

      Component: 53037-8 | LL4034-6 (clinical significance) (0..1)

      Pathogenic | Likely pathogenic | Uncertain significance | Likely benign | Benign
      Binding*:* LOINC Answer List LL4034-6 (extensible)

       

      Component: 81259-4 | (Associated phenotype) (0..*)

      Binding*:* (unbound) (example)

       

      Component: TBD code | (Associated cancer) (0..*)

      Binding*:* (unbound) (example)

       

      Component 79742-3 | LL3731-8 (Mode of inheritance) (0..1)

      Autosomal dominant|Autosomal recessive|X-linked dominant|X-linked recessive|Y-linked|Codominant|Mitochondrial
      Binding: LOINC Answer List LL3731-8 (preferred)

       

       

      Therapeutic Implication Profile 

      code: TBD | Therapeutic implication

       

      Value 0..0

       

      Component: 81259-4 | (Associated phenotype) (0..*)

      Binding*:* (unbound) (example)

       

      Component: TBD code | (Associated cancer) (0..*)

      Binding*:* (unbound) (example)

       

      Component: 51963-7 |  (medication-assessed) (0..*)

      Binding*:* (unbound) (example)

       

      Component: TBD |  (therapy-assessed) (0..*)

      Binding*:* (unbound) (example)

       

      Component: 53040-2 |  (effect-medication-metabolism) (0..1)

      Ultrarapid metabolizer | Rapid metabolizer | Normal metabolizer | Intermediate metabolizer | Poor metabolizer
      Binding*:* LOINC Answer List LL3856-3 (preferred)

       

      Component: 83009-1 | (effect-medication-high-risk) (0..1)

      Low risk | High risk
      Binding*:* LOINC Answer List LL2353-2 (extensible)

       

      Component: TBD | (effect-medication-transporter) (0..1)

      Increased function | Normal function | Decreased function | Poor function
      Binding*:* (unbound) (example)

       

      Component: 51961-1 | LL3856-3 (effect-medication-efficacy) (0..1)

      Resistant | Responsive | Presumed resistant | Presumed responsive | Unknown significance | Non-Responsive | Presumed non-responsive
      Binding*:* LOINC Answer List LL539-8 (preferred)

       

      Show
      Remove all current Implication profiles except abstract base, add 2 new profiles restructuring our current components and codes as Diagnostic Implication and Therapeutic Implication   Genomic Implication Profile Extension: RelatedArtifact (0..*)   derivedFrom (reference: Observation/Variant/Haplotype/Genotype) (1..*)   Component: 93044-6 | Level of Evidence / “clinical validity” (0..1) Binding*:* LOINC Answer List LL5356-2 ( preferred )   Component: TBD code | prognosis (0..1) E.g. Better outcome, poorer outcome Binding*:* (unbound) ( example )     Diagnostic Implication Profile code: TBD code | Diagnostic implication   Value 0..0   Component: 53037-8 | LL4034-6 (clinical significance) (0..1) Pathogenic | Likely pathogenic | Uncertain significance | Likely benign | Benign Binding*:* LOINC Answer List LL4034-6 ( extensible )   Component: 81259-4 | (Associated phenotype) (0..*) Binding*:* (unbound) ( example )   Component: TBD code | (Associated cancer) (0..*) Binding*:* (unbound) ( example )   Component 79742-3 | LL3731-8 (Mode of inheritance) (0..1) Autosomal dominant|Autosomal recessive|X-linked dominant|X-linked recessive|Y-linked|Codominant|Mitochondrial Binding: LOINC Answer List LL3731-8 ( preferred )     Therapeutic Implication Profile   code: TBD | Therapeutic implication   Value 0..0   Component: 81259-4 | (Associated phenotype) (0..*) Binding*:* (unbound) ( example )   Component: TBD code | (Associated cancer) (0..*) Binding*:* (unbound) ( example )   Component: 51963-7 |  (medication-assessed) (0..*) Binding*:* (unbound) ( example )   Component: TBD |  (therapy-assessed) (0..*) Binding*:* (unbound) ( example )   Component: 53040-2 |  (effect-medication-metabolism) (0..1) Ultrarapid metabolizer | Rapid metabolizer | Normal metabolizer | Intermediate metabolizer | Poor metabolizer Binding*:* LOINC Answer List LL3856-3 ( preferred )   Component: 83009-1 | (effect-medication-high-risk) (0..1) Low risk | High risk Binding*:* LOINC Answer List LL2353-2 ( extensible )   Component: TBD | (effect-medication-transporter) (0..1) Increased function | Normal function | Decreased function | Poor function Binding*:* (unbound) ( example )   Component: 51961-1 | LL3856-3 (effect-medication-efficacy) (0..1) Resistant | Responsive | Presumed resistant | Presumed responsive | Unknown significance | Non-Responsive | Presumed non-responsive Binding*:* LOINC Answer List LL539-8 ( preferred )  
    • Kevin Power / Bob Milius: 16-0-2
    • Enhancement
    • Non-compatible

      Existing Wording: General comments on 1.5.1 General Guidance

      Comment:

      We should explore integrating the somatic specialization into a more general version pharmacogenomics.

      Summary:

      Specialization for somatic variant might not be necessary

            Assignee:
            Unassigned
            Reporter:
            clemmcdonald
            Watchers:
            4 Start watching this issue

              Created:
              Updated:
              Resolved: