clingen-data-model / clinvar-ingest

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Fix missing interpretation_description values in new clinical_assertion tables #243

Closed theferrit32 closed 1 month ago

theferrit32 commented 1 month ago

Need to ensure the DrugForTherapeuticAssertion value is preserved somewhere. Add test for this.

<ClinicalAssertion ID="9794255" SubmissionDate="2024-06-27" DateLastUpdated="2024-06-29" DateCreated="2024-06-02">
        <ClinVarSubmissionID localKey="civic.AID:7" localKeyIsSubmitted="1" />
        <ClinVarAccession Accession="SCV005045669" DateUpdated="2024-06-29" DateCreated="2024-06-02" Type="SCV" Version="2" SubmitterName="Wagner Lab, Nationwide Children's Hospital" OrgID="509553" OrganizationCategory="laboratory" />
        <RecordStatus>current</RecordStatus>
        <Classification DateLastEvaluated="2018-05-15">
          <ReviewStatus>criteria provided, single submitter</ReviewStatus>
          <SomaticClinicalImpact 
              ClinicalImpactAssertionType="therapeutic" 
              ClinicalImpactClinicalSignificance="sensitivity/response"  
              DrugForTherapeuticAssertion="Dabrafenib;Trametinib">Tier I - Strong</SomaticClinicalImpact>
          <Citation>
            <ID Source="PubMed">25265492</ID>
          </Citation>
          <Citation>
            <ID Source="PubMed">23020132</ID>
          </Citation>
          <Citation>
            <ID Source="PubMed">28891408</ID>
          </Citation>
          <Citation>
            <ID Source="PubMed">25399551</ID>
          </Citation>
          <Comment>Combination treatment of BRAF inhibitor dabrafenib and MEK inhibitor trametinib is recommended for adjuvant treatment of stage III or recurrent melanoma with BRAF V600E mutation detected by the approved THxID kit, as well as first line treatment for metastatic melanoma. The treatments are FDA approved based on studies including the Phase III COMBI-V, COMBI-D and COMBI-AD Trials. Combination therapy is now recommended above BRAF inhibitor monotherapy. Cutaneous squamous-cell carcinoma and keratoacanthoma occur at lower rates with combination therapy than with BRAF inhibitor alone.</Comment>
        </Classification>
        <Assertion>variation to disease</Assertion>
        <AttributeSet>
          <Attribute Type="AssertionMethod">AMP/ASCO/CAP Guidelines, 2017</Attribute>
          <Citation>
            <ID Source="PubMed">27993330</ID>
          </Citation>
        </AttributeSet>
        <ObservedInList>
          <ObservedIn>
            <Sample>
              <Origin>somatic</Origin>
              <Species TaxonomyId="9606">human</Species>
              <AffectedStatus>yes</AffectedStatus>
            </Sample>
            <Method>
              <MethodType>curation</MethodType>
            </Method>
            <ObservedData>
              <Attribute Type="Description">not provided</Attribute>
            </ObservedData>
          </ObservedIn>
        </ObservedInList>
        <SimpleAllele>
          <GeneList>
            <Gene Symbol="BRAF" />
          </GeneList>
          <VariantType>Variation</VariantType>
          <OtherNameList>
            <Name Type="SubmitterVariantId">civic.mpid:12</Name>
          </OtherNameList>
          <AttributeSet>
            <Attribute Type="HGVS">NM_004333.4:c.1799T&gt;A</Attribute>
          </AttributeSet>
        </SimpleAllele>
        <TraitSet Type="Disease">
          <Trait Type="Disease">
            <Name>
              <ElementValue Type="Preferred">Melanoma</ElementValue>
            </Name>
          </Trait>
        </TraitSet>
        <SubmissionNameList>
          <SubmissionName>SUB14487648</SubmissionName>
          <SubmissionName>SUB14568896</SubmissionName>
        </SubmissionNameList>
      </ClinicalAssertion>