{ "resourceType" : "Questionnaire", "id" : "ReportableVariantResultPanel", "meta" : { "profile" : ["https://fhir.nwgenomics.nhs.uk/StructureDefinition/NWQuestionnaire"] }, "language" : "en", "text" : { "status" : "extensions", "div" : "

Generated Narrative: Questionnaire ReportableVariantResultPanel

Profile: Questionnaire

\r\n\r\n\r\n\r\n\r\n\r\n\r\n\r\n\r\n\r\n\r\n\r\n\r\n\r\n\r\n\r\n\r\n\r\n\r\n\r\n\r\n\r\n\r\n\r\n\r\n\r\n\r\n\r\n\r\n\r\n\r\n\r\n\r\n\r\n\r\n\r\n\r\n\r\n\r\n\r\n\r\n\r\n\r\n\r\n\r\n\r\n\r\n\r\n\r\n\r\n\r\n\r\n\r\n\r\n\r\n\r\n\r\n
LinkIDTextCardinalityTypeDescription & Constraints\"doco\"
\".\"\".\" Result panel for a [Variant (Reportable Variant)](StructureDefinition-Variant.html)\n`Observation`, structured around the HL7 v2 [Lab Results Interface (LRI)](https://confluence.hl7.org/download/attachments/25559919/2018%2004%2003%20-%20V2%20LRI%20-%20Ch.%205%20CG%20and%20Code%20System%20Tables.pdf?api=v2)'s\nown **Discrete Variant Panel** (LOINC `81250-3`, LRI Chapter 5 Table 5-2, plus the\nStructural Variant Addenda in Table 5-3) - the same panel the NTHL1 and CFTR examples\nare based on. LRI already defines this as a single panel covering both simple and\nstructural variants; this Questionnaire follows that same single-panel structure\nrather than iGene's separate per-variant-type field sets, mapping each item to both\nits LRI `OBX` row and its corresponding component in the HL7 Genomics Reporting IG's\n[Variant](https://build.fhir.org/ig/HL7/genomics-reporting/StructureDefinition-variant.html)\nprofile. See [OMICS DSS Result Integration](reportable-variants.html) for the full\nLRI/FHIR/iGene three-way mapping table.\n\n`item.definition`/`item.code` are cross-checked against this IG's current `Variant`\nexamples: [Variant - NTHL1](Observation-8385c2fd-313d-4fd5-b98e-d5ea4bae6f99.html) and\n[Variant - CFTR](Observation-bca547c1-78a5-41be-8cfc-03c05805ac85.html) (both based on\nLRI examples), `Observation-EGFR-Variant-ctDNA`, `Observation-BRCA1`, and the four\n`Variant` Observations (a small variant, an intragenic CNV, a multi-gene CNV and a\nstructural variant) in\n[Bundle-ctdna9737383222-testresults](Bundle-ctdna9737383222-testresults.html), plus\niGene's own custom field spec for variants (`NotGit/iGene Custom Fields Master\nDataset - Updated 13-Aug-26.xlsx`, "Variant Level Data" sheet) - only elements\ngenuinely populated by at least one of these is modelled, since these are the only\nelements needed for the iGene feed. See [OMICS DSS Result Integration - Result\nPanel: Elements Not Included](reportable-variants.html#result-panel-elements-not-included)\nfor the LRI/FHIR elements deliberately left out because no current example populates\nthem.\n\n**Known gaps between iGene, LRI and the FHIR profile, not yet resolved:**\n- **Loss of Heterozygosity** is one of iGene's five variant types, but has **no\n corresponding row anywhere in LRI's Discrete Variant Panel** - LRI's closest concept,\n Allelic State (`53034-5`, row B.23), does not offer an LOH answer option. No current\n FHIR example produces LOH data either.\n- **Coordinate System [Type]** (`92822-6`) and **Origin of Germline Genetic Variant\n [Type]** (`94186-4`), both used by the ctDNA Bundle examples, have **no row in LRI's\n Discrete Variant Panel** - LRI's closest concept to the latter is Allelic Phase\n (`82120-7`, row B.26), a different LOINC code whose answer list happens to include\n Maternal/Paternal as two of several "sets of variants in cis" options, not a\n dedicated parent-of-origin field.\n- **Structural Variant**: iGene expects a single `Complex variant HGVS name` field\n (LOINC `81262-8` - itself an LRI Complex Variant Panel code, row C.2, not part of the\n Discrete Variant Panel at all), but the ctDNA Bundle's structural-variant Observation\n does not populate `81262-8` - it uses several Discrete Variant Panel components\n instead (Genomic Reference Sequence, Coordinate System, Genomic Ref/Alt Allele, DNA\n Change Type, Genomic DNA Change).Questionnairehttps://fhir.nwgenomics.nhs.uk/Questionnaire/ReportableVariantResultPanel#2.2.0
\".\"\".\"\".\" DiscreteVariantPanelDiscrete Variant Panel0..*groupDefinition: Observation
\".\"\".\"\".\"\".\" DiscreteVariantPanel-designNoteLRI Table 5-2 row B - repeats for each discrete variant reported (OBX-4 sub-ID "2a", incrementing per repeat).0..1display
\".\"\".\"\".\"\".\" LRI/B.1Variant Category0..1choiceDefinition: Observation.component.valueCodeableConcept
\".\"\".\"\".\"\".\"\".\" LRI/B.1-designNoteLRI row B.1, OBX type CWE, R/O/C = O, [0..1]. LRI's own answer list (LL4165-8)\nonly distinguishes Simple Variant vs Structural Variant - not granular enough to\nroute a variant to the correct iGene slot type. Resolved: this IG binds this\ncomponent to its own [IGeneVariantCategory](CodeSystem-IGeneVariantCategory.html)\nvalue set instead (`SEQV`/`ICNV`/`MCNV`/`SV`/`LOH`), making the classification\nthat used to be inferred (see [OMICS DSS Result\nIntegration](reportable-variants.html#outstanding-issues)) an explicit, coded\nvalue - the FHIR Variant profile has no named slice for this at all, so it is\nmodelled here as an open-slice component, same as `Variant.component:variant-category`.\nPopulated by every current example.0..1display
\".\"\".\"\".\"\".\" TranscriptSpecificationTranscript Specification0..1groupDefinition: Observation.component
\".\"\".\"\".\"\".\"\".\" LRI/B.3Gene Studied0..1choiceDefinition: Observation.component.valueCodeableConcept
\".\"\".\"\".\"\".\"\".\"\".\" LRI/B.3-designNoteLRI row B.3, OBX type CWE, R/O/C = C, [0..1]. FHIR Variant profile: this IG's\nown `gene-studied` addition (not one of the international profile's named\nslices). iGene: rolled into the free-text Description field (SEQV/ICNV) or the\nGene(s) field (LOH). Used by NTHL1, CFTR, EGFR-ctDNA, and the ctDNA Bundle's\nsmall-variant and intragenic-CNV Observations.0..1display
\".\"\".\"\".\"\".\"\".\" LRI/B.4Transcript Reference Sequence0..1choiceDefinition: Observation.component.valueCodeableConcept
\".\"\".\"\".\"\".\"\".\"\".\" LRI/B.4-designNoteLRI row B.4, OBX type CWE, R/O/C = C, [0..1]. FHIR Variant profile slice:\n`representative-transcript-ref-seq`. iGene: rolled into the free-text\nDescription field (SEQV/ICNV). Used by NTHL1, CFTR and the ctDNA Bundle's\nsmall-variant Observation.0..1display
\".\"\".\"\".\"\".\"\".\" LRI/B.5DNA Change (c.HGVS)0..1choiceDefinition: Observation.component.valueCodeableConcept
\".\"\".\"\".\"\".\"\".\"\".\" LRI/B.5-designNoteLRI row B.5, OBX type CWE, R/O/C = C, [0..1]. FHIR Variant profile slice:\n`representative-coding-hgvs`. iGene: rolled into the free-text Description\nfield (SEQV/ICNV). Used by EGFR-ctDNA, BRCA1 and the ctDNA Bundle's\nsmall-variant Observation.0..1display
\".\"\".\"\".\"\".\"\".\" LRI/B.6Amino Acid Change (pHGVS)0..1choiceDefinition: Observation.component.valueCodeableConcept
\".\"\".\"\".\"\".\"\".\"\".\" LRI/B.6-designNoteLRI row B.6, OBX type CWE, R/O/C = C, [0..1]. FHIR Variant profile slice:\n`representative-protein-hgvs`. iGene: rolled into the free-text Description\nfield (SEQV only - ICNV's Description omits this). Used only by the ctDNA\nBundle's small-variant Observation.0..1display
\".\"\".\"\".\"\".\"\".\" LRI/B.7DNA Change Type0..1choiceDefinition: Observation.component.valueCodeableConcept
\".\"\".\"\".\"\".\"\".\"\".\" LRI/B.7-designNoteLRI row B.7, OBX type CWE, R/O/C = O, [0..1]. FHIR Variant profile slice:\n`coding-change-type`. Not a discrete iGene field - summarised within iGene's\nfree-text Description/Genomic_coordinates fields. Used by every current\nexample (Sequence Ontology or LOINC answer coding, e.g. duplication,\ndeletion, substitution, copy_number_variation).0..1display
\".\"\".\"\".\"\".\" GenomicSpecificationGenomic Specification0..1groupDefinition: Observation.component
\".\"\".\"\".\"\".\"\".\" LRI/B.9Genomic Reference Sequence0..1choiceDefinition: Observation.component.valueCodeableConcept
\".\"\".\"\".\"\".\"\".\"\".\" LRI/B.9-designNoteLRI row B.9, OBX type CWE, R/O/C = C, [0..1]. FHIR Variant profile slice:\n`genomic-ref-seq`. iGene: rolled into the free-text Genomic_coordinates field\n(all four variant types). Used by NTHL1 and all four ctDNA Bundle\nObservations.0..1display
\".\"\".\"\".\"\".\"\".\" LRI/B.10Genomic DNA Change (gHGVS)0..1choiceDefinition: Observation.component.valueCodeableConcept
\".\"\".\"\".\"\".\"\".\"\".\" LRI/B.10-designNoteLRI row B.10, OBX type CWE, R/O/C = C, [0..1]. FHIR Variant profile slice:\n`genomic-hgvs`. iGene: rolled into the free-text Genomic_coordinates field\n(all four variant types). Used by all four ctDNA Bundle Observations - not by\nNTHL1/CFTR, where it is commented out pending a confirmed mapping.0..1display
\".\"\".\"\".\"\".\"\".\" LRI/B.11Genomic Ref Allele0..1stringDefinition: Observation.component.valueString
\".\"\".\"\".\"\".\"\".\"\".\" LRI/B.11-designNoteLRI row B.11, OBX type ST, R/O/C = C, [0..1]. FHIR Variant profile slice:\n`ref-allele`. Not a discrete iGene field - summarised within iGene's\nGenomic_coordinates field. Used by NTHL1, CFTR and all four ctDNA Bundle\nObservations.0..1display
\".\"\".\"\".\"\".\"\".\" LRI/B.12Genomic Allele Start-End0..1stringDefinition: Observation.component.valueRange
\".\"\".\"\".\"\".\"\".\"\".\" LRI/B.12-designNoteLRI row B.12, OBX type NR, R/O/C = C, [0..1]. FHIR Variant profile slice:\n`exact-start-end`. Not a discrete iGene field. Used only by the ctDNA\nBundle's small-variant Observation - a Range with only the low bound\npopulated.0..1display
\".\"\".\"\".\"\".\"\".\" LRI/B.13Genomic Alt Allele0..1stringDefinition: Observation.component.valueString
\".\"\".\"\".\"\".\"\".\"\".\" LRI/B.13-designNoteLRI row B.13, OBX type ST, R/O/C = C, [0..1]. FHIR Variant profile slice:\n`alt-allele`. Not a discrete iGene field - summarised within iGene's\nGenomic_coordinates field. Used by the ctDNA Bundle's intragenic-CNV,\nmulti-gene-CNV and structural-variant Observations (as symbolic ALT alleles,\ne.g. "<DEL>") - not by the small-variant Observation, NTHL1 or CFTR.0..1display
\".\"\".\"\".\"\".\" OtherAttributesOther Attributes0..1groupDefinition: Observation.component
\".\"\".\"\".\"\".\"\".\" LRI/B.17Cytogenetic (Chromosome) Location0..1stringDefinition: Observation.component.valueCodeableConcept
\".\"\".\"\".\"\".\"\".\"\".\" LRI/B.17-designNoteLRI row B.17, OBX type CWE, R/O/C = O, [0..1]. Not one of the international\nFHIR Variant profile's named component slices (its closest named slice,\nCytogenomic Nomenclature 81291-7, is actually a different LRI field - Table\n5-1 row A.11, part of the report-level Master Panel, not this Discrete\nVariant Panel) - captured here as an open-slice addition, consistent with\nGenomicObservation's open component slicing. iGene: this is the sole field\nfor the Multigenic CNV Description, and part of the Genomic_coordinates\nfield for the other three variant types. Used only by the ctDNA Bundle's\nmulti-gene-CNV Observation (e.g. "Xq22.1-q28").0..1display
\".\"\".\"\".\"\".\"\".\" LRI/B.18Genomic Source Class0..1choiceDefinition: Observation.component.valueCodeableConcept
\".\"\".\"\".\"\".\"\".\"\".\" LRI/B.18-designNoteLRI row B.18, OBX type CNE, R/O/C = R (required when present), [0..*]. FHIR\nVariant profile slice: `genomic-source-class`. Not a discrete iGene field.\nUsed by NTHL1, CFTR, EGFR-ctDNA and the ctDNA Bundle's small-variant,\nintragenic-CNV and multi-gene-CNV Observations (Germline or Somatic) - not\nby the structural-variant Observation.0..1display
\".\"\".\"\".\"\".\" InterpretationsInterpretations0..1groupDefinition: Observation.component
\".\"\".\"\".\"\".\"\".\" LRI/B.20Classification0..1choiceDefinition: Observation.component.valueCodeableConcept
\".\"\".\"\".\"\".\"\".\"\".\" LRI/B.20-designNoteLRI row B.20 (LRI names it "Genetic sequence variation clinical\nsignificance"), OBX type CNE, R/O/C = O, [0..1]. FHIR Variant profile: not\none of the profile's own component slices (the profile relies on the generic\n`Observation.interpretation`/`valueCodeableConcept` pattern for this) -\nmodelled here as an open-slice component to match how every current example\nactually carries it. iGene: this is the Classification field for all four\nvariant types. Used by all four ctDNA Bundle Observations (e.g.\n"Pathogenic").0..1display
\".\"\".\"\".\"\".\" AllelicStatePhaseAllelic State/Phase Information0..1groupDefinition: Observation.component
\".\"\".\"\".\"\".\"\".\" LRI/B.23Allelic State0..1choiceDefinition: Observation.component.valueCodeableConcept
\".\"\".\"\".\"\".\"\".\"\".\" LRI/B.23-designNoteLRI row B.23, OBX type CNE, R/O/C = C, [0..1], answer list LL381-5\n(Heteroplasmic/Homoplasmic/Homozygous/Heterozygous/Hemizygous - no "Loss of\nHeterozygosity" option). FHIR Variant profile slice: `allelic-state`. iGene:\nthe Zygosity/Copy-number state field for all five variant types (iGene's LOH\n"State" field has no LOINC code and is a different concept - LRI has no LOH\nanswer here). Used by NTHL1, CFTR, BRCA1 and the ctDNA Bundle's small-variant\nObservation (Heterozygous).0..1display
\".\"\".\"\".\"\".\"\".\" LRI/B.24Allelic Frequency0..1decimalDefinition: Observation.component.valueQuantity
\".\"\".\"\".\"\".\"\".\"\".\" LRI/B.24-designNoteLRI row B.24 (LRI names it "Allelic Frequency [NFr]", the FHIR profile and\nour examples call it "Sample variant allelic frequency [NFr]" - same LOINC\ncode, slightly different display text), OBX type NM, R/O/C = C, [0..1]. FHIR\nVariant profile slice: `sample-allelic-frequency`. iGene: the Level (VAF %)\nfield for the four variant types that have one (not LOH). Used by EGFR-ctDNA\n(as a percentage) and all four ctDNA Bundle Observations (as a decimal\nfraction) - the units differ between the two sources.0..1display
\".\"\".\"\".\"\".\" StructuralVariantAddendaStructural Variant Addenda0..1groupDefinition: Observation.component
\".\"\".\"\".\"\".\"\".\" StructuralVariantAddenda-designNoteLRI Table 5-3 - part of the same Discrete Variant Panel in the HL7 v2 message, shown as a separate table in LRI purely for visual separation of structural-variant-only attributes.0..1display
\".\"\".\"\".\"\".\"\".\" LRI/B.28Genomic Structural Variant Copy Number0..1decimalDefinition: Observation.component.valueQuantity
\".\"\".\"\".\"\".\"\".\"\".\" LRI/B.28-designNoteLRI row B.28, OBX type NM, R/O/C = O, [0..1], OBX-4 sub-ID "2a.1". FHIR\nVariant profile slice: `copy-number`. Not a discrete iGene field - the\nclosest iGene concept is the Copy-number state dropdown (Allelic State,\nB.23), which is a category not a number. Used by the ctDNA Bundle's\nintragenic-CNV and multi-gene-CNV Observations - not the structural-variant\n(translocation-style) Observation, where a copy number doesn't apply.0..1display
\".\"\".\"\".\"\".\"\".\" LRI/B.32Structural Variant Inner Start-End0..1stringDefinition: Observation.component.valueRange
\".\"\".\"\".\"\".\"\".\"\".\" LRI/B.32-designNoteLRI row B.32, OBX type NR, R/O/C = O, [0..1], OBX-4 sub-ID "2a.1". FHIR\nVariant profile slice: `inner-start-end`. Not a discrete iGene field -\nsummarised within iGene's Genomic_coordinates field. Used by the ctDNA\nBundle's intragenic-CNV, multi-gene-CNV and structural-variant Observations.0..1display
\".\"\".\"\".\"\".\" NoLRIEquivalentFHIR/iGene Elements With No LRI Discrete Variant Panel Row0..1groupDefinition: Observation.component
\".\"\".\"\".\"\".\"\".\" NoLRIEquivalent-designNoteThese are used by a current FHIR example and/or iGene, but have no row anywhere in LRI's Discrete Variant Panel (Table 5-2/5-3) - see the Description's gap notes.0..1display
\".\"\".\"\".\"\".\"\".\" FHIR/CoordinateSystemCoordinate System0..1choiceDefinition: Observation.component.valueCodeableConcept
\".\"\".\"\".\"\".\"\".\"\".\" FHIR/CoordinateSystem-designNoteNo LRI row. FHIR Variant profile slice: `coordinate-system`. Not a discrete\niGene field - summarised within iGene's Genomic_coordinates field. Used by\nall four ctDNA Bundle Observations (1-based character counting).0..1display
\".\"\".\"\".\"\".\"\".\" FHIR/OriginOfGermlineVariantOrigin of Germline Genetic Variant0..1choiceDefinition: Observation.component.valueCodeableConcept
\".\"\".\"\".\"\".\"\".\"\".\" FHIR/OriginOfGermlineVariant-designNoteNo dedicated LRI row - the closest LRI concept is Allelic Phase (82120-7, row\nB.26), whose answer list happens to include Maternal/Paternal among several\n"set of variants in cis" options, not a dedicated parent-of-origin field.\nFHIR Variant profile slice: `variant-inheritance`. iGene: this is the\nInheritance field for the four variant types that have one (not LOH), though\niGene's own spec gives it no LOINC code. Used by the ctDNA Bundle's\nsmall-variant, intragenic-CNV and multi-gene-CNV Observations (Maternal) -\nnot the structural-variant Observation.0..1display
\".\"\".\"\".\"\".\" LossOfHeterozygosityLoss of Heterozygosity (iGene fields, mapped to a separate Molecular Consequence Observation)0..1groupDefinition: Observation
\".\"\".\"\".\"\".\"\".\" LossOfHeterozygosity-designNoteOne of iGene's five variant types (`LOH1`-`LOH2`), with no corresponding row\nanywhere in LRI's Discrete Variant Panel. Decided: this IG models LOH as a\nseparate [Molecular Consequence](StructureDefinition-MolecularConsequence.html)\nObservation, `derivedFrom` the `Variant` it accompanies, with a\n`functional-effect` component coded `SO_0001786 loss_of_heterozygosity` -\nsee [Observation-ctdna9737383222-seqv1-loh](Observation-ctdna9737383222-seqv1-loh.html)\nfor a worked example - rather than as items directly on this Discrete Variant\nPanel. The two items below describe iGene's own flat fields for reference, not\nhow this IG models them.0..1display
\".\"\".\"\".\"\".\"\".\" iGene/LOH_DescriptionGene(s)0..1stringDefinition: Observation.component.valueCodeableConcept
\".\"\".\"\".\"\".\"\".\" iGene/LOH_StateLoss of Heterozygosity (LOH)0..1choiceDefinition: Observation.component.valueCodeableConcept
\".\"\".\"\".\"\".\"\".\"\".\" iGene/LOH_State-designNoteNo LOINC code in iGene's own spec ("None"); iGene example value "Significant LOH". Not a value LRI's Allelic State (B.23) answer list supports.0..1display

\"doco\" Documentation for this format
" }, "extension" : [{ "url" : "http://hl7.org/fhir/StructureDefinition/artifact-versionAlgorithm", "valueCoding" : { "system" : "http://hl7.org/fhir/version-algorithm", "code" : "semver" } }], "url" : "https://fhir.nwgenomics.nhs.uk/Questionnaire/ReportableVariantResultPanel", "version" : "2.2.0", "title" : "Reportable Variant Result Panel", "status" : "draft", "date" : "2026-09-20T05:53:36+00:00", "publisher" : "NHS North West Genomics", "contact" : [{ "telecom" : [{ "system" : "url", "value" : "https://www.nwgenomics.nhs.uk/contact-us" }] }], "description" : "Result panel for a [Variant (Reportable Variant)](StructureDefinition-Variant.html)\n`Observation`, structured around the HL7 v2 [Lab Results Interface (LRI)](https://confluence.hl7.org/download/attachments/25559919/2018%2004%2003%20-%20V2%20LRI%20-%20Ch.%205%20CG%20and%20Code%20System%20Tables.pdf?api=v2)'s\nown **Discrete Variant Panel** (LOINC `81250-3`, LRI Chapter 5 Table 5-2, plus the\nStructural Variant Addenda in Table 5-3) - the same panel the NTHL1 and CFTR examples\nare based on. LRI already defines this as a single panel covering both simple and\nstructural variants; this Questionnaire follows that same single-panel structure\nrather than iGene's separate per-variant-type field sets, mapping each item to both\nits LRI `OBX` row and its corresponding component in the HL7 Genomics Reporting IG's\n[Variant](https://build.fhir.org/ig/HL7/genomics-reporting/StructureDefinition-variant.html)\nprofile. See [OMICS DSS Result Integration](reportable-variants.html) for the full\nLRI/FHIR/iGene three-way mapping table.\n\n`item.definition`/`item.code` are cross-checked against this IG's current `Variant`\nexamples: [Variant - NTHL1](Observation-8385c2fd-313d-4fd5-b98e-d5ea4bae6f99.html) and\n[Variant - CFTR](Observation-bca547c1-78a5-41be-8cfc-03c05805ac85.html) (both based on\nLRI examples), `Observation-EGFR-Variant-ctDNA`, `Observation-BRCA1`, and the four\n`Variant` Observations (a small variant, an intragenic CNV, a multi-gene CNV and a\nstructural variant) in\n[Bundle-ctdna9737383222-testresults](Bundle-ctdna9737383222-testresults.html), plus\niGene's own custom field spec for variants (`NotGit/iGene Custom Fields Master\nDataset - Updated 13-Aug-26.xlsx`, \"Variant Level Data\" sheet) - only elements\ngenuinely populated by at least one of these is modelled, since these are the only\nelements needed for the iGene feed. See [OMICS DSS Result Integration - Result\nPanel: Elements Not Included](reportable-variants.html#result-panel-elements-not-included)\nfor the LRI/FHIR elements deliberately left out because no current example populates\nthem.\n\n**Known gaps between iGene, LRI and the FHIR profile, not yet resolved:**\n- **Loss of Heterozygosity** is one of iGene's five variant types, but has **no\n corresponding row anywhere in LRI's Discrete Variant Panel** - LRI's closest concept,\n Allelic State (`53034-5`, row B.23), does not offer an LOH answer option. No current\n FHIR example produces LOH data either.\n- **Coordinate System [Type]** (`92822-6`) and **Origin of Germline Genetic Variant\n [Type]** (`94186-4`), both used by the ctDNA Bundle examples, have **no row in LRI's\n Discrete Variant Panel** - LRI's closest concept to the latter is Allelic Phase\n (`82120-7`, row B.26), a different LOINC code whose answer list happens to include\n Maternal/Paternal as two of several \"sets of variants in cis\" options, not a\n dedicated parent-of-origin field.\n- **Structural Variant**: iGene expects a single `Complex variant HGVS name` field\n (LOINC `81262-8` - itself an LRI Complex Variant Panel code, row C.2, not part of the\n Discrete Variant Panel at all), but the ctDNA Bundle's structural-variant Observation\n does not populate `81262-8` - it uses several Discrete Variant Panel components\n instead (Genomic Reference Sequence, Coordinate System, Genomic Ref/Alt Allele, DNA\n Change Type, Genomic DNA Change).", "jurisdiction" : [{ "coding" : [{ "system" : "urn:iso:std:iso:3166", "code" : "GB", "display" : "United Kingdom of Great Britain and Northern Ireland" }] }], "code" : [{ "system" : "http://loinc.org", "code" : "69548-6", "display" : "Genetic variant assessment" }], "item" : [{ "linkId" : "DiscreteVariantPanel", "definition" : "http://hl7.org/fhir/StructureDefinition/Observation#Observation", "code" : [{ "system" : "http://loinc.org", "code" : "81250-3", "display" : "Discrete genetic variant panel" }], "text" : "Discrete Variant Panel", "type" : "group", "repeats" : true, "item" : [{ "extension" : [{ "url" : "http://hl7.org/fhir/StructureDefinition/questionnaire-itemControl", "valueCodeableConcept" : { "coding" : [{ "system" : "http://hl7.org/fhir/questionnaire-item-control", "code" : "help" }] } }], "linkId" : "DiscreteVariantPanel-designNote", "text" : "LRI Table 5-2 row B - repeats for each discrete variant reported (OBX-4 sub-ID \"2a\", incrementing per repeat).", "type" : "display" }, { "linkId" : "LRI/B.1", "definition" : "http://hl7.org/fhir/StructureDefinition/Observation#Observation.component.valueCodeableConcept", "code" : [{ "system" : "http://loinc.org", "code" : "83005-9", "display" : "Variant category" }], "text" : "Variant Category", "type" : "choice", "item" : [{ "extension" : [{ "url" : "http://hl7.org/fhir/StructureDefinition/questionnaire-itemControl", "valueCodeableConcept" : { "coding" : [{ "system" : "http://hl7.org/fhir/questionnaire-item-control", "code" : "help" }] } }], "linkId" : "LRI/B.1-designNote", "text" : "LRI row B.1, OBX type CWE, R/O/C = O, [0..1]. LRI's own answer list (LL4165-8)\nonly distinguishes Simple Variant vs Structural Variant - not granular enough to\nroute a variant to the correct iGene slot type. Resolved: this IG binds this\ncomponent to its own [IGeneVariantCategory](CodeSystem-IGeneVariantCategory.html)\nvalue set instead (`SEQV`/`ICNV`/`MCNV`/`SV`/`LOH`), making the classification\nthat used to be inferred (see [OMICS DSS Result\nIntegration](reportable-variants.html#outstanding-issues)) an explicit, coded\nvalue - the FHIR Variant profile has no named slice for this at all, so it is\nmodelled here as an open-slice component, same as `Variant.component:variant-category`.\nPopulated by every current example.", "type" : "display" }] }, { "linkId" : "TranscriptSpecification", "definition" : "http://hl7.org/fhir/StructureDefinition/Observation#Observation.component", "text" : "Transcript Specification", "type" : "group", "item" : [{ "linkId" : "LRI/B.3", "definition" : "http://hl7.org/fhir/StructureDefinition/Observation#Observation.component.valueCodeableConcept", "code" : [{ "system" : "http://loinc.org", "code" : "48018-6", "display" : "Gene studied [ID]" }], "text" : "Gene Studied", "type" : "choice", "item" : [{ "extension" : [{ "url" : "http://hl7.org/fhir/StructureDefinition/questionnaire-itemControl", "valueCodeableConcept" : { "coding" : [{ "system" : "http://hl7.org/fhir/questionnaire-item-control", "code" : "help" }] } }], "linkId" : "LRI/B.3-designNote", "text" : "LRI row B.3, OBX type CWE, R/O/C = C, [0..1]. FHIR Variant profile: this IG's\nown `gene-studied` addition (not one of the international profile's named\nslices). iGene: rolled into the free-text Description field (SEQV/ICNV) or the\nGene(s) field (LOH). Used by NTHL1, CFTR, EGFR-ctDNA, and the ctDNA Bundle's\nsmall-variant and intragenic-CNV Observations.", "type" : "display" }] }, { "linkId" : "LRI/B.4", "definition" : "http://hl7.org/fhir/StructureDefinition/Observation#Observation.component.valueCodeableConcept", "code" : [{ "system" : "http://loinc.org", "code" : "51958-7", "display" : "Transcript reference sequence [ID]" }], "text" : "Transcript Reference Sequence", "type" : "choice", "item" : [{ "extension" : [{ "url" : "http://hl7.org/fhir/StructureDefinition/questionnaire-itemControl", "valueCodeableConcept" : { "coding" : [{ "system" : "http://hl7.org/fhir/questionnaire-item-control", "code" : "help" }] } }], "linkId" : "LRI/B.4-designNote", "text" : "LRI row B.4, OBX type CWE, R/O/C = C, [0..1]. FHIR Variant profile slice:\n`representative-transcript-ref-seq`. iGene: rolled into the free-text\nDescription field (SEQV/ICNV). Used by NTHL1, CFTR and the ctDNA Bundle's\nsmall-variant Observation.", "type" : "display" }] }, { "linkId" : "LRI/B.5", "definition" : "http://hl7.org/fhir/StructureDefinition/Observation#Observation.component.valueCodeableConcept", "code" : [{ "system" : "http://loinc.org", "code" : "48004-6", "display" : "DNA change (c.HGVS)" }], "text" : "DNA Change (c.HGVS)", "type" : "choice", "item" : [{ "extension" : [{ "url" : "http://hl7.org/fhir/StructureDefinition/questionnaire-itemControl", "valueCodeableConcept" : { "coding" : [{ "system" : "http://hl7.org/fhir/questionnaire-item-control", "code" : "help" }] } }], "linkId" : "LRI/B.5-designNote", "text" : "LRI row B.5, OBX type CWE, R/O/C = C, [0..1]. FHIR Variant profile slice:\n`representative-coding-hgvs`. iGene: rolled into the free-text Description\nfield (SEQV/ICNV). Used by EGFR-ctDNA, BRCA1 and the ctDNA Bundle's\nsmall-variant Observation.", "type" : "display" }] }, { "linkId" : "LRI/B.6", "definition" : "http://hl7.org/fhir/StructureDefinition/Observation#Observation.component.valueCodeableConcept", "code" : [{ "system" : "http://loinc.org", "code" : "48005-3", "display" : "Amino acid change (pHGVS)" }], "text" : "Amino Acid Change (pHGVS)", "type" : "choice", "item" : [{ "extension" : [{ "url" : "http://hl7.org/fhir/StructureDefinition/questionnaire-itemControl", "valueCodeableConcept" : { "coding" : [{ "system" : "http://hl7.org/fhir/questionnaire-item-control", "code" : "help" }] } }], "linkId" : "LRI/B.6-designNote", "text" : "LRI row B.6, OBX type CWE, R/O/C = C, [0..1]. FHIR Variant profile slice:\n`representative-protein-hgvs`. iGene: rolled into the free-text Description\nfield (SEQV only - ICNV's Description omits this). Used only by the ctDNA\nBundle's small-variant Observation.", "type" : "display" }] }, { "linkId" : "LRI/B.7", "definition" : "http://hl7.org/fhir/StructureDefinition/Observation#Observation.component.valueCodeableConcept", "code" : [{ "system" : "http://loinc.org", "code" : "48019-4", "display" : "DNA change [Type]" }], "text" : "DNA Change Type", "type" : "choice", "item" : [{ "extension" : [{ "url" : "http://hl7.org/fhir/StructureDefinition/questionnaire-itemControl", "valueCodeableConcept" : { "coding" : [{ "system" : "http://hl7.org/fhir/questionnaire-item-control", "code" : "help" }] } }], "linkId" : "LRI/B.7-designNote", "text" : "LRI row B.7, OBX type CWE, R/O/C = O, [0..1]. FHIR Variant profile slice:\n`coding-change-type`. Not a discrete iGene field - summarised within iGene's\nfree-text Description/Genomic_coordinates fields. Used by every current\nexample (Sequence Ontology or LOINC answer coding, e.g. duplication,\ndeletion, substitution, copy_number_variation).", "type" : "display" }] }] }, { "linkId" : "GenomicSpecification", "definition" : "http://hl7.org/fhir/StructureDefinition/Observation#Observation.component", "text" : "Genomic Specification", "type" : "group", "item" : [{ "linkId" : "LRI/B.9", "definition" : "http://hl7.org/fhir/StructureDefinition/Observation#Observation.component.valueCodeableConcept", "code" : [{ "system" : "http://loinc.org", "code" : "48013-7", "display" : "Genomic reference sequence [ID]" }], "text" : "Genomic Reference Sequence", "type" : "choice", "item" : [{ "extension" : [{ "url" : "http://hl7.org/fhir/StructureDefinition/questionnaire-itemControl", "valueCodeableConcept" : { "coding" : [{ "system" : "http://hl7.org/fhir/questionnaire-item-control", "code" : "help" }] } }], "linkId" : "LRI/B.9-designNote", "text" : "LRI row B.9, OBX type CWE, R/O/C = C, [0..1]. FHIR Variant profile slice:\n`genomic-ref-seq`. iGene: rolled into the free-text Genomic_coordinates field\n(all four variant types). Used by NTHL1 and all four ctDNA Bundle\nObservations.", "type" : "display" }] }, { "linkId" : "LRI/B.10", "definition" : "http://hl7.org/fhir/StructureDefinition/Observation#Observation.component.valueCodeableConcept", "code" : [{ "system" : "http://loinc.org", "code" : "81290-9", "display" : "Genomic DNA change (gHGVS)" }], "text" : "Genomic DNA Change (gHGVS)", "type" : "choice", "item" : [{ "extension" : [{ "url" : "http://hl7.org/fhir/StructureDefinition/questionnaire-itemControl", "valueCodeableConcept" : { "coding" : [{ "system" : "http://hl7.org/fhir/questionnaire-item-control", "code" : "help" }] } }], "linkId" : "LRI/B.10-designNote", "text" : "LRI row B.10, OBX type CWE, R/O/C = C, [0..1]. FHIR Variant profile slice:\n`genomic-hgvs`. iGene: rolled into the free-text Genomic_coordinates field\n(all four variant types). Used by all four ctDNA Bundle Observations - not by\nNTHL1/CFTR, where it is commented out pending a confirmed mapping.", "type" : "display" }] }, { "linkId" : "LRI/B.11", "definition" : "http://hl7.org/fhir/StructureDefinition/Observation#Observation.component.valueString", "code" : [{ "system" : "http://loinc.org", "code" : "69547-8", "display" : "Genomic ref allele [ID]" }], "text" : "Genomic Ref Allele", "type" : "string", "item" : [{ "extension" : [{ "url" : "http://hl7.org/fhir/StructureDefinition/questionnaire-itemControl", "valueCodeableConcept" : { "coding" : [{ "system" : "http://hl7.org/fhir/questionnaire-item-control", "code" : "help" }] } }], "linkId" : "LRI/B.11-designNote", "text" : "LRI row B.11, OBX type ST, R/O/C = C, [0..1]. FHIR Variant profile slice:\n`ref-allele`. Not a discrete iGene field - summarised within iGene's\nGenomic_coordinates field. Used by NTHL1, CFTR and all four ctDNA Bundle\nObservations.", "type" : "display" }] }, { "linkId" : "LRI/B.12", "definition" : "http://hl7.org/fhir/StructureDefinition/Observation#Observation.component.valueRange", "code" : [{ "system" : "http://loinc.org", "code" : "81254-5", "display" : "Genomic allele start-end" }], "text" : "Genomic Allele Start-End", "type" : "string", "item" : [{ "extension" : [{ "url" : "http://hl7.org/fhir/StructureDefinition/questionnaire-itemControl", "valueCodeableConcept" : { "coding" : [{ "system" : "http://hl7.org/fhir/questionnaire-item-control", "code" : "help" }] } }], "linkId" : "LRI/B.12-designNote", "text" : "LRI row B.12, OBX type NR, R/O/C = C, [0..1]. FHIR Variant profile slice:\n`exact-start-end`. Not a discrete iGene field. Used only by the ctDNA\nBundle's small-variant Observation - a Range with only the low bound\npopulated.", "type" : "display" }] }, { "linkId" : "LRI/B.13", "definition" : "http://hl7.org/fhir/StructureDefinition/Observation#Observation.component.valueString", "code" : [{ "system" : "http://loinc.org", "code" : "69551-0", "display" : "Genomic alt allele [ID]" }], "text" : "Genomic Alt Allele", "type" : "string", "item" : [{ "extension" : [{ "url" : "http://hl7.org/fhir/StructureDefinition/questionnaire-itemControl", "valueCodeableConcept" : { "coding" : [{ "system" : "http://hl7.org/fhir/questionnaire-item-control", "code" : "help" }] } }], "linkId" : "LRI/B.13-designNote", "text" : "LRI row B.13, OBX type ST, R/O/C = C, [0..1]. FHIR Variant profile slice:\n`alt-allele`. Not a discrete iGene field - summarised within iGene's\nGenomic_coordinates field. Used by the ctDNA Bundle's intragenic-CNV,\nmulti-gene-CNV and structural-variant Observations (as symbolic ALT alleles,\ne.g. \"\") - not by the small-variant Observation, NTHL1 or CFTR.", "type" : "display" }] }] }, { "linkId" : "OtherAttributes", "definition" : "http://hl7.org/fhir/StructureDefinition/Observation#Observation.component", "text" : "Other Attributes", "type" : "group", "item" : [{ "linkId" : "LRI/B.17", "definition" : "http://hl7.org/fhir/StructureDefinition/Observation#Observation.component.valueCodeableConcept", "code" : [{ "system" : "http://loinc.org", "code" : "48001-2", "display" : "Cytogenetic (chromosome) location" }], "text" : "Cytogenetic (Chromosome) Location", "type" : "string", "item" : [{ "extension" : [{ "url" : "http://hl7.org/fhir/StructureDefinition/questionnaire-itemControl", "valueCodeableConcept" : { "coding" : [{ "system" : "http://hl7.org/fhir/questionnaire-item-control", "code" : "help" }] } }], "linkId" : "LRI/B.17-designNote", "text" : "LRI row B.17, OBX type CWE, R/O/C = O, [0..1]. Not one of the international\nFHIR Variant profile's named component slices (its closest named slice,\nCytogenomic Nomenclature 81291-7, is actually a different LRI field - Table\n5-1 row A.11, part of the report-level Master Panel, not this Discrete\nVariant Panel) - captured here as an open-slice addition, consistent with\nGenomicObservation's open component slicing. iGene: this is the sole field\nfor the Multigenic CNV Description, and part of the Genomic_coordinates\nfield for the other three variant types. Used only by the ctDNA Bundle's\nmulti-gene-CNV Observation (e.g. \"Xq22.1-q28\").", "type" : "display" }] }, { "linkId" : "LRI/B.18", "definition" : "http://hl7.org/fhir/StructureDefinition/Observation#Observation.component.valueCodeableConcept", "code" : [{ "system" : "http://loinc.org", "code" : "48002-0", "display" : "Genomic source class [Type]" }], "text" : "Genomic Source Class", "type" : "choice", "item" : [{ "extension" : [{ "url" : "http://hl7.org/fhir/StructureDefinition/questionnaire-itemControl", "valueCodeableConcept" : { "coding" : [{ "system" : "http://hl7.org/fhir/questionnaire-item-control", "code" : "help" }] } }], "linkId" : "LRI/B.18-designNote", "text" : "LRI row B.18, OBX type CNE, R/O/C = R (required when present), [0..*]. FHIR\nVariant profile slice: `genomic-source-class`. Not a discrete iGene field.\nUsed by NTHL1, CFTR, EGFR-ctDNA and the ctDNA Bundle's small-variant,\nintragenic-CNV and multi-gene-CNV Observations (Germline or Somatic) - not\nby the structural-variant Observation.", "type" : "display" }] }] }, { "linkId" : "Interpretations", "definition" : "http://hl7.org/fhir/StructureDefinition/Observation#Observation.component", "text" : "Interpretations", "type" : "group", "item" : [{ "linkId" : "LRI/B.20", "definition" : "http://hl7.org/fhir/StructureDefinition/Observation#Observation.component.valueCodeableConcept", "code" : [{ "system" : "http://loinc.org", "code" : "53037-8", "display" : "Genetic variation clinical significance [Imp]" }], "text" : "Classification", "type" : "choice", "item" : [{ "extension" : [{ "url" : "http://hl7.org/fhir/StructureDefinition/questionnaire-itemControl", "valueCodeableConcept" : { "coding" : [{ "system" : "http://hl7.org/fhir/questionnaire-item-control", "code" : "help" }] } }], "linkId" : "LRI/B.20-designNote", "text" : "LRI row B.20 (LRI names it \"Genetic sequence variation clinical\nsignificance\"), OBX type CNE, R/O/C = O, [0..1]. FHIR Variant profile: not\none of the profile's own component slices (the profile relies on the generic\n`Observation.interpretation`/`valueCodeableConcept` pattern for this) -\nmodelled here as an open-slice component to match how every current example\nactually carries it. iGene: this is the Classification field for all four\nvariant types. Used by all four ctDNA Bundle Observations (e.g.\n\"Pathogenic\").", "type" : "display" }] }] }, { "linkId" : "AllelicStatePhase", "definition" : "http://hl7.org/fhir/StructureDefinition/Observation#Observation.component", "text" : "Allelic State/Phase Information", "type" : "group", "item" : [{ "linkId" : "LRI/B.23", "definition" : "http://hl7.org/fhir/StructureDefinition/Observation#Observation.component.valueCodeableConcept", "code" : [{ "system" : "http://loinc.org", "code" : "53034-5", "display" : "Allelic state" }], "text" : "Allelic State", "type" : "choice", "item" : [{ "extension" : [{ "url" : "http://hl7.org/fhir/StructureDefinition/questionnaire-itemControl", "valueCodeableConcept" : { "coding" : [{ "system" : "http://hl7.org/fhir/questionnaire-item-control", "code" : "help" }] } }], "linkId" : "LRI/B.23-designNote", "text" : "LRI row B.23, OBX type CNE, R/O/C = C, [0..1], answer list LL381-5\n(Heteroplasmic/Homoplasmic/Homozygous/Heterozygous/Hemizygous - no \"Loss of\nHeterozygosity\" option). FHIR Variant profile slice: `allelic-state`. iGene:\nthe Zygosity/Copy-number state field for all five variant types (iGene's LOH\n\"State\" field has no LOINC code and is a different concept - LRI has no LOH\nanswer here). Used by NTHL1, CFTR, BRCA1 and the ctDNA Bundle's small-variant\nObservation (Heterozygous).", "type" : "display" }] }, { "linkId" : "LRI/B.24", "definition" : "http://hl7.org/fhir/StructureDefinition/Observation#Observation.component.valueQuantity", "code" : [{ "system" : "http://loinc.org", "code" : "81258-6", "display" : "Allelic Frequency [NFr]" }], "text" : "Allelic Frequency", "type" : "decimal", "item" : [{ "extension" : [{ "url" : "http://hl7.org/fhir/StructureDefinition/questionnaire-itemControl", "valueCodeableConcept" : { "coding" : [{ "system" : "http://hl7.org/fhir/questionnaire-item-control", "code" : "help" }] } }], "linkId" : "LRI/B.24-designNote", "text" : "LRI row B.24 (LRI names it \"Allelic Frequency [NFr]\", the FHIR profile and\nour examples call it \"Sample variant allelic frequency [NFr]\" - same LOINC\ncode, slightly different display text), OBX type NM, R/O/C = C, [0..1]. FHIR\nVariant profile slice: `sample-allelic-frequency`. iGene: the Level (VAF %)\nfield for the four variant types that have one (not LOH). Used by EGFR-ctDNA\n(as a percentage) and all four ctDNA Bundle Observations (as a decimal\nfraction) - the units differ between the two sources.", "type" : "display" }] }] }, { "linkId" : "StructuralVariantAddenda", "definition" : "http://hl7.org/fhir/StructureDefinition/Observation#Observation.component", "code" : [{ "system" : "http://loinc.org", "code" : "81297-4", "display" : "Structural variant addendum panel" }], "text" : "Structural Variant Addenda", "type" : "group", "item" : [{ "extension" : [{ "url" : "http://hl7.org/fhir/StructureDefinition/questionnaire-itemControl", "valueCodeableConcept" : { "coding" : [{ "system" : "http://hl7.org/fhir/questionnaire-item-control", "code" : "help" }] } }], "linkId" : "StructuralVariantAddenda-designNote", "text" : "LRI Table 5-3 - part of the same Discrete Variant Panel in the HL7 v2 message, shown as a separate table in LRI purely for visual separation of structural-variant-only attributes.", "type" : "display" }, { "linkId" : "LRI/B.28", "definition" : "http://hl7.org/fhir/StructureDefinition/Observation#Observation.component.valueQuantity", "code" : [{ "system" : "http://loinc.org", "code" : "82155-3", "display" : "Genomic structural variant copy number" }], "text" : "Genomic Structural Variant Copy Number", "type" : "decimal", "item" : [{ "extension" : [{ "url" : "http://hl7.org/fhir/StructureDefinition/questionnaire-itemControl", "valueCodeableConcept" : { "coding" : [{ "system" : "http://hl7.org/fhir/questionnaire-item-control", "code" : "help" }] } }], "linkId" : "LRI/B.28-designNote", "text" : "LRI row B.28, OBX type NM, R/O/C = O, [0..1], OBX-4 sub-ID \"2a.1\". FHIR\nVariant profile slice: `copy-number`. Not a discrete iGene field - the\nclosest iGene concept is the Copy-number state dropdown (Allelic State,\nB.23), which is a category not a number. Used by the ctDNA Bundle's\nintragenic-CNV and multi-gene-CNV Observations - not the structural-variant\n(translocation-style) Observation, where a copy number doesn't apply.", "type" : "display" }] }, { "linkId" : "LRI/B.32", "definition" : "http://hl7.org/fhir/StructureDefinition/Observation#Observation.component.valueRange", "code" : [{ "system" : "http://loinc.org", "code" : "81302-2", "display" : "Structural variant inner start and end" }], "text" : "Structural Variant Inner Start-End", "type" : "string", "item" : [{ "extension" : [{ "url" : "http://hl7.org/fhir/StructureDefinition/questionnaire-itemControl", "valueCodeableConcept" : { "coding" : [{ "system" : "http://hl7.org/fhir/questionnaire-item-control", "code" : "help" }] } }], "linkId" : "LRI/B.32-designNote", "text" : "LRI row B.32, OBX type NR, R/O/C = O, [0..1], OBX-4 sub-ID \"2a.1\". FHIR\nVariant profile slice: `inner-start-end`. Not a discrete iGene field -\nsummarised within iGene's Genomic_coordinates field. Used by the ctDNA\nBundle's intragenic-CNV, multi-gene-CNV and structural-variant Observations.", "type" : "display" }] }] }, { "linkId" : "NoLRIEquivalent", "definition" : "http://hl7.org/fhir/StructureDefinition/Observation#Observation.component", "text" : "FHIR/iGene Elements With No LRI Discrete Variant Panel Row", "type" : "group", "item" : [{ "extension" : [{ "url" : "http://hl7.org/fhir/StructureDefinition/questionnaire-itemControl", "valueCodeableConcept" : { "coding" : [{ "system" : "http://hl7.org/fhir/questionnaire-item-control", "code" : "help" }] } }], "linkId" : "NoLRIEquivalent-designNote", "text" : "These are used by a current FHIR example and/or iGene, but have no row anywhere in LRI's Discrete Variant Panel (Table 5-2/5-3) - see the Description's gap notes.", "type" : "display" }, { "linkId" : "FHIR/CoordinateSystem", "definition" : "http://hl7.org/fhir/StructureDefinition/Observation#Observation.component.valueCodeableConcept", "code" : [{ "system" : "http://loinc.org", "code" : "92822-6", "display" : "Genomic coordinate system [Type]" }], "text" : "Coordinate System", "type" : "choice", "item" : [{ "extension" : [{ "url" : "http://hl7.org/fhir/StructureDefinition/questionnaire-itemControl", "valueCodeableConcept" : { "coding" : [{ "system" : "http://hl7.org/fhir/questionnaire-item-control", "code" : "help" }] } }], "linkId" : "FHIR/CoordinateSystem-designNote", "text" : "No LRI row. FHIR Variant profile slice: `coordinate-system`. Not a discrete\niGene field - summarised within iGene's Genomic_coordinates field. Used by\nall four ctDNA Bundle Observations (1-based character counting).", "type" : "display" }] }, { "linkId" : "FHIR/OriginOfGermlineVariant", "definition" : "http://hl7.org/fhir/StructureDefinition/Observation#Observation.component.valueCodeableConcept", "code" : [{ "system" : "http://loinc.org", "code" : "94186-4", "display" : "Origin of germline genetic variant [Type]" }], "text" : "Origin of Germline Genetic Variant", "type" : "choice", "item" : [{ "extension" : [{ "url" : "http://hl7.org/fhir/StructureDefinition/questionnaire-itemControl", "valueCodeableConcept" : { "coding" : [{ "system" : "http://hl7.org/fhir/questionnaire-item-control", "code" : "help" }] } }], "linkId" : "FHIR/OriginOfGermlineVariant-designNote", "text" : "No dedicated LRI row - the closest LRI concept is Allelic Phase (82120-7, row\nB.26), whose answer list happens to include Maternal/Paternal among several\n\"set of variants in cis\" options, not a dedicated parent-of-origin field.\nFHIR Variant profile slice: `variant-inheritance`. iGene: this is the\nInheritance field for the four variant types that have one (not LOH), though\niGene's own spec gives it no LOINC code. Used by the ctDNA Bundle's\nsmall-variant, intragenic-CNV and multi-gene-CNV Observations (Maternal) -\nnot the structural-variant Observation.", "type" : "display" }] }] }, { "linkId" : "LossOfHeterozygosity", "definition" : "http://hl7.org/fhir/StructureDefinition/Observation#Observation", "text" : "Loss of Heterozygosity (iGene fields, mapped to a separate Molecular Consequence Observation)", "type" : "group", "item" : [{ "extension" : [{ "url" : "http://hl7.org/fhir/StructureDefinition/questionnaire-itemControl", "valueCodeableConcept" : { "coding" : [{ "system" : "http://hl7.org/fhir/questionnaire-item-control", "code" : "help" }] } }], "linkId" : "LossOfHeterozygosity-designNote", "text" : "One of iGene's five variant types (`LOH1`-`LOH2`), with no corresponding row\nanywhere in LRI's Discrete Variant Panel. Decided: this IG models LOH as a\nseparate [Molecular Consequence](StructureDefinition-MolecularConsequence.html)\nObservation, `derivedFrom` the `Variant` it accompanies, with a\n`functional-effect` component coded `SO_0001786 loss_of_heterozygosity` -\nsee [Observation-ctdna9737383222-seqv1-loh](Observation-ctdna9737383222-seqv1-loh.html)\nfor a worked example - rather than as items directly on this Discrete Variant\nPanel. The two items below describe iGene's own flat fields for reference, not\nhow this IG models them.", "type" : "display" }, { "linkId" : "iGene/LOH_Description", "definition" : "http://hl7.org/fhir/StructureDefinition/Observation#Observation.component.valueCodeableConcept", "code" : [{ "system" : "http://loinc.org", "code" : "48018-6", "display" : "Gene studied [ID]" }], "text" : "Gene(s)", "type" : "string" }, { "linkId" : "iGene/LOH_State", "definition" : "http://hl7.org/fhir/StructureDefinition/Observation#Observation.component.valueCodeableConcept", "text" : "Loss of Heterozygosity (LOH)", "type" : "choice", "item" : [{ "extension" : [{ "url" : "http://hl7.org/fhir/StructureDefinition/questionnaire-itemControl", "valueCodeableConcept" : { "coding" : [{ "system" : "http://hl7.org/fhir/questionnaire-item-control", "code" : "help" }] } }], "linkId" : "iGene/LOH_State-designNote", "text" : "No LOINC code in iGene's own spec (\"None\"); iGene example value \"Significant LOH\". Not a value LRI's Allelic State (B.23) answer list supports.", "type" : "display" }] }] }] }] }