FHIR IG analytics| Package | fhir.nwgenomics.nhs.uk |
| Resource Type | Questionnaire |
| Id | Questionnaire-ReportableVariantResultPanel.json |
| FHIR Version | R4 |
| Source | https://build.fhir.org/ig/nw-gmsa/nw-gmsa.github.com/Questionnaire-ReportableVariantResultPanel.html |
| URL | https://fhir.nwgenomics.nhs.uk/Questionnaire/ReportableVariantResultPanel |
| Version | 2.2.0 |
| Status | draft |
| Date | 2026-09-27T08:17:18+00:00 |
| Title | Reportable Variant Result Panel |
| Realm | us |
| Authority | hl7 |
| Description | Result panel for a [Variant (Reportable Variant)](StructureDefinition-Variant.html) `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 own **Discrete Variant Panel** (LOINC `81250-3`, LRI Chapter 5 Table 5-2, plus the Structural Variant Addenda in Table 5-3) - the same panel the NTHL1 and CFTR examples are based on. LRI already defines this as a single panel covering both simple and structural variants; this Questionnaire follows that same single-panel structure rather than iGene's separate per-variant-type field sets, mapping each item to both its LRI `OBX` row and its corresponding component in the HL7 Genomics Reporting IG's [Variant](https://build.fhir.org/ig/HL7/genomics-reporting/StructureDefinition-variant.html) profile. See [OMICS DSS Result Integration](reportable-variants.html) for the full LRI/FHIR/iGene three-way mapping table. `item.definition`/`item.code` are cross-checked against this IG's current `Variant` examples: [Variant - NTHL1](Observation-8385c2fd-313d-4fd5-b98e-d5ea4bae6f99.html) and [Variant - CFTR](Observation-bca547c1-78a5-41be-8cfc-03c05805ac85.html) (both based on LRI examples), `Observation-EGFR-Variant-ctDNA`, `Observation-BRCA1`, and the four `Variant` Observations (a small variant, an intragenic CNV, a multi-gene CNV and a structural variant) in [Bundle-ctdna9737383222-testresults](Bundle-ctdna9737383222-testresults.html), plus iGene's own custom field spec for variants (`NotGit/iGene Custom Fields Master Dataset - Updated 13-Aug-26.xlsx`, "Variant Level Data" sheet) - only elements genuinely populated by at least one of these is modelled, since these are the only elements needed for the iGene feed. See [OMICS DSS Result Integration - Result Panel: Elements Not Included](reportable-variants.html#result-panel-elements-not-included) for the LRI/FHIR elements deliberately left out because no current example populates them. **Known gaps between iGene, LRI and the FHIR profile, not yet resolved:** - **Loss of Heterozygosity** is one of iGene's five variant types, but has **no corresponding row anywhere in LRI's Discrete Variant Panel** - LRI's closest concept, Allelic State (`53034-5`, row B.23), does not offer an LOH answer option. No current FHIR example produces LOH data either. - **Coordinate System [Type]** (`92822-6`) and **Origin of Germline Genetic Variant [Type]** (`94186-4`), both used by the ctDNA Bundle examples, have **no row in LRI's Discrete Variant Panel** - LRI's closest concept to the latter is Allelic Phase (`82120-7`, row B.26), a different LOINC code whose answer list happens to include Maternal/Paternal as two of several "sets of variants in cis" options, not a dedicated parent-of-origin field. - **Structural Variant**: iGene expects a single `Complex variant HGVS name` field (LOINC `81262-8` - itself an LRI Complex Variant Panel code, row C.2, not part of the Discrete Variant Panel at all), but the ctDNA Bundle's structural-variant Observation does not populate `81262-8` - it uses several Discrete Variant Panel components instead (Genomic Reference Sequence, Coordinate System, Genomic Ref/Alt Allele, DNA Change Type, Genomic DNA Change). |
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Note: links and images are rebased to the (stated) source
Generated Narrative: Questionnaire ReportableVariantResultPanel
Profile: Questionnaire
| LinkID | Text | Cardinality | Type | Description & Constraints |
|---|---|---|---|---|
  | Result panel for a [Variant (Reportable Variant)](StructureDefinition-Variant.html) `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 own **Discrete Variant Panel** (LOINC `81250-3`, LRI Chapter 5 Table 5-2, plus the Structural Variant Addenda in Table 5-3) - the same panel the NTHL1 and CFTR examples are based on. LRI already defines this as a single panel covering both simple and structural variants; this Questionnaire follows that same single-panel structure rather than iGene's separate per-variant-type field sets, mapping each item to both its LRI `OBX` row and its corresponding component in the HL7 Genomics Reporting IG's [Variant](https://build.fhir.org/ig/HL7/genomics-reporting/StructureDefinition-variant.html) profile. See [OMICS DSS Result Integration](reportable-variants.html) for the full LRI/FHIR/iGene three-way mapping table. `item.definition`/`item.code` are cross-checked against this IG's current `Variant` examples: [Variant - NTHL1](Observation-8385c2fd-313d-4fd5-b98e-d5ea4bae6f99.html) and [Variant - CFTR](Observation-bca547c1-78a5-41be-8cfc-03c05805ac85.html) (both based on LRI examples), `Observation-EGFR-Variant-ctDNA`, `Observation-BRCA1`, and the four `Variant` Observations (a small variant, an intragenic CNV, a multi-gene CNV and a structural variant) in [Bundle-ctdna9737383222-testresults](Bundle-ctdna9737383222-testresults.html), plus iGene's own custom field spec for variants (`NotGit/iGene Custom Fields Master Dataset - Updated 13-Aug-26.xlsx`, "Variant Level Data" sheet) - only elements genuinely populated by at least one of these is modelled, since these are the only elements needed for the iGene feed. See [OMICS DSS Result Integration - Result Panel: Elements Not Included](reportable-variants.html#result-panel-elements-not-included) for the LRI/FHIR elements deliberately left out because no current example populates them. **Known gaps between iGene, LRI and the FHIR profile, not yet resolved:** - **Loss of Heterozygosity** is one of iGene's five variant types, but has **no corresponding row anywhere in LRI's Discrete Variant Panel** - LRI's closest concept, Allelic State (`53034-5`, row B.23), does not offer an LOH answer option. No current FHIR example produces LOH data either. - **Coordinate System [Type]** (`92822-6`) and **Origin of Germline Genetic Variant [Type]** (`94186-4`), both used by the ctDNA Bundle examples, have **no row in LRI's Discrete Variant Panel** - LRI's closest concept to the latter is Allelic Phase (`82120-7`, row B.26), a different LOINC code whose answer list happens to include Maternal/Paternal as two of several "sets of variants in cis" options, not a dedicated parent-of-origin field. - **Structural Variant**: iGene expects a single `Complex variant HGVS name` field (LOINC `81262-8` - itself an LRI Complex Variant Panel code, row C.2, not part of the Discrete Variant Panel at all), but the ctDNA Bundle's structural-variant Observation does not populate `81262-8` - it uses several Discrete Variant Panel components instead (Genomic Reference Sequence, Coordinate System, Genomic Ref/Alt Allele, DNA Change Type, Genomic DNA Change). | Questionnaire | https://fhir.nwgenomics.nhs.uk/Questionnaire/ReportableVariantResultPanel#2.2.0 | |
  DiscreteVariantPanel | Discrete Variant Panel | 0..* | group | Definition: Observation |
   DiscreteVariantPanel-designNote | LRI Table 5-2 row B - repeats for each discrete variant reported (OBX-4 sub-ID "2a", incrementing per repeat). | 0..1 | display | |
 LRI/B.1 | Variant Category | 0..1 | choice | Definition: Observation.component.valueCodeableConcept |
 LRI/B.1-designNote | LRI row B.1, OBX type CWE, R/O/C = O, [0..1]. LRI's own answer list (LL4165-8) only distinguishes Simple Variant vs Structural Variant - not granular enough to route a variant to the correct iGene slot type. Resolved: this IG binds this component to its own [IGeneVariantCategory](CodeSystem-IGeneVariantCategory.html) value set instead (`SEQV`/`ICNV`/`MCNV`/`SV`/`LOH`), making the classification that used to be inferred (see [OMICS DSS Result Integration](reportable-variants.html#outstanding-issues)) an explicit, coded value - the FHIR Variant profile has no named slice for this at all, so it is modelled here as an open-slice component, same as `Variant.component:variant-category`. Populated by every current example. | 0..1 | display | |
| TranscriptSpecification | Transcript Specification | 0..1 | group | Definition: Observation.component |
| LRI/B.3 | Gene Studied | 0..1 | choice | Definition: Observation.component.valueCodeableConcept |
| LRI/B.3-designNote | LRI row B.3, OBX type CWE, R/O/C = C, [0..1]. FHIR Variant profile: this IG's own `gene-studied` addition (not one of the international profile's named slices). iGene: rolled into the free-text Description field (SEQV/ICNV) or the Gene(s) field (LOH). Used by NTHL1, CFTR, EGFR-ctDNA, and the ctDNA Bundle's small-variant and intragenic-CNV Observations. | 0..1 | display | |
| LRI/B.4 | Transcript Reference Sequence | 0..1 | choice | Definition: Observation.component.valueCodeableConcept |
| LRI/B.4-designNote | LRI row B.4, OBX type CWE, R/O/C = C, [0..1]. FHIR Variant profile slice: `representative-transcript-ref-seq`. iGene: rolled into the free-text Description field (SEQV/ICNV). Used by NTHL1, CFTR and the ctDNA Bundle's small-variant Observation. | 0..1 | display | |
| LRI/B.5 | DNA Change (c.HGVS) | 0..1 | choice | Definition: Observation.component.valueCodeableConcept |
| LRI/B.5-designNote | LRI row B.5, OBX type CWE, R/O/C = C, [0..1]. FHIR Variant profile slice: `representative-coding-hgvs`. iGene: rolled into the free-text Description field (SEQV/ICNV). Used by EGFR-ctDNA, BRCA1 and the ctDNA Bundle's small-variant Observation. | 0..1 | display | |
| LRI/B.6 | Amino Acid Change (pHGVS) | 0..1 | choice | Definition: Observation.component.valueCodeableConcept |
| LRI/B.6-designNote | LRI row B.6, OBX type CWE, R/O/C = C, [0..1]. FHIR Variant profile slice: `representative-protein-hgvs`. iGene: rolled into the free-text Description field (SEQV only - ICNV's Description omits this). Used only by the ctDNA Bundle's small-variant Observation. | 0..1 | display | |
| LRI/B.7 | DNA Change Type | 0..1 | choice | Definition: Observation.component.valueCodeableConcept |
| LRI/B.7-designNote | LRI row B.7, OBX type CWE, R/O/C = O, [0..1]. FHIR Variant profile slice: `coding-change-type`. Not a discrete iGene field - summarised within iGene's free-text Description/Genomic_coordinates fields. Used by every current example (Sequence Ontology or LOINC answer coding, e.g. duplication, deletion, substitution, copy_number_variation). | 0..1 | display | |
| GenomicSpecification | Genomic Specification | 0..1 | group | Definition: Observation.component |
| LRI/B.9 | Genomic Reference Sequence | 0..1 | choice | Definition: Observation.component.valueCodeableConcept |
| LRI/B.9-designNote | LRI row B.9, OBX type CWE, R/O/C = C, [0..1]. FHIR Variant profile slice: `genomic-ref-seq`. iGene: rolled into the free-text Genomic_coordinates field (all four variant types). Used by NTHL1 and all four ctDNA Bundle Observations. | 0..1 | display | |
| LRI/B.10 | Genomic DNA Change (gHGVS) | 0..1 | choice | Definition: Observation.component.valueCodeableConcept |
| LRI/B.10-designNote | LRI row B.10, OBX type CWE, R/O/C = C, [0..1]. FHIR Variant profile slice: `genomic-hgvs`. iGene: rolled into the free-text Genomic_coordinates field (all four variant types). Used by all four ctDNA Bundle Observations - not by NTHL1/CFTR, where it is commented out pending a confirmed mapping. | 0..1 | display | |
 LRI/B.11 | Genomic Ref Allele | 0..1 | string | Definition: Observation.component.valueString |
| LRI/B.11-designNote | LRI row B.11, OBX type ST, R/O/C = C, [0..1]. FHIR Variant profile slice: `ref-allele`. Not a discrete iGene field - summarised within iGene's Genomic_coordinates field. Used by NTHL1, CFTR and all four ctDNA Bundle Observations. | 0..1 | display | |
| LRI/B.12 | Genomic Allele Start-End | 0..1 | string | Definition: Observation.component.valueRange |
| LRI/B.12-designNote | LRI row B.12, OBX type NR, R/O/C = C, [0..1]. FHIR Variant profile slice: `exact-start-end`. Not a discrete iGene field. Used only by the ctDNA Bundle's small-variant Observation - a Range with only the low bound populated. | 0..1 | display | |
| LRI/B.13 | Genomic Alt Allele | 0..1 | string | Definition: Observation.component.valueString |
| LRI/B.13-designNote | LRI row B.13, OBX type ST, R/O/C = C, [0..1]. FHIR Variant profile slice: `alt-allele`. Not a discrete iGene field - summarised within iGene's Genomic_coordinates field. Used by the ctDNA Bundle's intragenic-CNV, multi-gene-CNV and structural-variant Observations (as symbolic ALT alleles, e.g. "<DEL>") - not by the small-variant Observation, NTHL1 or CFTR. | 0..1 | display | |
| OtherAttributes | Other Attributes | 0..1 | group | Definition: Observation.component |
| LRI/B.17 | Cytogenetic (Chromosome) Location | 0..1 | string | Definition: Observation.component.valueCodeableConcept |
| LRI/B.17-designNote | LRI row B.17, OBX type CWE, R/O/C = O, [0..1]. Not one of the international FHIR Variant profile's named component slices (its closest named slice, Cytogenomic Nomenclature 81291-7, is actually a different LRI field - Table 5-1 row A.11, part of the report-level Master Panel, not this Discrete Variant Panel) - captured here as an open-slice addition, consistent with GenomicObservation's open component slicing. iGene: this is the sole field for the Multigenic CNV Description, and part of the Genomic_coordinates field for the other three variant types. Used only by the ctDNA Bundle's multi-gene-CNV Observation (e.g. "Xq22.1-q28"). | 0..1 | display | |
| LRI/B.18 | Genomic Source Class | 0..1 | choice | Definition: Observation.component.valueCodeableConcept |
| LRI/B.18-designNote | LRI row B.18, OBX type CNE, R/O/C = R (required when present), [0..*]. FHIR Variant profile slice: `genomic-source-class`. Not a discrete iGene field. Used by NTHL1, CFTR, EGFR-ctDNA and the ctDNA Bundle's small-variant, intragenic-CNV and multi-gene-CNV Observations (Germline or Somatic) - not by the structural-variant Observation. | 0..1 | display | |
| Interpretations | Interpretations | 0..1 | group | Definition: Observation.component |
| LRI/B.20 | Classification | 0..1 | choice | Definition: Observation.component.valueCodeableConcept |
| LRI/B.20-designNote | LRI row B.20 (LRI names it "Genetic sequence variation clinical significance"), OBX type CNE, R/O/C = O, [0..1]. FHIR Variant profile: not one of the profile's own component slices (the profile relies on the generic `Observation.interpretation`/`valueCodeableConcept` pattern for this) - modelled here as an open-slice component to match how every current example actually carries it. iGene: this is the Classification field for all four variant types. Used by all four ctDNA Bundle Observations (e.g. "Pathogenic"). | 0..1 | display | |
| AllelicStatePhase | Allelic State/Phase Information | 0..1 | group | Definition: Observation.component |
| LRI/B.23 | Allelic State | 0..1 | choice | Definition: Observation.component.valueCodeableConcept |
| LRI/B.23-designNote | LRI row B.23, OBX type CNE, R/O/C = C, [0..1], answer list LL381-5 (Heteroplasmic/Homoplasmic/Homozygous/Heterozygous/Hemizygous - no "Loss of Heterozygosity" option). FHIR Variant profile slice: `allelic-state`. iGene: the Zygosity/Copy-number state field for all five variant types (iGene's LOH "State" field has no LOINC code and is a different concept - LRI has no LOH answer here). Used by NTHL1, CFTR, BRCA1 and the ctDNA Bundle's small-variant Observation (Heterozygous). | 0..1 | display | |
 LRI/B.24 | Allelic Frequency | 0..1 | decimal | Definition: Observation.component.valueQuantity |
| LRI/B.24-designNote | LRI row B.24 (LRI names it "Allelic Frequency [NFr]", the FHIR profile and our examples call it "Sample variant allelic frequency [NFr]" - same LOINC code, slightly different display text), OBX type NM, R/O/C = C, [0..1]. FHIR Variant profile slice: `sample-allelic-frequency`. iGene: the Level (VAF %) field for the four variant types that have one (not LOH). Used by EGFR-ctDNA (as a percentage) and all four ctDNA Bundle Observations (as a decimal fraction) - the units differ between the two sources. | 0..1 | display | |
| StructuralVariantAddenda | Structural Variant Addenda | 0..1 | group | Definition: Observation.component |
| StructuralVariantAddenda-designNote | 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. | 0..1 | display | |
| LRI/B.28 | Genomic Structural Variant Copy Number | 0..1 | decimal | Definition: Observation.component.valueQuantity |
| LRI/B.28-designNote | LRI row B.28, OBX type NM, R/O/C = O, [0..1], OBX-4 sub-ID "2a.1". FHIR Variant profile slice: `copy-number`. Not a discrete iGene field - the closest iGene concept is the Copy-number state dropdown (Allelic State, B.23), which is a category not a number. Used by the ctDNA Bundle's intragenic-CNV and multi-gene-CNV Observations - not the structural-variant (translocation-style) Observation, where a copy number doesn't apply. | 0..1 | display | |
| LRI/B.32 | Structural Variant Inner Start-End | 0..1 | string | Definition: Observation.component.valueRange |
| LRI/B.32-designNote | LRI row B.32, OBX type NR, R/O/C = O, [0..1], OBX-4 sub-ID "2a.1". FHIR Variant profile slice: `inner-start-end`. Not a discrete iGene field - summarised within iGene's Genomic_coordinates field. Used by the ctDNA Bundle's intragenic-CNV, multi-gene-CNV and structural-variant Observations. | 0..1 | display | |
| NoLRIEquivalent | FHIR/iGene Elements With No LRI Discrete Variant Panel Row | 0..1 | group | Definition: Observation.component |
| NoLRIEquivalent-designNote | 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. | 0..1 | display | |
| FHIR/CoordinateSystem | Coordinate System | 0..1 | choice | Definition: Observation.component.valueCodeableConcept |
| FHIR/CoordinateSystem-designNote | No LRI row. FHIR Variant profile slice: `coordinate-system`. Not a discrete iGene field - summarised within iGene's Genomic_coordinates field. Used by all four ctDNA Bundle Observations (1-based character counting). | 0..1 | display | |
| FHIR/OriginOfGermlineVariant | Origin of Germline Genetic Variant | 0..1 | choice | Definition: Observation.component.valueCodeableConcept |
| FHIR/OriginOfGermlineVariant-designNote | No dedicated LRI row - the closest LRI concept is Allelic Phase (82120-7, row B.26), whose answer list happens to include Maternal/Paternal among several "set of variants in cis" options, not a dedicated parent-of-origin field. FHIR Variant profile slice: `variant-inheritance`. iGene: this is the Inheritance field for the four variant types that have one (not LOH), though iGene's own spec gives it no LOINC code. Used by the ctDNA Bundle's small-variant, intragenic-CNV and multi-gene-CNV Observations (Maternal) - not the structural-variant Observation. | 0..1 | display | |
| LossOfHeterozygosity | Loss of Heterozygosity (iGene fields, mapped to a separate Molecular Consequence Observation) | 0..1 | group | Definition: Observation |
| LossOfHeterozygosity-designNote | One of iGene's five variant types (`LOH1`-`LOH2`), with no corresponding row anywhere in LRI's Discrete Variant Panel. Decided: this IG models LOH as a separate [Molecular Consequence](StructureDefinition-MolecularConsequence.html) Observation, `derivedFrom` the `Variant` it accompanies, with a `functional-effect` component coded `SO_0001786 loss_of_heterozygosity` - see [Observation-ctdna9737383222-seqv1-loh](Observation-ctdna9737383222-seqv1-loh.html) for a worked example - rather than as items directly on this Discrete Variant Panel. The two items below describe iGene's own flat fields for reference, not how this IG models them. | 0..1 | display | |
| iGene/LOH_Description | Gene(s) | 0..1 | string | Definition: Observation.component.valueCodeableConcept |
| iGene/LOH_State | Loss of Heterozygosity (LOH) | 0..1 | choice | Definition: Observation.component.valueCodeableConcept |
| iGene/LOH_State-designNote | 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. | 0..1 | display | |
| Documentation for this format | ||||
FHIR
FHIRsmith{
"resourceType": "Questionnaire",
"id": "ReportableVariantResultPanel",
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"title": "Reportable Variant Result Panel",
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"date": "2026-09-27T08:17:18+00:00",
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"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).",
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}
],
"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. \"<DEL>\") - 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"
}
]
}
]
}
]
}
]
}