description: Logical Model for a single entry in the DNPM DIP MTB Patient Record ngsReports array
package_name: de.medizininformatikinitiative.kerndatensatz.mtb
derivation: specialization
name: DNPM_LM_NGSReport
type: https://dnpm-dip.net/fhir/StructureDefinition/dnpm-lm-ngs-report
elements:
  dnpmId: {type: string, short: NGS Report UUID (DNPM internal ID), index: 0}
  patient:
    type: BackboneElement
    short: Patient reference
    index: 1
    elements:
      id: {type: string, short: Patient ID, index: 2}
      type: {type: string, short: Reference type (Patient), index: 3}
    required: [id, type]
  specimen:
    type: BackboneElement
    short: Tumor specimen reference
    index: 4
    elements:
      id: {type: string, short: Specimen ID, index: 5}
      type: {type: string, short: Reference type (TumorSpecimen), index: 6}
    required: [id, type]
  issuedOn: {type: string, short: Report issue date (YYYY-MM-DD), index: 7}
  type:
    type: BackboneElement
    short: NGS analysis type (e.g. exome, panel)
    index: 8
    elements:
      code: {type: string, short: Type code, index: 9}
      display: {type: string, short: Type display, index: 10}
      system: {type: string, short: Type system URI, index: 11}
    required: [system, code]
  metadata:
    type: BackboneElement
    short: NGS run metadata
    index: 12
    elements:
      referenceGenome:
        type: BackboneElement
        short: Reference genome used
        index: 13
        elements:
          code: {type: string, short: Genome build code (e.g. GRCh38), index: 14}
          display: {type: string, short: Genome build display, index: 15}
          system: {type: string, short: Genome build system URI, index: 16}
        required: [system, code]
      sequencer:
        type: BackboneElement
        short: Sequencer instrument
        index: 17
        elements:
          code: {type: string, short: Sequencer code, index: 18}
          display: {type: string, short: Sequencer display, index: 19}
          system: {type: string, short: Sequencer system URI, index: 20}
        required: [system, code]
      kitManufacturer: {type: string, short: Kit manufacturer name, index: 21}
      kitType: {type: string, short: Kit type name, index: 22}
      pipeline: {type: string, short: Bioinformatics pipeline identifier, index: 23}
      tumorCellContent:
        type: BackboneElement
        short: Tumor cell content metadata estimate
        index: 24
        elements:
          method:
            type: BackboneElement
            short: Estimation method
            index: 25
            elements:
              code: {type: string, short: Method code, index: 26}
              display: {type: string, short: Method display, index: 27}
              system: {type: string, short: Method system URI, index: 28}
            required: [system, code]
          value: {type: decimal, short: Tumor cell content fraction (0.0 – 1.0), index: 29}
        required: [value]
  results:
    type: BackboneElement
    short: NGS analysis results
    index: 30
    elements:
      tumorCellContent:
        type: BackboneElement
        short: Bioinformatically determined tumor cell content
        index: 31
        elements:
          id: {type: string, short: Result ID, index: 32}
          patient:
            type: BackboneElement
            short: Patient reference
            index: 33
            elements:
              id: {type: string, short: Patient ID, index: 34}
              type: {type: string, short: Reference type, index: 35}
            required: [id, type]
          specimen:
            type: BackboneElement
            short: Specimen reference
            index: 36
            elements:
              id: {type: string, short: Specimen ID, index: 37}
              type: {type: string, short: Reference type, index: 38}
            required: [id, type]
          method:
            type: BackboneElement
            short: Determination method
            index: 39
            elements:
              code: {type: string, short: Method code, index: 40}
              display: {type: string, short: Method display, index: 41}
              system: {type: string, short: Method system URI, index: 42}
            required: [system, code]
          value: {type: decimal, short: Tumor cell content fraction (0.0 – 1.0), index: 43}
        required: [method, id, value, specimen, patient]
      tmb:
        type: BackboneElement
        short: Tumor Mutational Burden
        index: 44
        elements:
          id: {type: string, short: TMB result ID, index: 45}
          patient:
            type: BackboneElement
            short: Patient reference
            index: 46
            elements:
              id: {type: string, short: Patient ID, index: 47}
              type: {type: string, short: Reference type, index: 48}
            required: [id, type]
          specimen:
            type: BackboneElement
            short: Specimen reference
            index: 49
            elements:
              id: {type: string, short: Specimen ID, index: 50}
              type: {type: string, short: Reference type, index: 51}
            required: [id, type]
          value:
            type: BackboneElement
            short: TMB quantity
            index: 52
            elements:
              value: {type: decimal, short: Numeric TMB value, index: 53}
              unit: {type: string, short: Unit (e.g. Mutations per megabase), index: 54}
            required: [value, unit]
          interpretation:
            type: BackboneElement
            short: TMB interpretation
            index: 55
            elements:
              code: {type: string, short: Interpretation code (e.g. high), index: 56}
              display: {type: string, short: Interpretation display, index: 57}
              system: {type: string, short: Interpretation system URI, index: 58}
            required: [system, code]
        required: [id, value, specimen, patient]
      brcaness:
        type: BackboneElement
        short: BRCAness score
        index: 59
        elements:
          id: {type: string, short: BRCAness result ID, index: 60}
          patient:
            type: BackboneElement
            short: Patient reference
            index: 61
            elements:
              id: {type: string, short: Patient ID, index: 62}
              type: {type: string, short: Reference type, index: 63}
            required: [id, type]
          specimen:
            type: BackboneElement
            short: Specimen reference
            index: 64
            elements:
              id: {type: string, short: Specimen ID, index: 65}
              type: {type: string, short: Reference type, index: 66}
            required: [id, type]
          value: {type: decimal, short: BRCAness score (0.0 – 1.0), index: 67}
          confidenceRange:
            type: BackboneElement
            short: Confidence range
            index: 68
            elements:
              min: {type: decimal, short: Minimum confidence value, index: 69}
              max: {type: decimal, short: Maximum confidence value, index: 70}
            required: [min, max]
        required: [id, value, specimen, patient]
      hrdScore:
        type: BackboneElement
        short: Homologous Recombination Deficiency Score
        index: 71
        elements:
          id: {type: string, short: HRD result ID, index: 72}
          patient:
            type: BackboneElement
            short: Patient reference
            index: 73
            elements:
              id: {type: string, short: Patient ID, index: 74}
              type: {type: string, short: Reference type, index: 75}
            required: [id, type]
          specimen:
            type: BackboneElement
            short: Specimen reference
            index: 76
            elements:
              id: {type: string, short: Specimen ID, index: 77}
              type: {type: string, short: Reference type, index: 78}
            required: [id, type]
          value: {type: decimal, short: HRD composite score, index: 79}
          components:
            type: BackboneElement
            short: HRD component scores
            index: 80
            elements:
              lst: {type: decimal, short: Large-scale state transitions (LST), index: 81}
              loh: {type: decimal, short: Loss of heterozygosity (LOH), index: 82}
              tai: {type: decimal, short: Telomeric allelic imbalance (TAI), index: 83}
          interpretation:
            type: BackboneElement
            short: HRD interpretation
            index: 84
            elements:
              code: {type: string, short: Interpretation code (e.g. low), index: 85}
              display: {type: string, short: Interpretation display, index: 86}
              system: {type: string, short: Interpretation system URI, index: 87}
            required: [system, code]
        required: [id, value, specimen, patient]
      simpleVariants:
        type: BackboneElement
        short: Simple variants (SNV / small indels)
        array: true
        index: 88
        elements:
          patient:
            type: BackboneElement
            short: Patient reference
            index: 90
            elements:
              id: {type: string, short: Patient ID, index: 91}
              type: {type: string, short: Reference type, index: 92}
            required: [id, type]
          chromosome: {type: string, short: Chromosome (e.g. chr4), index: 96}
          readDepth: {type: integer, short: Read depth at variant position, index: 116}
          interpretation:
            type: BackboneElement
            short: ClinVar / clinical interpretation
            index: 118
            elements:
              code: {type: string, short: Interpretation code, index: 119}
              display: {type: string, short: Interpretation display, index: 120}
              system: {type: string, short: Interpretation system URI, index: 121}
            required: [system, code]
          transcriptId:
            type: BackboneElement
            short: Transcript identifier
            index: 105
            elements:
              value: {type: string, short: Transcript ID value (e.g. ENST...), index: 106}
              system: {type: string, short: Transcript system URI, index: 107}
            required: [value, system]
          localization:
            type: BackboneElement
            short: Variant localisation in gene
            array: true
            index: 101
            elements:
              code: {type: string, short: Localisation code, index: 102}
              display: {type: string, short: Localisation display, index: 103}
              system: {type: string, short: Localisation system URI, index: 104}
            required: [system, code]
          dnaChange: {type: string, short: cDNA / DNA change in HGVS notation (e.g. c.570G>T), index: 114}
          externalIds:
            type: BackboneElement
            short: External variant identifiers (e.g. dbSNP rs-number)
            array: true
            index: 93
            elements:
              value: {type: string, short: Identifier value, index: 94}
              system: {type: string, short: Identifier system URI, index: 95}
            required: [value, system]
          allelicFrequency: {type: decimal, short: Variant allelic frequency, index: 117}
          id: {type: string, short: Variant ID, index: 89}
          gene:
            type: BackboneElement
            short: Affected gene
            index: 97
            elements:
              code: {type: string, short: HGNC gene code, index: 98}
              display: {type: string, short: Gene symbol, index: 99}
              system: {type: string, short: Gene nomenclature system URI, index: 100}
            required: [system, code]
          exonId: {type: string, short: Exon identifier, index: 108}
          position:
            type: BackboneElement
            short: Genomic position (1-based)
            index: 109
            elements:
              start: {type: integer, short: Start position, index: 110}
              end: {type: integer, short: End position, index: 111}
            required: [start]
          refAllele: {type: string, short: Reference allele, index: 113}
          proteinChange: {type: string, short: Protein change in HGVS notation (e.g. p.(Glu125Asp)), index: 115}
          altAllele: {type: string, short: Alternate allele, index: 112}
        required: [chromosome, id, gene, altAllele, refAllele, patient]
      copyNumberVariants:
        type: BackboneElement
        short: Copy number variants (CNV)
        array: true
        index: 122
        elements:
          patient:
            type: BackboneElement
            short: Patient reference
            index: 124
            elements:
              id: {type: string, short: Patient ID, index: 125}
              type: {type: string, short: Reference type, index: 126}
            required: [id, type]
          reportedAffectedGenes:
            type: BackboneElement
            short: Reported affected genes
            array: true
            index: 142
            elements:
              code: {type: string, short: HGNC gene code, index: 143}
              display: {type: string, short: Gene symbol, index: 144}
              system: {type: string, short: Gene nomenclature system URI, index: 145}
            required: [system, code]
          chromosome: {type: string, short: Chromosome (e.g. chr7), index: 127}
          relativeCopyNumber: {type: decimal, short: Relative copy number, index: 139}
          focality:
            type: BackboneElement
            short: CNV focality
            index: 146
            elements:
              code: {type: string, short: Focality code (e.g. focal), index: 147}
              display: {type: string, short: Focality display, index: 148}
              system: {type: string, short: Focality system URI, index: 149}
            required: [system, code]
          totalCopyNumber: {type: integer, short: Total copy number, index: 138}
          cnB: {type: integer, short: Copy number allele B, index: 141}
          startRange:
            type: BackboneElement
            short: Start position range
            index: 132
            elements:
              start: {type: integer, short: Range start, index: 133}
              end: {type: integer, short: Range end, index: 134}
            required: [start, end]
          localization:
            type: BackboneElement
            short: CNV localisation
            array: true
            index: 128
            elements:
              code: {type: string, short: Localisation code, index: 129}
              display: {type: string, short: Localisation display, index: 130}
              system: {type: string, short: Localisation system URI, index: 131}
            required: [system, code]
          type:
            type: BackboneElement
            short: CNV type (gain / loss)
            index: 150
            elements:
              code: {type: string, short: CNV type code, index: 151}
              display: {type: string, short: CNV type display, index: 152}
              system: {type: string, short: CNV type system URI, index: 153}
            required: [system, code]
          id: {type: string, short: CNV ID, index: 123}
          endRange:
            type: BackboneElement
            short: End position range
            index: 135
            elements:
              start: {type: integer, short: Range start, index: 136}
              end: {type: integer, short: Range end, index: 137}
            required: [start, end]
          cnA: {type: integer, short: Copy number allele A, index: 140}
        required: [chromosome, id, type, patient]
      dnaFusions:
        type: BackboneElement
        short: DNA-level gene fusions
        array: true
        index: 154
        elements:
          id: {type: string, short: DNA fusion ID, index: 155}
          patient:
            type: BackboneElement
            short: Patient reference
            index: 156
            elements:
              id: {type: string, short: Patient ID, index: 157}
              type: {type: string, short: Reference type, index: 158}
            required: [id, type]
          localization:
            type: BackboneElement
            short: Fusion localisation
            array: true
            index: 159
            elements:
              code: {type: string, short: Localisation code, index: 160}
              display: {type: string, short: Localisation display, index: 161}
              system: {type: string, short: Localisation system URI, index: 162}
            required: [system, code]
          fusionPartner5prime:
            type: BackboneElement
            short: 5-prime fusion partner
            index: 163
            elements:
              gene:
                type: BackboneElement
                short: 5-prime partner gene
                index: 164
                elements:
                  code: {type: string, short: HGNC gene code, index: 165}
                  display: {type: string, short: Gene symbol, index: 166}
                  system: {type: string, short: Gene nomenclature system URI, index: 167}
                required: [system, code]
              position: {type: integer, short: Breakpoint position, index: 168}
            required: [gene, position]
          fusionPartner3prime:
            type: BackboneElement
            short: 3-prime fusion partner
            index: 169
            elements:
              gene:
                type: BackboneElement
                short: 3-prime partner gene
                index: 170
                elements:
                  code: {type: string, short: HGNC gene code, index: 171}
                  display: {type: string, short: Gene symbol, index: 172}
                  system: {type: string, short: Gene nomenclature system URI, index: 173}
                required: [system, code]
              position: {type: integer, short: Breakpoint position, index: 174}
            required: [gene, position]
          reportedNumReads: {type: integer, short: Number of reads supporting fusion, index: 175}
        required: [id, patient]
      rnaFusions:
        type: BackboneElement
        short: RNA-level gene fusions
        array: true
        index: 176
        elements:
          id: {type: string, short: RNA fusion ID, index: 177}
          patient:
            type: BackboneElement
            short: Patient reference
            index: 178
            elements:
              id: {type: string, short: Patient ID, index: 179}
              type: {type: string, short: Reference type, index: 180}
            required: [id, type]
          externalIds:
            type: BackboneElement
            short: External identifiers (e.g. COSMIC fusion ID)
            array: true
            index: 181
            elements:
              value: {type: string, short: Identifier value, index: 182}
              system: {type: string, short: Identifier system URI, index: 183}
            required: [value, system]
          localization:
            type: BackboneElement
            short: Fusion localisation
            array: true
            index: 184
            elements:
              code: {type: string, short: Localisation code, index: 185}
              display: {type: string, short: Localisation display, index: 186}
              system: {type: string, short: Localisation system URI, index: 187}
            required: [system, code]
          fusionPartner5prime:
            type: BackboneElement
            short: 5-prime fusion partner
            index: 188
            elements:
              gene:
                type: BackboneElement
                short: 5-prime partner gene
                index: 189
                elements:
                  code: {type: string, short: HGNC gene code, index: 190}
                  display: {type: string, short: Gene symbol, index: 191}
                  system: {type: string, short: Gene nomenclature system URI, index: 192}
                required: [system, code]
              transcript:
                type: BackboneElement
                short: 5-prime transcript
                index: 193
                elements:
                  value: {type: string, short: Transcript ID (e.g. ENST...), index: 194}
                  system: {type: string, short: Transcript system URI, index: 195}
                required: [value, system]
              exon: {type: string, short: Exon identifier, index: 196}
              position: {type: integer, short: Breakpoint position, index: 197}
              strand: {type: string, short: Strand (+ or -), index: 198}
            required: [gene, position]
          fusionPartner3prime:
            type: BackboneElement
            short: 3-prime fusion partner
            index: 199
            elements:
              gene:
                type: BackboneElement
                short: 3-prime partner gene
                index: 200
                elements:
                  code: {type: string, short: HGNC gene code, index: 201}
                  display: {type: string, short: Gene symbol, index: 202}
                  system: {type: string, short: Gene nomenclature system URI, index: 203}
                required: [system, code]
              transcript:
                type: BackboneElement
                short: 3-prime transcript
                index: 204
                elements:
                  value: {type: string, short: Transcript ID (e.g. ENST...), index: 205}
                  system: {type: string, short: Transcript system URI, index: 206}
                required: [value, system]
              exon: {type: string, short: Exon identifier, index: 207}
              position: {type: integer, short: Breakpoint position, index: 208}
              strand: {type: string, short: Strand (+ or -), index: 209}
            required: [gene, position]
          effect:
            type: BackboneElement
            short: RNA fusion effect
            index: 210
            elements:
              code: {type: string, short: Effect code (e.g. in-frame), index: 211}
              display: {type: string, short: Effect display, index: 212}
              system: {type: string, short: Effect system URI, index: 213}
            required: [system, code]
          reportedNumReads: {type: integer, short: Number of reads supporting fusion, index: 214}
        required: [id, patient]
package_version: 2027.0.0-ballot.1
class: logical
kind: logical
url: https://dnpm-dip.net/fhir/StructureDefinition/dnpm-lm-ngs-report
base: http://hl7.org/fhir/StructureDefinition/Element
version: 2027.0.0-ballot.1
required: [results, dnpmId, issuedOn, specimen, type, patient]