MII IG Kerndatensatz-Modul Onkologie
2027.0.0-ballot.1 -
Germany
MII IG Kerndatensatz-Modul Onkologie
2027.0.0-ballot.1 -
Germany
This page is part of the MII IG Kerndatensatz-Modul Onkologie (v2027.0.0-ballot.1: Release) based on FHIR (HL7® FHIR® Standard) R4. This is the current published version in its permanent home (it will always be available at this URL). For a full list of available versions, see the Directory of published versions
The oBDS records genetic variants in a coarse-grained way (free-text designation
plus one qualifier out of M/W/P/N/U, or free text instead, oBDS
23.1/23.2 — see the section Qualifiers of the genetics report). For a
structured, interoperable representation, the
MII Molecular Genetics Report (MolGen)
SHOULD be used where available; it is based on the HL7 Clinical Genomics
Genomics Reporting IG and uses international nomenclatures (HGNC,
HGVS, ISCN, Sequence Ontology).
For the variant and marker types typical of oncological practice, this page gives
a concrete recommendation on which MolGen structure to use for representing
them (as of molgen 2026.x, also valid for 2027). It is based on an example
marker list (57 genes, approximately 300 gene × variant combinations); the
recommendation is deliberately not normative, but an implementation aid.
Profile reference:
MII_PR_MolGen_Variante(parent:http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/variant)
| oBDS/list type | Example | Recommended MolGen representation |
|---|---|---|
| Gene (identity) | BRAF, ALK |
Variante.component:gene-studied → HGNC (http://www.genenames.org/geneId) |
| Specific mutation (protein) | BRAF V600E = p.Val600Glu |
component:representative-protein-hgvs (p.HGVS) |
| Specific mutation (DNA) | c.1799T>A |
component:representative-coding-hgvs (c.HGVS) |
| Formula / HGVS free text | any HGVS statement | matching *-hgvs component; otherwise value/note |
| Exon statement | EGFR exon 19, FGFR2 exon 12 |
component:dna-region (LOINC 47999-8, DNA region name), where applicable plus exact-start-end |
| Fusion | EML4::ALK, BCR::ABL1 |
component:gene-fusion → HGNC pair GENE1::GENE2 (ValueSet hgnc-vs) |
| Amplification | ERBB2/HER2 amplification |
component:copy-number (copy number) |
| Translocation / rearrangement | del(17)(p13), ROS1 rearrangement |
component:cytogenetic-location (ISCN) |
| LOH / co-deletion | LOH 1p/19q |
component:cytogenetic-location or copy-number |
| Promoter hypermethylation | MGMT |
special case — a dedicated methylation observation (LOINC), not a variant |
| Unknown | gene without further detail | component:gene-studied + value = indeterminate |
| IHC marker | PD-L1, HER2 IHC, p16, p53 |
not a variant → MII_PR_MTB_Immunohistochemistry (Molecular Tumour Board module) |
The §65c platform marker list (Genetische Marker,
as of 2023-11-27, ~300 gene×variant combinations) prescribes a fixed
two-position notation for transmission, combined in Bezeichnung with ||:
ALK_IHC/HER2_IHC, and cytogenetic entries such as del(17)(p13)) — for the
FHIR representation the special cases of the table above apply (IHC → MTB
profile, cytogenetics → cytogenetic-location).| Kind (list) | Position-2 notation | Example |
|---|---|---|
<Formel> |
formula "e.g. according to HGVSp or HGVSc" (official wording) | p.Val600Glu, c.1799T>A |
| specific mutation | codon level: gene symbol-codon | BRAF-V600 |
| exon | Exon <no> |
Exon 19 |
| fusion | GENE1::GENE2, optionally with a trailing additional mutation |
EML4::ALK, BCR::ABL1 T315I |
| amplification / translocation / rearrangement / promoter hypermethylation | literal keyword | Amplifikation |
| IHC | empty (score via Sonstige_Auspraegung) |
— |
<Freitext> |
free text for unlisted alterations | — |
| unknown | empty | — |
For the structured FHIR view this notation is the parser contract: position 1
becomes gene-studied (HGNC); position 2 maps, depending on its kind, to the
matching component of the marker-type table above (HGVS formulas to *-hgvs,
GENE1::GENE2 to gene-fusion — a trailing additional mutation such as T315I
is carried as a separate HGVS component of the same variant).
Gene identity (HGNC). The gene symbols in the list are already HGNC-approved
symbols. In MolGen the gene is carried in structured form via gene-studied
(HGNC); the oBDS free-text entry Observation.note is therefore not needed for
the structured view.
Exon level. Statements such as "exon 19" do not describe an individual
variant, but a region. MolGen/Genomics Reporting represents this via dna-region
(named DNA region) — a dedicated GA4GH Cat-VRS is not required for this.
Cat-VRS remains reserved for genuine categories (e.g. "any activating EGFR
mutation") and is to be considered later on (post-2027).
Fusions. gene-fusion.value is bound to the HGNC ValueSet and expects the
notation GENESYMBOL1::GENESYMBOL2 (e.g. EML4::ALK). Plain "fusion without
partner" statements are carried via the gene studied (gene-studied) plus a
fusion flag.
IHC markers (MTB). Immunohistochemical markers (PD-L1, HER2 IHC, p16, p53,
panTRK, ROS1 IHC, …) are protein expression findings, not sequence variants. The
MII extension module Molecular Tumour Board (MTB) provides dedicated profiles
for them (base: MII_PR_MTB_Immunohistochemistry, parent
MII_PR_MTB_Molekularer_Biomarker):
| Marker | MTB profile | Code (authoritative) |
|---|---|---|
| generic (all IHC) | mii-pr-mtb-immunohistochemistry |
SNOMED 1234806008 "Observation using immunohistochemistry" + target via component:gene-studied |
| HER2 IHC | mii-pr-mtb-immunohistochemistry-her2 |
LOINC 18474-7 "HER2 Ag [Presence] in Tissue by Immune stain" |
| PD-L1 IHC | mii-pr-mtb-immunohistochemistry-pdl1 |
scores: NCIt C184941 (TPS), C176582 (CPS), C199175 (ICS), LOINC 83053-9 (TC) |
| MMR (dMMR/pMMR) | mii-pr-mtb-immunohistochemistry-mmr |
LOINC per protein: MLH1 81691-8, MSH2 81692-6, MSH6 81693-4, PMS2 81694-2 |
For markers without a specific profile (p16, p53, panTRK, ROS1 IHC, …) use the
base profile mii-pr-mtb-immunohistochemistry with the generic SNOMED code plus
component:gene-studied.
Note (architecture and maturity): The MTB module integrates genetic findings above Oncology and MolGen — it declares
kerndatensatz.onkologieandkerndatensatz.molgenas dependencies itself. Oncology can therefore not take MTB as a dependency (circular reference); the MTB references here are documentary (recommended target location), not technically resolved. The modules involved are in draft/STU/trial-use — this assignment is a guide and may still change as MolGen/MTB mature.
IGHV mutation status (CLL). The §65c marker list carries IGHV as a single
entry — clinically it covers two statements that must be represented separately:
component:gene-studied as a gene statement. HGNC holds no collective "IGHV"
entity, only the 167 individual segments — they are listed in
mii-vs-onko-ighv-gensegmente-hgnc.M = mutation, W = wild type / unmutated), i.e. in FHIR via the
value of the variant observation (valueCodeableConcept, present / wild type).
No separate status resource is required — see the qualifier table below.Menge_Genetik_Typ)The marker type (table above) is only one axis of the report. The second axis is
the qualifier of the finding. The oBDS type Menge_Genetik_Typ provides for
exactly one statement per Genetische_Variante — either a code from the
selection list Auspraegung or the free-text field Sonstige_Auspraegung
(xs:choice). The selection list comprises five codes; the module terminology
adds S as the code for the free-text case.
| oBDS code | Meaning (oBDS XSD) | SNOMED CT (module ConceptMap) | Recommendation MolGen/FHIR |
|---|---|---|---|
M |
mutation/positive | 55446002 Genetic mutation (finding) |
Observation.value[x] = LOINC LA9633-4 "Present" (for Observation.code = LOINC 69548-6) |
W |
wild type/not mutated/negative | 412730000 Genetic finding not detected (finding) |
negative finding; additionally component:coding-change-type (LOINC 48019-4) = SO SO:0002073 no_sequence_alteration (LOINC equivalent LA9658-1 "Wild type") |
P |
polymorphism | 50334000 Genetic polymorphism (finding) |
variant present (value[x] = LA9633-4); the assessment as a polymorphism does not belong in the variant, but in a separate finding interpretation (Genomics Reporting profile diagnostic-implication) |
N |
cannot be determined | 1156316003 Cannot be determined (qualifier value) |
no value[x]; instead Observation.dataAbsentReason, e.g. not-performed |
U |
unknown | 261665006 Unknown (qualifier value) |
no value[x]; Observation.dataAbsentReason = unknown |
S |
other (module addition for Sonstige_Auspraegung) |
74964007 Other (qualifier value) |
free text into Observation.note; structured only insofar as the content corresponds to one of the cases above |
The SNOMED column reflects the ConceptMap maintained in the module,
mii-cm-onko-genetische-variante-auspraegung-sct,
and is therefore binding for the module. The MolGen column — like the marker type
table above — is a non-normative implementation recommendation.
Relation to the example marker list. In the underlying marker list, almost
all rows provide only for M/W; P, N and U do not occur there, and the
immunohistochemistry rows (scores 0/+/++/+++ and IC/TPS/CPS)
already point to the free-text route Sonstige_Auspraegung. The list is
therefore a subset of the oBDS system, not a divergent value range.
Sources. Authoritative for the qualifier list is the type
Menge_Genetik_Typ of the oBDS XML schema (oBDS_v3.0.4.xsd /
oBDS_v3.0.5.xsd, unchanged there), described in the section 65c platform
documentation:
Menge_Genetik_Typ.
Gene and variant are currently transmitted combined in Bezeichnung with the
separator || — this composite free text is the starting point for the marker
type assignment in the table above.
If MolGen cannot be implemented at a site, the direct mapping of the oBDS
fields according to the profile
Genetische Variante
continues to apply: Observation.note (variant name) and
Observation.interpretation (qualifier).
This page is the clinical documentation basis for representing the variant types. The tiered strategy is partly profiled:
Observation.component:gene-studied is bound extensibly in profile
MII_PR_Onko_Genetische_Variante
to the value set
mii-vs-onko-marker-gene-hgnc
(40 HGNC genes from the §65c marker list). Extensible means: the list covers
the common oncological marker genes, further genes are explicitly permitted.
The free-text gene name per oBDS 23.1 remains in note.text.