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Coding Best Practices

Avoiding redundancy

Problem

Not every diagnosis needs every available coding system. Excessive multiple coding can lead to:

• Redundancy and data bloat
• Inconsistencies between different coding systems
• Reduced maintainability

Solution: targeted coding

Recommended coding strategy

1. Primary coding systems by diagnosis type

For CLINICAL diagnoses

• ICD-10-GM: mandatory (billing/statistics in the German healthcare system)
• Orpha codes: mandatory for rare diseases
• HPO codes: recommended for phenotypic description

For GENETIC diagnoses

• Orpha codes: mandatory for rare diseases
• OMIM codes: strongly recommended for genetic entities
• ICD-10-GM: optional (often unspecific for genetic variants)

2. Context-dependent coding systems

HPO codes

• Use for: clinical diagnoses (MII_PR_SE_ClinicalDiagnosis)
• Purpose: phenotypic description
• Optional for: genetic diagnoses (if the phenotype is relevant)

OMIM codes

• Use for: genetic diagnoses (MII_PR_SE_GeneticDiagnosis)
• Purpose: genetic disease entity
• Do not use for: purely clinical diagnoses without genetic confirmation

SNOMED CT

• Use when:
  • No more specific coding is available
  • International interoperability is required
  • Complex clinical concepts need to be represented
• Avoid when: Orpha/OMIM are sufficient

Decision matrix

Diagnosis type	ICD-10-GM	Orpha	HPO	OMIM	SNOMED CT
Clinical RD diagnosis	✅ Mandatory	✅ Mandatory	✅ Recommended	❌ Do not use	⚠️ Optional
Genetic RD diagnosis	⚠️ Optional	✅ Mandatory	⚠️ Optional	✅ Strongly recommended	⚠️ Optional
Suspected diagnosis	✅ Mandatory	⚠️ If possible	✅ For symptoms	❌ Do not use	⚠️ Optional

Practical examples

✅ CORRECT: focused coding

Clinical diagnosis (ICD-10-GM required)

Instance: marfan-clinical-focused
InstanceOf: MII_PR_SE_ClinicalDiagnosis
* code.coding[icd10-gm] = $ICD10GM#Q87.4 "Marfan-Syndrom"
* code.coding[orphanet] = http://www.orpha.net#558 "Marfan syndrome"
* code.coding[omim] = http://omim.org#154700 "Marfan syndrome"
// OMIM used for genetic coding

Genetic diagnosis (ICD-10-GM optional)

Instance: sma-genetic-focused
InstanceOf: MII_PR_SE_GeneticDiagnosis
* code.coding[orphanet] = http://www.orpha.net#83330 "SMA type 1"
* code.coding[omim] = http://omim.org#253300 "Spinal muscular atrophy, type I"
// ICD-10-GM can be omitted for a purely genetic diagnosis
// HPO optional, only if the phenotype is to be documented

Genetic diagnosis with ICD-10 (if clinically relevant)

Instance: cf-genetic-with-clinical
InstanceOf: MII_PR_SE_GeneticDiagnosis
* code.coding[icd10-gm] = $ICD10GM#E84.0 "Zystische Fibrose mit Lungenmanifestationen"
* code.coding[orphanet] = http://www.orpha.net#586 "Cystic fibrosis"
* code.coding[omim] = http://omim.org#219700 "Cystic fibrosis"
// ICD-10 useful here because the clinical manifestation is specified

❌ WRONG: excessive coding

Instance: overencoded-diagnosis
InstanceOf: Condition
* code.coding[0] = $ICD10GM#Q87.4 "Marfan-Syndrom"
* code.coding[1] = http://www.orpha.net#558 "Marfan syndrome"
* code.coding[2] = $SCT#19346006 "Marfan syndrome"
* code.coding[3] = http://omim.org#154700 "Marfan syndrome"
* code.coding[4] = $UMLS#C0024796 "Marfan Syndrome"
* code.coding[5] = $MeSH#D008382 "Marfan Syndrome"
// Too many redundant codes!

Special scenarios

Diagnosis progression

When modeling diagnostic courses:

1. Suspicion (screening)
   • ICD-10-GM: mandatory
   • Orpha: if a specific RD is suspected
   • HPO: for symptom description
   • OMIM: do not use
2. Clinical diagnosis
   • ICD-10-GM: mandatory
   • Orpha: mandatory
   • HPO: recommended
   • OMIM: do not use
3. Genetically confirmed
   • ICD-10-GM: optional (only if clinically relevant)
   • Orpha: mandatory
   • HPO: optional (if phenotypically relevant)
   • OMIM: strongly recommended

Purely genetic vs. clinical-genetic diagnoses

Purely genetic findings

// Example: carrier status without symptoms
Instance: carrier-status-sma
InstanceOf: MII_PR_SE_GeneticDiagnosis
* code.coding[orphanet] = http://www.orpha.net#83330 "SMA"
* code.coding[omim] = http://omim.org#253300 "SMA type I"
* code.text = "Heterozygote SMN1-Mutation (Anlageträger)"
// No ICD-10, since no clinical manifestation

Clinical-genetic diagnosis

// Example: symptomatic patient with genetic confirmation
Instance: symptomatic-genetic-diagnosis
InstanceOf: MII_PR_SE_GeneticDiagnosis
* code.coding[icd10-gm] = $ICD10GM#G12.0 "Infantile spinale Muskelatrophie"
* code.coding[orphanet] = http://www.orpha.net#83330 "SMA type 1"
* code.coding[omim] = http://omim.org#253300 "SMA type I"
// ICD-10 useful, since a clinical manifestation is present

Quality criteria

Minimal requirements

Clinical diagnosis

• ICD-10-GM code present
• Orpha code for the rare disease
• Appropriate verificationStatus

Genetic diagnosis

• Orpha code for the rare disease
• OMIM code (if available)
• Evidence link to MolGen resources
• Appropriate verificationStatus (usually "confirmed")

Optimal coding

• No redundant codes
• Context-appropriate use of HPO/OMIM
• Clear separation between clinical and genetic diagnosis
• Evidence linking appropriate to the diagnosis type

When to use ICD-10-GM for genetic diagnoses?

✅ ICD-10-GM useful for:

• Symptomatic patients
• Clinically manifest diseases
• When specific clinical subtypes are coded (e.g. CF with pulmonary manifestations)
• Diagnoses relevant to billing

❌ Omit ICD-10-GM for:

• Pure carriers without symptoms
• Predictive genetic tests
• Genetic variants of unclear significance (VUS)
• When ICD-10 offers no adequate specificity

Important note: excluded diagnoses

⚠️ MANDATORY: documentation of excluded diagnoses

Excluded diagnoses (refuted) MUST also be coded and documented!

This applies in particular to:

• Suspected diagnoses that were refuted
• Differential diagnoses that were excluded
• Negative genetic test results for suspected diseases

Coding excluded diagnoses

* verificationStatus = #refuted
* clinicalStatus = #inactive
* code.coding[orphanet] = // Orpha code of the excluded disease
* note.text = // justification of the exclusion

Why is this important?

• Avoiding redundant diagnostics: tests already performed are not repeated
• Complete documentation: the diagnostic process remains traceable
• Research: important for epidemiology and differential diagnostics
• Patient safety: prevents unnecessary examinations

Summary

Basic principle: as much as necessary, as little as possible

1. Clinical diagnosis: ICD-10-GM + Orpha + HPO
2. Genetic diagnosis: Orpha + OMIM (ICD-10-GM only if clinically relevant)
3. Excluded diagnosis: same coding + verificationStatus = refuted
4. SNOMED CT: only if it adds value
5. Other systems: only in justified exceptional cases

The choice of coding systems should take into account the context of the diagnosis (clinical vs. genetic) and the purpose (billing, research, registration).