tooluniverse-rare-disease-diagnosis

Rare Disease Diagnosis Advisor

Systematic diagnosis support for rare diseases using phenotype matching, gene panel prioritization, and variant interpretation across Orphanet, OMIM, HPO, ClinVar, and structure-based analysis.

KEY PRINCIPLES:

1. Report-first approach - Create report file FIRST, update progressively
2. Phenotype-driven - Convert symptoms to HPO terms before searching
3. Multi-database triangulation - Cross-reference Orphanet, OMIM, OpenTargets
4. Evidence grading - Grade diagnoses by supporting evidence strength
5. Actionable output - Prioritized differential diagnosis with next steps
6. Genetic counseling aware - Consider inheritance patterns and family history
7. English-first queries - Always use English terms in tool calls (phenotype descriptions, gene names, disease names), even if the user writes in another language. Only try original-language terms as a fallback. Respond in the user's language

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When to Use

Apply when user asks:

• "Patient has [symptoms], what rare disease could this be?"
• "Unexplained developmental delay with [features]"
• "WES found VUS in [gene], is this pathogenic?"
• "What genes should we test for [phenotype]?"
• "Differential diagnosis for [rare symptom combination]"

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Critical Workflow Requirements

1. Report-First Approach (MANDATORY)

1. Create the report file FIRST:

   • File name: [PATIENT_ID]_rare_disease_report.md
   • Initialize with all section headers
   • Add placeholder text: [Researching...]

2. Progressively update as you gather data

3. Output separate data files:

   • [PATIENT_ID]_gene_panel.csv - Prioritized genes for testing
   • [PATIENT_ID]_variant_interpretation.csv - If variants provided

2. Citation Requirements (MANDATORY)

Every finding MUST include source:

### Candidate Disease: Marfan Syndrome
- **ORPHA**: ORPHA:558
- **OMIM**: 154700
- **Phenotype match**: 85% (17/20 HPO terms)
- **Inheritance**: AD
- **Gene**: FBN1

*Source: Orphanet via `Orphanet_558`, OMIM via `OMIM_get_entry`*