tooluniverse-rare-disease-diagnosis

Match patient phenotypes and genetics to rare diseases with HPO terms.

1.6k|244|Updated Mar 3, 2025
One-click install
npx skills add https://github.com/mims-harvard/ToolUniverse --skill tooluniverse-rare-disease-diagnosis
Or copy as Structured Prompt for Agent
Please help me install this Agent Skill.
Skill: tooluniverse-rare-disease-diagnosis
Source: https://github.com/mims-harvard/ToolUniverse/tree/main/skills/tooluniverse-rare-disease-diagnosis
Command: npx skills add https://github.com/mims-harvard/ToolUniverse --skill tooluniverse-rare-disease-diagnosis

SYSTEM DOCUMENTATION & REQUIREMENTS

What problem does it solve?

This Skill streamlines rare disease diagnosis by translating patient phenotypes into standardized HPO terms, integrating genetic data, and generating structured differential diagnoses.

Core Features & Use Cases

  • Phenotype to disease mapping: Converts patient features to HPO terms and matches them to Orphanet/OMIM diseases.
  • Gene panel prioritization: Identifies high-priority genes for testing based on ClinGen, haploinsufficiency, and tissue expression.
  • Variant interpretation workflow: Provides a framework to interpret VUS with population data, pathogenicity predictions, and literature context.
  • Use Case: A child with developmental delay and epilepsy receives a ranked differential with recommended genetic tests and a plan for follow-up.

Quick Start

Enter patient phenotype and optional genetic data to generate a prioritized differential and testing plan. The tool will convert symptoms to HPO terms, match diseases from Orphanet and OMIM, and propose a gene panel and variant interpretation workflow.

Frequently Asked Questions about tooluniverse-rare-disease-diagnosis

High-intent search queries and answers about installing and using this skill.

FAQPage Schema
How do I diagnose a rare disease from phenotype and genes?

To diagnose a rare disease from phenotype and genes, translate patient features into standardized HPO terms and match them against Orphanet and OMIM databases to generate a prioritized differential. This structured process integrates genetic data to identify likely conditions.

How do I prioritize a gene panel for unexplained developmental delay and seizures?

Prioritize a gene panel for developmental delay and seizures by matching patient HPO phenotypes to disease databases, then filtering genes using ClinGen, haploinsufficiency predictions, and tissue expression data like GTEx to recommend targeted genetic tests.

Can I use HPO terms to generate a differential diagnosis from Orphanet and OMIM?

Yes, you can use HPO terms to generate a differential diagnosis from Orphanet and OMIM. The workflow converts patient symptoms into standardized HPO terms and matches them directly to diseases within these databases to rank likely conditions.

What is the best way to interpret VUS in rare disease genetic testing?

The best way to interpret VUS in rare disease genetic testing is using a structured workflow that combines population data from gnomAD, pathogenicity predictions, and literature context to provide evidence-grade annotations for unexplained presentations.

Does this rare disease diagnosis workflow integrate ClinVar and gnomAD data?

Yes, this rare disease diagnosis workflow integrates ClinVar and gnomAD data. It uses these databases alongside ClinGen, GTEx, Orphanet, OMIM, and HPO to support phenotype-to-disease matching and variant interpretation.