Genomic-Agent-Discovery

Share an important finding with other agents. Publish your 3-5 most significant discoveries per analysis. Findings are deduplicated — if a very similar finding already exists, you'll be asked to find a new angle.

Read all findings published by other agents. Use to understand cross-domain patterns, avoid duplicating research, and build on others' discoveries.

Send a message to another agent or broadcast to all. Use to share discoveries, ask questions, or alert others to important cross-domain connections. Messages appear in a shared chatroom visible to all agents and the human operator.

Check the agent chatroom for messages. Call every 5-10 tool uses to stay coordinated with other agents. Returns messages addressed to you or broadcast.

Log a web search you are about to perform. Call BEFORE every web search to avoid duplicate research across agents. Returns a warning if another agent already searched for something similar.

See all web searches performed by all agents. Use to avoid duplicating research and discover what others have already looked up.

Get the ACMG Secondary Findings v3.2 gene list — 73 genes recommended for clinical reporting. Returns gene name, associated condition, and inheritance pattern. Use this to systematically check all medically actionable genes.

Get the CPIC gene-drug interaction lookup table. Returns pharmacogenes mapped to their affected medications with clinical guideline levels and safety notes. Use this to identify drug interaction risks for a patient's metabolizer profile.

Run Exomiser to prioritize patient variants by phenotype match. Provide HPO terms describing the patient's symptoms/conditions and Exomiser will rank which genetic variants most likely explain those symptoms. This is the gold-standard tool for rare disease variant prioritization. Requires Exomiser to be installed (npm run setup-exomiser). Returns nothing if Exomiser is not available — use other query tools instead.

Get a high-level summary of the patient's genotype data: total variant count, chromosome distribution, sex (from X chromosome heterozygosity), and basic stats. Call this first to understand the scope of data available.

Look up the patient's genotype for a specific rsID. Returns chromosome, position, and the patient's alleles (e.g. 'AG', 'CC', 'TT').

Look up patient genotypes for multiple rsIDs at once (up to 200). More efficient than individual lookups when checking many variants.

Find ALL known variants for a gene by cross-referencing ClinVar, GWAS, and AlphaMissense. Then checks which of those variants the patient actually carries. This is the best starting point for investigating a specific gene.

Look up ClinVar clinical significance for a variant. Shows pathogenicity classifications, associated phenotypes, and review status (star rating).

Look up GWAS Catalog associations for a variant. Shows traits, p-values, effect sizes, and study references from genome-wide association studies.

Look up AlphaMissense AI pathogenicity prediction for a missense variant. Returns predicted pathogenicity class and score (0-1).

Look up CADD (Combined Annotation Dependent Depletion) score for a variant. PHRED-scaled scores above 20 suggest top 1% most deleterious variants.

Find Human Phenotype Ontology terms associated with a gene. Shows which clinical phenotypes (symptoms, findings) are linked to variants in this gene.

Find genes associated with a disease or condition using DisGeNET. Useful to discover which genes to investigate for a particular health concern. Returns genes ranked by association score.

Search CIViC (Clinical Interpretation of Variants in Cancer) database. Returns clinical evidence for cancer-relevant variants including therapeutic, diagnostic, and prognostic annotations.

Look up PharmGKB pharmacogenomic annotations for a variant. Shows drug-gene interactions, dosing guidelines, and clinical annotations.

Look up SNPedia summary for a variant. SNPedia is a community-curated wiki of SNP associations, providing plain-language explanations of what genotypes mean.

Get pharmacogenomic results for a specific gene. Queries CPIC tables from the unified database for allele definitions and drug recommendations, then checks the patient's genotypes at defining variant positions.

Get a complete pharmacogenomics panel across all 34 CPIC pharmacogenes. For each gene, retrieves the patient's genotypes at key defining variant positions and looks up CPIC allele definitions to derive star alleles. This is the comprehensive starting point for pharmacogenomic analysis.