Tooluniverse Gwas Drug Discovery

GWAS-to-drug translation succeeds when you think causally. A genetic association provides causal direction that observational data cannot: if a loss-of-function variant protects against disease, an inhibitor of that gene's product is the hypothesis to test. The direction of effect (LOF vs. GOF) determines whether you need an inhibitor or an agonist — get this wrong and the drug works backwards. GWAS effect sizes are small (odds ratios of 1.1–1.5 are typical), but the drug effect may be much larger or smaller than the genetic effect; the genetic signal validates the target, not the dose. Always integrate multiple lines of evidence (eQTL colocalization, pQTL, L2G score) before committing to a target, because many GWAS variants tag the causal gene only indirectly.

LOOK UP DON'T GUESS: Do not assume which gene a GWAS variant implicates — use OpenTargets_get_variant_credible_sets or gwas_get_associations_for_snp to get the actual mapped gene and L2G score. Do not guess the direction of effect, odds ratio, or whether a drug already exists for the target; always query the tools.

Workflow Steps

Step 1: GWAS Gene Discovery

Input: Disease/trait name (e.g., "type 2 diabetes", "Alzheimer disease")

Process: Query GWAS Catalog for associations, filter by significance (p < 5x10^-8), map variants to genes, aggregate evidence.

Tools:

• gwas_get_associations_for_trait - Get associations by disease
• gwas_search_associations - Flexible search
• gwas_get_associations_for_snp - SNP-specific associations
• OpenTargets_search_gwas_studies_by_disease - Curated GWAS data
• OpenTargets_get_variant_credible_sets - Fine-mapped loci with L2G predictions

Step 2: Druggability Assessment

Input: Gene list from Step 1

Process: Check target class, assess tractability, evaluate safety, check for tool compounds or structures.

Tools:

• OpenTargets_get_target_tractability_by_ensemblID - Druggability assessment
• OpenTargets_get_target_classes_by_ensemblID - Target classification
• OpenTargets_get_target_safety_profile_by_ensemblID - Safety data
• OpenTargets_get_target_genomic_location_by_ensemblID - Genomic context

Step 3: Target Prioritization

Scoring Formula:

Target Score = (GWAS Score x 0.4) + (Druggability x 0.3) + (Clinical Evidence x 0.2) + (Novelty x 0.1)

Rank targets by composite score. Generate target dossiers.

Step 4: Existing Drug Search

Process: Search drug-target associations, find approved drugs and clinical candidates, get MOA and indication data.

Tools:

• OpenTargets_get_associated_drugs_by_disease_efoId - Known drugs for disease
• OpenTargets_get_drug_mechanisms_of_action_by_chemblId - Drug MOA
• ChEMBL_get_target_activities - Bioactivity data
• ChEMBL_get_drug_mechanisms / ChEMBL_search_drugs - Drug data

Step 5: Clinical Evidence & Safety

Tools:

• FDA_get_adverse_reactions_by_drug_name - Safety data
• FDA_get_active_ingredient_info_by_drug_name - Drug composition
• OpenTargets_get_drug_warnings_by_chemblId - Drug warnings

Step 6: Repurposing Opportunities

Match drug targets to new disease genes, assess mechanistic fit, check contraindications, estimate repurposing probability.

Quick Start

from tooluniverse import ToolUniverse
tu = ToolUniverse(use_cache=True)
tu.load_tools()

# Step 1: Get GWAS associations (use disease_trait not trait; no p_value_threshold param)
associations = tu.tools.gwas_get_associations_for_trait(disease_trait="type 2 diabetes")

# Step 2: Assess druggability (ensemblId lowercase d)
tractability = tu.tools.OpenTargets_get_target_tractability_by_ensemblID(ensemblId="ENSG00000148737")

# Step 3: Find existing drugs per target via DGIdb (OpenTargets drug query may return HTTP 400)
drugs = tu.tools.DGIdb_get_drug_gene_interactions(genes=["TCF7L2"])

All Tools by Category

GWAS & Genetics:

• gwas_get_associations_for_trait / gwas_search_associations / gwas_get_associations_for_snp
• OpenTargets_search_gwas_studies_by_disease / OpenTargets_get_variant_credible_sets

Target Assessment:

• OpenTargets_get_target_tractability_by_ensemblID / OpenTargets_get_target_classes_by_ensemblID
• OpenTargets_get_target_safety_profile_by_ensemblID / OpenTargets_get_target_genomic_location_by_ensemblID

Drug Discovery:

• OpenTargets_get_associated_drugs_by_disease_efoId / OpenTargets_get_drug_mechanisms_of_action_by_chemblId
• ChEMBL_get_target_activities / ChEMBL_get_drug_mechanisms / ChEMBL_search_drugs

Safety & Clinical:

• FDA_get_adverse_reactions_by_drug_name / FDA_get_active_ingredient_info_by_drug_name
• OpenTargets_get_drug_warnings_by_chemblId

Literature:

• PubMed_search_articles / EuropePMC_search_articles / ClinicalTrials_search_studies

Best Practices

1. Multi-ancestry GWAS: Include trans-ethnic meta-analyses for robust signals
2. Functional validation: Confirm with eQTL, pQTL, colocalization analysis
3. Network analysis: Group GWAS hits by pathway (KEGG, Reactome)
4. Safety assessment: Check gnomAD pLI, GTEx expression, PharmaGKB
5. Batch operations: Use tu.run_batch() for parallel queries across targets

Parameter Gotchas

Interpretation: From GWAS Hit to Drug Target

GWAS Signal Strength Assessment

Target Prioritization Decision Tree

After identifying GWAS-linked genes, rank them by answering:

1. Is the gene druggable? (DGIdb category: kinase/GPCR/ion channel = yes; transcription factor/scaffold = harder)

   • If approved drug exists → REPURPOSING opportunity (fastest path)
   • If druggable but no drug → NOVEL TARGET (standard drug discovery)
   • If not druggable → consider antisense/PROTAC/genetic medicine

2. Is the genetic direction clear?

   • LOF variants increase disease risk → need an AGONIST or gene therapy
   • GOF variants increase disease risk → need an INHIBITOR (typical small molecule)
   • Direction unclear → need functional studies before drug design

3. What's the effect size? (Odds ratio from GWAS)

   • OR > 2.0: strong effect, likely penetrant → Mendelian-like, high confidence
   • OR 1.2-2.0: moderate, common in complex disease → validate with independent data
   • OR < 1.2: small effect → may not be clinically meaningful alone

4. Is there clinical precedent?

   • Drug for same target approved for ANY disease → safety data exists → lower risk
   • Drug in clinical trials → partial de-risking
   • No precedent → full de novo development risk

Troubleshooting

Reference Files

• REFERENCE.md - Detailed concepts, druggability tiers, clinical translation, limitations, ethics
• EXAMPLES.md - Use cases (Huntington's, Alzheimer's, diabetes) with success stories
• REPORT_TEMPLATE.md - Output report template with scoring criteria
• PROCEDURES.md - Step-by-step implementation procedures
• QUICK_START.md - Quick start guide
• Related skills: tooluniverse-drug-repurposing, disease-intelligence-gatherer, tooluniverse-sdk