Genome Report

Genome Report

Generate clinical reports and import biomarker data.

Vault Configuration

• Database: data/genome.db
• Templates: Templates/Biomarker Entry.md
• Genetic predictions: skills/genome-report/references/genetic_predictions.md
• Reports: Reports/
• Biomarkers: Biomarkers/

Sub-Workflows

A: Biomarker Import

Triggered by: /biomarker, "import lab results", PDF shared

1. Read PDF and extract lab markers (values, units, reference ranges)
2. Normalize German lab names if needed (Leukozyten → WBC, GPT → ALT)
3. Create entry at Biomarkers/YYYY-MM-DD Lab Results.md using template
4. Compare each marker against genetic predictions:
   • PNPLA3 G;G → expect elevated ALT
   • HFE het → monitor ferritin/transferrin
   • IL1B G;G → expect elevated CRP
   • SH2B3 C;T → expect lower platelets
5. Flag clinical thresholds:
   • CRP > 3 mg/L → SSRI augmentation consideration
   • Ferritin > 300 → phlebotomy discussion
   • ALT > 2x ULN → hepatology referral
6. Generate missing markers list (prioritized)
7. Run trend analysis if previous biomarkers exist
8. Update Meta/Biomarker Tracking Dashboard.md

B: Wallet Card Generation

Triggered by: /wallet-card, "create wallet card"

Generate Reports/Wallet Card.md:

• Query CYP enzyme status from database
• List: AVOID (hard contraindications), CAUTION (dose adjustments), LIMIT (max doses)
• Include: current medication, carrier status, cannabis interaction note
• Format: printable 1-page reference

C: Pharmacogenomics Card

Full enzyme status table with drug interaction matrix.

D: Prescriber Summary

One-page overview for doctors unfamiliar with PGx.

E: SSRI Response Profile

CRP-guided treatment algorithm, sertraline vs alternatives.

Validation

All prescriber-facing reports require multi-agent validation gate (2 agents must agree). Run /genome-validate automatically if config/agents.yaml has gates configured.

Output

• Report note in Reports/ or Biomarkers/
• Updated dashboards
• Validation report (for prescriber docs)