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genome-report

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UpdatedMarch 29, 2026 at 13:05

Generate prescriber-facing reports and import biomarker lab results. Triggers on: /biomarker, /wallet-card, "import lab results", "analyze bloodwork", "generate prescriber summary", "create wallet card", "update PGx card".

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glebis

glebis/genome-toolkit

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Related occupationsSOC

Based on SOC occupation classification

Software DevelopersComputer and Mathematical Occupations·SOC 15-1252

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2 files

SKILL.md

readonly

name	genome-report
description	Generate prescriber-facing reports and import biomarker lab results. Triggers on: /biomarker, /wallet-card, "import lab results", "analyze bloodwork", "generate prescriber summary", "create wallet card", "update PGx card".

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

Read PDF and extract lab markers (values, units, reference ranges)
Normalize German lab names if needed (Leukozyten → WBC, GPT → ALT)
Create entry at Biomarkers/YYYY-MM-DD Lab Results.md using template
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
Flag clinical thresholds:
- CRP > 3 mg/L → SSRI augmentation consideration
- Ferritin > 300 → phlebotomy discussion
- ALT > 2x ULN → hepatology referral
Generate missing markers list (prioritized)
Run trend analysis if previous biomarkers exist
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)

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Multi-agent validation pipeline for fact-checking claims, verifying evidence tiers, and ensuring prescriber document accuracy. Uses Codex CLI, NotebookLM, PubMed subagents, and Tavily search. Supports: audit (full vault), gene SYMBOL (single gene fact-check), protocol NAME (protocol/report fact-check). Triggers on: /genome-validate, "validate this note", "fact-check", "cross-check claims", "verify evidence", "audit this report", "fact-check gene X", "check protocol X".

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Run analysis scripts: PRS, enrichment, vault audit, PubMed monitoring, consistency checks. Triggers on: /genome-analytics, "run PRS", "audit vault", "check PubMed", "run enrichment", "check consistency", "analyze pathway".

2026-03-2939

name	genome-report
description	Generate prescriber-facing reports and import biomarker lab results. Triggers on: /biomarker, /wallet-card, "import lab results", "analyze bloodwork", "generate prescriber summary", "create wallet card", "update PGx card".

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

Read PDF and extract lab markers (values, units, reference ranges)
Normalize German lab names if needed (Leukozyten → WBC, GPT → ALT)
Create entry at Biomarkers/YYYY-MM-DD Lab Results.md using template
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
Flag clinical thresholds:
- CRP > 3 mg/L → SSRI augmentation consideration
- Ferritin > 300 → phlebotomy discussion
- ALT > 2x ULN → hepatology referral
Generate missing markers list (prioritized)
Run trend analysis if previous biomarkers exist
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)