prs-os DomainOS

Status: Graduated (production, ADR-009)
Engine: prs-os
Domain: Polygenic risk scores (LDpred, PRSice, cross-ancestry transfer)

Polygenic-risk-score DomainOS: PRS construction (LDpred, PRSice), cross-ancestry transfer, and risk stratification. Graduated 2026-04-12 (ADR-009) with ~16 skills. Overlaps GWASos; the sub-router prefers prs-os for explicit PRS-tool mentions.

Field	Value
Product	prs-os
Engine id	prs-os
Intent key	prs_os
Repository	Hordago-Labs/prs-os
Plugin	prs-os
Maturity (registry)	Graduated (production, ADR-009)

Overview

Polygenic-risk-score DomainOS: PRS construction (LDpred, PRSice), cross-ancestry transfer, and risk stratification. Graduated 2026-04-12 (ADR-009) with ~16 skills. Overlaps GWASos; the sub-router prefers prs-os for explicit PRS-tool mentions.

Scientific approach

prs-os structures every run as 5 phases. Gates marked HITL require an explicit human-in-the-loop approval before the run advances.

#	Phase	Gate	HITL
1	Base/Target Harmonization	Harmonize base and target datasets.	No
2	Effect-Size Modeling	Fit LDpred/PRSice effect sizes.	No
3	Score Construction	Construct polygenic scores.	No
4	Ancestry Transfer	Evaluate cross-ancestry portability.	No
5	Risk Stratification	Approve risk-stratification model.	Yes

Capabilities & evidence objects

Domain tools / skills

• ldpred
• prsice
• ancestry-transfer
• risk-stratification

Evidence objects

Object	Role	Consumer
result.json	produces	co-writer
provenance.json	produces	evidence-audit

Canonical artifacts (5-artifact contract)

Planned

The 5-artifact contract below is the target shape. Canonical-artifact emission is tracked as inherited debt (Wave 3C) and is not yet guaranteed.

Artifact	Description
result.json	Structured primary result payload for the domain run.
report.md	Human-readable narrative summary of the analysis.
provenance.json	Tool versions, reference data, and algorithm lineage for reproducibility.
gate_status.json	Per-phase gate pass/fail decisions.
session_summary.json	Session metadata for replay and audit.

Standalone quickstart

Zero platform dependency

This quickstart runs the DomainOS standalone. The Hordago platform is not required; platform composition is opt-in (see Composition below).

1. Install the standalone prs-os plugin (Hordago-Labs/prs-os) -- no Hordago platform required.
2. Invoke the domain skill with a prs-os intent (see the intent keywords below).
3. Review the emitted artifacts under the run's output directory.

Intent keywords (route to this engine):

polygenic risk \bprs\b ^prs$ ldpred prsice genetic risk score polygenic score risk prediction

Worked example

LDpred PRS with cross-ancestry evaluation

A user requests an LDpred polygenic score. prs-os harmonizes base and target cohorts, fits effect sizes, constructs the score, and reports cross-ancestry portability before proposing a risk-stratification model.

Validation & benchmarks

Benchmarks

• Held-out AUC / R^2
• Cross-ancestry portability regression

Reproducibility. provenance.json pins LD reference panel and effect-size model.

Reference

MCP fallback servers (used when the plugin is unavailable): pubmed, open-targets

Source documents

• Scaffold-domains ledger (prs-os): references/scaffold-domains.md

Composition

Platform opt-in

prs-os runs standalone. When composed under the Hordago platform it gains cross-domain routing, the Shared Compiler gate, and evidence-audit provenance enforcement. Platform composition is opt-in; the quickstart above has zero platform dependency.

Cross-domain dependencies

Engine	Relationship
gwas-os	Consumes GWAS summary statistics; generic 'polygenic' routes to gwas-os while explicit PRS tools route here.