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Apply published polygenic scores from PGS Catalog to approved local personal DNA and return raw weighted score plus overlap QC.
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Based on SOC occupation classification
Use this skill for genetics, genome source, variant, gene, phenotype, disease, screen, pharmacogenomics, and Genomi install/setup maintenance questions.
Build and inspect ClinVar exact-match evidence and candidate inventories. Use for clinical labels, VUS/conflict, carrier context, and drug-response rows.
Activate this skill for "/genomi decode", "decode my genome", "decode my DNA", "show me the dashboard", "the Genomi dashboard", "one-shot rundown", or any all-at-once request that asks Genomi to compose every capability's findings into a single artifact. This is the whole-genome dashboard kicker — it sweeps every relevant Genomi capability in one shot, not a per-target lookup. Composes evidence from every relevant Genomi capability into a single self-contained Genomi Dashboard.html and returns localhost serve metadata. Active genome required.
Answer drug-response, medication, PharmGKB-style, PGxDB, ATC, DrugBank, gene-drug, and variant-drug questions using public PGx evidence plus local sample genotype support when an Active Genome Index is selected.
Plan rare disease, hereditary disease, cancer risk, carrier-relevance, and observed-condition source investigation from public targets or selected active genome evidence.
Answer specific rsID, allele, gene, region, genotype, and absence/callability questions using explicit session context or public evidence.
| name | prs |
| description | Apply published polygenic scores from PGS Catalog to approved local personal DNA and return raw weighted score plus overlap QC. |
| tools | ["prs.search_scores","prs.fetch_score_metadata","prs.list_imported_scores","prs.check_score_overlap","prs.calculate_score","prs.build_source_context"] |
Use this skill when the user asks about polygenic risk scores, PRS, PGS Catalog scores, common disease or trait risk from many variants, or applying a published scoring file to their genome.
GRCh38 when omitted; use GRCh37 only when the
Active Genome Index is GRCh37/hg19.score_mean and score_sd
are supplied for the same score, build, cohort/reference distribution, and
scoring convention.prs.search_scores for public trait or score discovery. If the user
already supplies a PGS ID, use that ID directly.prs.fetch_score_metadata when the source publication, build, variant
count, scoring-file URLs, licensing, or cohort/evaluation context matters.prs.calculate_score with the chosen pgs_id and the user's genome
source to get the raw weighted score plus overlap QC.prs.check_score_overlap when you only need readiness and QC without a
calculated score.prs.list_imported_scores when the user asks what scores are already
available locally.prs.build_source_context when the user asks what PRS can or cannot
tell them.PGS Catalog rarely publishes a reference cohort mean/SD, so a raw weighted score has units on an arbitrary scale. Deliver a defensible directional or quantitative answer for this specific question by combining capabilities that contribute orthogonal evidence — population allele frequencies feeding a closed-form z, direct effect-allele dosages at well-replicated lead loci, additional published scores derived by different methods, treatment-response context when the outcome is treatable, mechanism context from functional or pathway evidence, or whatever else Genomi currently exposes that fits. Disclose the assumptions of any closed-form estimate (HWE, variant independence, ancestry of the allele-frequency source).
When an Active Genome Index is scored or its overlap changes the result, report the score ID/source, genome build, overlap status, matched/missing/excluded variant counts, and whether the result is raw or calibrated. Do not add a routine Active Genome Index status line for public score metadata lookups.
Use careful language:
Directional language ("leans above population average", "in the upper tertile of the analytic z distribution") is appropriate when grounded in the orthogonal evidence the synthesis combined.
Avoid:
A scope-limited result from this capability is not a final user-facing answer when other Genomi capabilities can contribute orthogonal evidence to the same question. Returning "cannot answer" while applicable capabilities remain unexamined is a host-agent failure mode.
Explain PGS Catalog provenance, local scoring workflow, genome-build defaults, calibration limits, and PRS risk boundaries.
Use when: The user asks what PRS can and cannot tell them, whether PRS means common risk analysis, or how Genomi applies published scores.
Why necessary: PRS answers require explicit boundaries around calibration, cohort portability, missing variants, and clinical non-diagnosis.
Not for: Calculating a personal score; use prs.calculate_score after Active Genome Index access approval.
Example prompts: Explain how Genomi implements PRS. Does PRS give common disease risk?
Result semantics: Returns public method context only; it does not read Active Genome Index.
Apply a published polygenic score to an approved Active Genome Index and return raw weighted score plus QC.
Use when: The user asks to calculate or apply a published PRS/PGS score to their genome.
Why necessary: This keeps Active Genome Index local, applies only selected published weights, reports overlap and build defaults, and avoids unsupported risk-category claims.
Not for: Training a new PRS model. Diagnosis, monogenic disease interpretation, medication response, or absolute-risk prediction without a validated calibration model. Ancestry or identity inference.
Example prompts: Calculate PGS000001 for my Active Genome Index. Apply this local scoring file to my GRCh38 genome.
Result semantics: Output is a raw weighted score and QC unless explicit calibration parameters are supplied. Do not phrase it as diagnosis, absolute disease risk, ethnicity, or clinical actionability.
Check how many variants from a polygenic score are usable in an approved Active Genome Index.
Use when: The agent needs PRS overlap/readiness before calculating or interpreting a published polygenic score.
Why necessary: A PRS score can be misleading with low variant overlap, build mismatch, unharmonized palindromic alleles, or missing genotype records.
Not for: Public score search; use prs.search_scores. Diagnosis or absolute risk classification.
Example prompts: Does my genome have enough overlap with PGS000001?
Result semantics: Reports overlap and calculation readiness only; missing score variants are not negative evidence for disease risk.
Fetch detailed public PGS Catalog metadata for one score ID, including scoring-file URLs and source publication context.
Use when: The agent needs the exact PGS Catalog record context — trait, build, variant count, source publication, cohort, ancestry/evaluation, licensing — before explaining or applying a score.
Why necessary: The score metadata carries build, trait, source publication, cohort, ancestry/evaluation, and licensing context that determines whether applying a score is appropriate.
Not for: Calculating a personal score; use prs.calculate_score with the chosen pgs_id.
Example prompts: Fetch metadata for PGS000001.
Result semantics: Returns public PGS Catalog metadata only and may report source_unavailable if the external source cannot be reached.
Import a PGS Catalog or local scoring file into Genomi's local PRS score cache for a declared genome build.
Use when: A score has been selected and needs to be materialized locally before overlap checking or scoring.
Why necessary: Private genotype scoring must run against local score artifacts rather than uploading genotypes to external services.
Not for: Reading Active Genome Index; import is public/local score materialization only. Interpreting the score as risk; use prs.calculate_score and preserve its limitations.
Example prompts: Import PGS000001 for GRCh38. Import this local scoring file for GRCh37.
Result semantics: Creates a local cache of variant weights and manifest metadata. The default genome_build is GRCh38 when omitted and is disclosed in defaults_applied.
List polygenic scores available locally for use without reading Active Genome Index.
Use when: The user asks which polygenic scores are available locally.
Why necessary: Knowing which scores are already available locally helps the agent pick a matching genome build and avoid re-fetching.
Not for: Calculating personal PRS values; use prs.calculate_score after approval.
Example prompts: Which PRS scores are imported locally?
Result semantics: Lists local score-cache metadata only; it does not read Active Genome Index.
Search public PGS Catalog score metadata by trait, score ID, EFO term, or free-text query without reading Active Genome Index.
Use when: The user asks which published PGS/PRS scores exist for a trait or provides a PGS Catalog score ID.
Why necessary: Score selection is source-specific and must expose trait, build, variant count, publication, evaluation, and licensing context before using a score on Active Genome Index.
Not for: Reading or scoring a user's genome; pass the chosen pgs_id to prs.calculate_score after Active Genome Index access approval. Training a new PRS from GWAS summary statistics.
Example prompts: Find PGS Catalog scores for coronary artery disease. What is PGS000001?
Result semantics: Returns public score candidates and source metadata only; it does not read Active Genome Index.