prs

Polygenic Scores

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.

Boundaries

• PRS/PGS here means applying published variant weights from a scoring file. Genomi does not train new PRS models from GWAS summary statistics.
• Default genome build is GRCh38 when omitted; use GRCh37 only when the Active Genome Index is GRCh37/hg19.
• Active Genome Index artifacts stay local. Public score metadata may use PGS Catalog, but private genotypes are not uploaded to external services.
• A raw PRS is common-risk or trait context, not a diagnosis, absolute disease risk, treatment recommendation, or clinical category.
• Only state standardized score context when valid score_mean and score_sd are supplied for the same score, build, cohort/reference distribution, and scoring convention.
• Do not use PRS output for ethnicity, identity, monogenic diagnosis, medication response, or rare-disease causality.

Workflow

1. Use prs.search_scores for public trait or score discovery. If the user already supplies a PGS ID, use that ID directly.
2. Use prs.fetch_score_metadata when the source publication, build, variant count, scoring-file URLs, licensing, or cohort/evaluation context matters.
3. Use prs.calculate_score with the chosen pgs_id and the user's genome source to get the raw weighted score plus overlap QC.
4. Use prs.check_score_overlap when you only need readiness and QC without a calculated score.
5. Use prs.list_imported_scores when the user asks what scores are already available locally.
6. Use prs.build_source_context when the user asks what PRS can or cannot tell them.

When published calibration is missing

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).