Polygenic Score (PGS) ID: PGS002627

Predicted Trait
Reported Trait Age at menarche
Mapped Trait(s) age at menarche (EFO_0004703)
Released in PGS Catalog: June 9, 2022
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Score Details

Score Construction
PGS Name repro_MENARCHE_AGE.PolyFun-pred
Development Method
Name PolyFun-pred
Parameters NR
Variants
Original Genome Build GRCh37
Number of Variants 831,098
Effect Weight Type beta
PGS Source
PGS Catalog Publication (PGP) ID PGP000332
Citation (link to publication) Weissbrod O et al. Nat Genet (2022)
Ancestry Distribution
Source of Variant
Associations (GWAS)
European: 100%
176,155 individuals (100%)
PGS Evaluation
African: 25%
East Asian: 25%
European: 25%
South Asian: 25%
4 Sample Sets

Development Samples

Source of Variant Associations (GWAS)
Study Identifiers Sample Numbers Sample Ancestry Cohort(s)
— 176,155 individuals European UKB

Performance Metrics

Disclaimer: The performance metrics are displayed as reported by the source studies. It is important to note that metrics are not necessarily comparable with each other. For example, metrics depend on the sample characteristics (described by the PGS Catalog Sample Set [PSS] ID), phenotyping, and statistical modelling. Please refer to the source publication for additional guidance on performance.

PGS Performance
Metric ID (PPM) 		PGS Sample Set ID
(PSS) 		Performance Source Trait PGS Effect Sizes
(per SD change) 		Classification Metrics Other Metrics Covariates Included in the Model PGS Performance:
Other Relevant Information
PPM014343 PSS009683|
African Ancestry|
3,392 individuals
 PGP000332 |
Weissbrod O et al. Nat Genet (2022)
 Reported Trait: Age of Menarche — — Incremental R2 (full model when combined with BOLT-LMM vs. covariates alone): 0.0078 age, sex, age*sex, assessment center, genotyping array, 10 PCs See repro_MENARCHE_AGE.mixweights file at http://data.broadinstitute.org/alkesgroup/polypred_results for combination weights
PPM014392 PSS009684|
East Asian Ancestry|
554 individuals
 PGP000332 |
Weissbrod O et al. Nat Genet (2022)
 Reported Trait: Age of Menarche — — Incremental R2 (full model when combined with BOLT-LMM vs. covariates alone): 0.007 age, sex, age*sex, assessment center, genotyping array, 10 PCs See repro_MENARCHE_AGE.mixweights file at http://data.broadinstitute.org/alkesgroup/polypred_results for combination weights
PPM014441 PSS009685|
European Ancestry|
23,774 individuals
 PGP000332 |
Weissbrod O et al. Nat Genet (2022)
 Reported Trait: Age of Menarche — — Incremental R2 (full model when combined with BOLT-LMM vs. covariates alone): 0.1008 age, sex, age*sex, assessment center, genotyping array, 10 PCs See repro_MENARCHE_AGE.mixweights file at http://data.broadinstitute.org/alkesgroup/polypred_results for combination weights
PPM014490 PSS009686|
South Asian Ancestry|
3,465 individuals
 PGP000332 |
Weissbrod O et al. Nat Genet (2022)
 Reported Trait: Age of Menarche — — Incremental R2 (full model when combined with BOLT-LMM vs. covariates alone): 0.0318 age, sex, age*sex, assessment center, genotyping array, 10 PCs See repro_MENARCHE_AGE.mixweights file at http://data.broadinstitute.org/alkesgroup/polypred_results for combination weights

Evaluated Samples

PGS Sample Set ID
(PSS) 		Phenotype Definitions and Methods Participant Follow-up Time Sample Numbers Age of Study Participants Sample Ancestry Additional Ancestry Description Cohort(s) Additional Sample/Cohort Information
PSS009684 — — 554 individuals — East Asian — UKB —
PSS009685 — — 23,774 individuals — European Non-British European UKB —
PSS009686 — — 3,465 individuals — South Asian — UKB —
PSS009683 — — 3,392 individuals — African unspecified — UKB —