Polygenic Score (PGS) ID: PGS002131

Predicted Trait
Reported Trait Age when periods started (menarche)
Mapped Trait(s) age at menarche (EFO_0004703)
Additional Trait Information sex-specific factors
Released in PGS Catalog: Jan. 10, 2022
Download Score FTP directory
Terms and Licenses
PGS obtained from the Catalog should be cited appropriately, and used in accordance with any licensing restrictions set by the authors. See EBI Terms of Use (https://www.ebi.ac.uk/about/terms-of-use/) for additional details.

Score Details

Score Construction
PGS Name portability-ldpred2_F_menarche
Development Method
Name LDpred2 (bigsnpr)
Parameters LDpred2-auto using HapMap3 variants
Variants
Original Genome Build GRCh37
Number of Variants 854,735
Effect Weight Type beta
PGS Source
PGS Catalog Publication (PGP) ID PGP000263
Citation (link to publication) Privé F et al. Am J Hum Genet (2022)
Ancestry Distribution
Score Development/Training
European: 100%
391,124 individuals (100%)
PGS Evaluation
European: 37.5%
African: 25%
East Asian: 12.5%
Greater Middle Eastern: 12.5%
South Asian: 12.5%
8 Sample Sets

Development Samples

Score Development/Training
Study Identifiers Sample Numbers Sample Ancestry Cohort(s) Phenotype Definitions & Methods Age of Study Participants Participant Follow-up Time Additional Ancestry Description Additional Sample/Cohort Information
— 391,124 individuals European UKB — — — UK (+ Ireland) —

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
PPM011908 PSS008033|
East Asian Ancestry|
611 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: Age when periods started (menarche) — — Partial Correlation (partial-r): 0.0879 [0.0074, 0.1673] sex, age, birth date, deprivation index, 16 PCs —
PPM011903 PSS009375|
European Ancestry|
5,746 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: Age when periods started (menarche) — — Partial Correlation (partial-r): 0.2831 [0.2591, 0.3067] sex, age, birth date, deprivation index, 16 PCs —
PPM011904 PSS009149|
European Ancestry|
1,292 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: Age when periods started (menarche) — — Partial Correlation (partial-r): 0.245 [0.1926, 0.296] sex, age, birth date, deprivation index, 16 PCs —
PPM011905 PSS008703|
European Ancestry|
1,920 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: Age when periods started (menarche) — — Partial Correlation (partial-r): 0.2575 [0.215, 0.299] sex, age, birth date, deprivation index, 16 PCs —
PPM011906 PSS008477|
Greater Middle Eastern Ancestry|
221 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: Age when periods started (menarche) — — Partial Correlation (partial-r): 0.1354 [-0.0027, 0.2685] sex, age, birth date, deprivation index, 16 PCs —
PPM011907 PSS008255|
South Asian Ancestry|
1,460 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: Age when periods started (menarche) — — Partial Correlation (partial-r): 0.0945 [0.0431, 0.1454] sex, age, birth date, deprivation index, 16 PCs —
PPM011909 PSS007819|
African Ancestry|
771 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: Age when periods started (menarche) — — Partial Correlation (partial-r): 0.1018 [0.0306, 0.1721] sex, age, birth date, deprivation index, 16 PCs —
PPM011910 PSS008923|
African Ancestry|
994 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: Age when periods started (menarche) — — Partial Correlation (partial-r): 0.1087 [0.0462, 0.1703] sex, age, birth date, deprivation index, 16 PCs —

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
PSS007819 — — 771 individuals — African American or Afro-Caribbean Carribean UKB —
PSS008477 — — 221 individuals — Greater Middle Eastern (Middle Eastern, North African or Persian) Iran (Middle East) UKB —
PSS008255 — — 1,460 individuals — South Asian India (South Asia) UKB —
PSS009375 — — 5,746 individuals — European UK (+ Ireland) UKB —
PSS008923 — — 994 individuals — African unspecified Nigeria (West Africa) UKB —
PSS009149 — — 1,292 individuals — European Poland (NE Europe) UKB —
PSS008703 — — 1,920 individuals — European Italy (South Europe) UKB —
PSS008033 — — 611 individuals — East Asian China (East Asia) UKB —