Polygenic Score (PGS) ID: PGS001915

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
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Score Details

Score Construction
PGS Name portability-PLR_F_menarche
Development Method
Name Penalized regression (bigstatsr)
Parameters HapMap3 variants
Variants
Original Genome Build GRCh37
Number of Variants 38,940
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
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
391,124 individuals European UK (+ Ireland) 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
PPM010203 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): 0.2798 [0.2557, 0.3035] sex, age, birth date, deprivation index, 16 PCs
PPM010204 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): 0.2408 [0.1884, 0.2919] sex, age, birth date, deprivation index, 16 PCs
PPM010205 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): 0.2576 [0.2152, 0.2992] sex, age, birth date, deprivation index, 16 PCs
PPM010206 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): 0.1617 [0.0242, 0.2932] sex, age, birth date, deprivation index, 16 PCs
PPM010207 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): 0.0834 [0.0319, 0.1345] sex, age, birth date, deprivation index, 16 PCs
PPM010209 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): 0.0913 [0.02, 0.1618] sex, age, birth date, deprivation index, 16 PCs
PPM010210 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): 0.0772 [0.0145, 0.1393] sex, age, birth date, deprivation index, 16 PCs
PPM010208 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): 0.1105 [0.0302, 0.1894] 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