Polygenic Score (PGS) ID: PGS003508

Predicted Trait
Reported Trait Age when periods started (menarche)
Mapped Trait(s) age at menarche (EFO_0004703)
Released in PGS Catalog: April 12, 2023
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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 cont-decay-F_menarche
Development Method
Name LDpred2-auto
Parameters vec_p_init = seq_log(1e-4, 0.9, length.out = 10), burn_in = 100, num_iter = 500, report_step = 5
Variants
Original Genome Build GRCh37
Number of Variants 979,739
Effect Weight Type beta
PGS Source
PGS Catalog Publication (PGP) ID PGP000457
Citation (link to publication) Ding Y et al. bioRxiv (2022) Preprint
Ancestry Distribution
Score Development/Training
European: 100%
193,808 individuals (100%)
PGS Evaluation
European: 44.4%
African: 22.2%
East Asian: 11.1%
Greater Middle Eastern: 11.1%
South Asian: 11.1%
9 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
— 193,808 individuals,
0.0 % Male samples
 European UKB — Mean = 56.7 years
Sd = 7.9 years		 — white British —

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
PPM017436 PSS010869|
European Ancestry|
10,448 individuals
 PGP000457 |
Ding Y et al. bioRxiv (2022)
|Pre		 Reported Trait: Age when periods started (menarche) — — partial-R2: 0.1 sex, age, deprivation index, PC1-16 —
PPM017520 PSS010785|
European Ancestry|
2,448 individuals
 PGP000457 |
Ding Y et al. bioRxiv (2022)
|Pre		 Reported Trait: Age when periods started (menarche) — — partial-R2: 0.08 sex, age, deprivation index, PC1-16 —
PPM017604 PSS010617|
European Ancestry|
3,478 individuals
 PGP000457 |
Ding Y et al. bioRxiv (2022)
|Pre		 Reported Trait: Age when periods started (menarche) — — partial-R2: 0.08 sex, age, deprivation index, PC1-16 —
PPM017688 PSS010533|
Greater Middle Eastern Ancestry|
442 individuals
 PGP000457 |
Ding Y et al. bioRxiv (2022)
|Pre		 Reported Trait: Age when periods started (menarche) — — partial-R2: 0.05 sex, age, deprivation index, PC1-16 —
PPM017772 PSS010197|
European Ancestry|
1,248 individuals
 PGP000457 |
Ding Y et al. bioRxiv (2022)
|Pre		 Reported Trait: Age when periods started (menarche) — — partial-R2: 0.1 sex, age, deprivation index, PC1-16 —
PPM017856 PSS010449|
South Asian Ancestry|
2,633 individuals
 PGP000457 |
Ding Y et al. bioRxiv (2022)
|Pre		 Reported Trait: Age when periods started (menarche) — — partial-R2: 0.03 sex, age, deprivation index, PC1-16 —
PPM017940 PSS010365|
East Asian Ancestry|
1,138 individuals
 PGP000457 |
Ding Y et al. bioRxiv (2022)
|Pre		 Reported Trait: Age when periods started (menarche) — — partial-R2: 0.02 sex, age, deprivation index, PC1-16 —
PPM018024 PSS010281|
African Ancestry|
1,469 individuals
 PGP000457 |
Ding Y et al. bioRxiv (2022)
|Pre		 Reported Trait: Age when periods started (menarche) — — partial-R2: 0.03 sex, age, deprivation index, PC1-16 —
PPM018108 PSS010701|
African Ancestry|
1,905 individuals
 PGP000457 |
Ding Y et al. bioRxiv (2022)
|Pre		 Reported Trait: Age when periods started (menarche) — — partial-R2: 0.01 sex, age, deprivation index, PC1-16 —

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
PSS010785 — — 2,448 individuals,
0.0 % Male samples
 Mean = 54.5 years
Sd = 7.6 years		 European Polish UKB —
PSS010533 — — 442 individuals,
0.0 % Male samples
 Mean = 52.2 years
Sd = 8.0 years		 Greater Middle Eastern (Middle Eastern, North African or Persian) Iranian UKB —
PSS010869 — — 10,448 individuals,
0.0 % Male samples
 Mean = 56.7 years
Sd = 7.8 years		 European white British UKB —
PSS010281 — — 1,469 individuals,
0.0 % Male samples
 Mean = 52.2 years
Sd = 7.9 years		 African American or Afro-Caribbean Caribbean UKB —
PSS010701 — — 1,905 individuals,
0.0 % Male samples
 Mean = 52.3 years
Sd = 8.0 years		 African unspecified Nigerian UKB —
PSS010449 — — 2,633 individuals,
0.0 % Male samples
 Mean = 52.8 years
Sd = 8.0 years		 South Asian Indian UKB —
PSS010197 — — 1,248 individuals,
0.0 % Male samples
 Mean = 57.8 years
Sd = 7.0 years		 European Ashkenazi UKB —
PSS010617 — — 3,478 individuals,
0.0 % Male samples
 Mean = 54.2 years
Sd = 8.3 years		 European Italian UKB —
PSS010365 — — 1,138 individuals,
0.0 % Male samples
 Mean = 52.4 years
Sd = 7.5 years		 East Asian Chinese UKB —