Polygenic Score (PGS) ID: PGS003506

Predicted Trait
Reported Trait Length of menstrual cycle
Mapped Trait(s) menstrual cycle measurement (EFO_0007786)
Released in PGS Catalog: April 12, 2023
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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 cont-decay-F_length_menstrual_cycle
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%
32,543 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
— 32,543 individuals,
0.0 % Male samples
 European UKB — Mean = 45.9 years
Sd = 3.8 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
PPM017434 PSS010867|
European Ancestry|
1,768 individuals
 PGP000457 |
Ding Y et al. bioRxiv (2022)
|Pre		 Reported Trait: Length of menstrual cycle — — partial-R2: 0.01 sex, age, deprivation index, PC1-16 —
PPM017518 PSS010783|
European Ancestry|
589 individuals
 PGP000457 |
Ding Y et al. bioRxiv (2022)
|Pre		 Reported Trait: Length of menstrual cycle — — partial-R2: 0.02 sex, age, deprivation index, PC1-16 —
PPM017686 PSS010531|
Greater Middle Eastern Ancestry|
145 individuals
 PGP000457 |
Ding Y et al. bioRxiv (2022)
|Pre		 Reported Trait: Length of menstrual cycle — — partial-R2: 0.02 sex, age, deprivation index, PC1-16 —
PPM017770 PSS010195|
European Ancestry|
157 individuals
 PGP000457 |
Ding Y et al. bioRxiv (2022)
|Pre		 Reported Trait: Length of menstrual cycle — — partial-R2: 0.01 sex, age, deprivation index, PC1-16 —
PPM017854 PSS010447|
South Asian Ancestry|
724 individuals
 PGP000457 |
Ding Y et al. bioRxiv (2022)
|Pre		 Reported Trait: Length of menstrual cycle — — partial-R2: 0.02 sex, age, deprivation index, PC1-16 —
PPM017938 PSS010363|
East Asian Ancestry|
388 individuals
 PGP000457 |
Ding Y et al. bioRxiv (2022)
|Pre		 Reported Trait: Length of menstrual cycle — — partial-R2: 0.03 sex, age, deprivation index, PC1-16 —
PPM018022 PSS010279|
African Ancestry|
431 individuals
 PGP000457 |
Ding Y et al. bioRxiv (2022)
|Pre		 Reported Trait: Length of menstrual cycle — — partial-R2: 0.0 sex, age, deprivation index, PC1-16 —
PPM018106 PSS010699|
African Ancestry|
527 individuals
 PGP000457 |
Ding Y et al. bioRxiv (2022)
|Pre		 Reported Trait: Length of menstrual cycle — — partial-R2: 0.0 sex, age, deprivation index, PC1-16 —
PPM017602 PSS010615|
European Ancestry|
920 individuals
 PGP000457 |
Ding Y et al. bioRxiv (2022)
|Pre		 Reported Trait: Length of menstrual cycle — — 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
PSS010783 — — 589 individuals,
0.0 % Male samples
 Mean = 45.7 years
Sd = 3.9 years		 European Polish UKB —
PSS010531 — — 145 individuals,
0.0 % Male samples
 Mean = 45.9 years
Sd = 4.5 years		 Greater Middle Eastern (Middle Eastern, North African or Persian) Iranian UKB —
PSS010279 — — 431 individuals,
0.0 % Male samples
 Mean = 45.8 years
Sd = 3.8 years		 African American or Afro-Caribbean Caribbean UKB —
PSS010699 — — 527 individuals,
0.0 % Male samples
 Mean = 45.0 years
Sd = 3.6 years		 African unspecified Nigerian UKB —
PSS010447 — — 724 individuals,
0.0 % Male samples
 Mean = 45.2 years
Sd = 4.4 years		 South Asian Indian UKB —
PSS010195 — — 157 individuals,
0.0 % Male samples
 Mean = 47.0 years
Sd = 3.9 years		 European Ashkenazi UKB —
PSS010867 — — 1,768 individuals,
0.0 % Male samples
 Mean = 45.9 years
Sd = 3.9 years		 European white British UKB —
PSS010615 — — 920 individuals,
0.0 % Male samples
 Mean = 45.2 years
Sd = 3.8 years		 European Italian UKB —
PSS010363 — — 388 individuals,
0.0 % Male samples
 Mean = 45.6 years
Sd = 3.8 years		 East Asian Chinese UKB —