Polygenic Score (PGS) ID: PGS002129

Predicted Trait
Reported Trait Length of menstrual cycle
Mapped Trait(s) menstrual cycle measurement (EFO_0007786)
Additional Trait Information sex-specific factors
Released in PGS Catalog: Jan. 10, 2022
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Score Details

Score Construction
PGS Name portability-ldpred2_F_length_menstrual_cycle
Development Method
Name LDpred2 (bigsnpr)
Parameters LDpred2-auto using HapMap3 variants
Variants
Original Genome Build GRCh37
Number of Variants 491,888
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
PPM011887 PSS009373|
European Ancestry|
987 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: Length of menstrual cycle — — Partial Correlation (partial-r): 0.1022 [0.0394, 0.1641] sex, age, birth date, deprivation index, 16 PCs —
PPM011888 PSS009147|
European Ancestry|
308 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: Length of menstrual cycle — — Partial Correlation (partial-r): 0.157 [0.0424, 0.2676] sex, age, birth date, deprivation index, 16 PCs —
PPM011889 PSS008701|
European Ancestry|
538 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: Length of menstrual cycle — — Partial Correlation (partial-r): 0.0269 [-0.0593, 0.1127] sex, age, birth date, deprivation index, 16 PCs —
PPM011890 PSS008475|
Greater Middle Eastern Ancestry|
72 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: Length of menstrual cycle — — Partial Correlation (partial-r): 0.0688 [-0.2053, 0.3329] sex, age, birth date, deprivation index, 16 PCs —
PPM011891 PSS008253|
South Asian Ancestry|
402 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: Length of menstrual cycle — — Partial Correlation (partial-r): 0.1682 [0.0691, 0.2639] sex, age, birth date, deprivation index, 16 PCs —
PPM011892 PSS008031|
East Asian Ancestry|
197 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: Length of menstrual cycle — — Partial Correlation (partial-r): 0.1261 [-0.0213, 0.2682] sex, age, birth date, deprivation index, 16 PCs —
PPM011893 PSS007817|
African Ancestry|
211 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: Length of menstrual cycle — — Partial Correlation (partial-r): -0.0358 [-0.1765, 0.1064] sex, age, birth date, deprivation index, 16 PCs —
PPM011894 PSS008921|
African Ancestry|
282 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: Length of menstrual cycle — — Partial Correlation (partial-r): -0.0043 [-0.1252, 0.1167] 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
PSS008253 — — 402 individuals — South Asian India (South Asia) UKB —
PSS007817 — — 211 individuals — African American or Afro-Caribbean Carribean UKB —
PSS008701 — — 538 individuals — European Italy (South Europe) UKB —
PSS009147 — — 308 individuals — European Poland (NE Europe) UKB —
PSS008921 — — 282 individuals — African unspecified Nigeria (West Africa) UKB —
PSS008475 — — 72 individuals — Greater Middle Eastern (Middle Eastern, North African or Persian) Iran (Middle East) UKB —
PSS009373 — — 987 individuals — European UK (+ Ireland) UKB —
PSS008031 — — 197 individuals — East Asian China (East Asia) UKB —