Polygenic Score (PGS) ID: PGS002079

Predicted Trait
Reported Trait Irregular menstrual cycle/bleeding
Mapped Trait(s) menstrual cycle measurement (EFO_0007786)
Additional Trait Information genitourinary
Released in PGS Catalog: Jan. 10, 2022
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Score Details

Score Construction
PGS Name portability-ldpred2_626.1
Development Method
Name LDpred2 (bigsnpr)
Parameters LDpred2-auto using HapMap3 variants
Variants
Original Genome Build GRCh37
Number of Variants 719,789
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
PPM011493 PSS009343|
European Ancestry|
10,063 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: Irregular menstrual cycle/bleeding — — Partial Correlation (partial-r): 0.0369 [0.0173, 0.0564] sex, age, birth date, deprivation index, 16 PCs —
PPM011495 PSS008671|
European Ancestry|
3,394 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: Irregular menstrual cycle/bleeding — — Partial Correlation (partial-r): 0.0311 [-0.0027, 0.0647] sex, age, birth date, deprivation index, 16 PCs —
PPM011496 PSS008445|
Greater Middle Eastern Ancestry|
441 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: Irregular menstrual cycle/bleeding — — Partial Correlation (partial-r): 0.0755 [-0.0201, 0.1697] sex, age, birth date, deprivation index, 16 PCs —
PPM011497 PSS008225|
South Asian Ancestry|
2,690 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: Irregular menstrual cycle/bleeding — — Partial Correlation (partial-r): 0.0716 [0.0337, 0.1092] sex, age, birth date, deprivation index, 16 PCs —
PPM011498 PSS008006|
East Asian Ancestry|
1,113 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: Irregular menstrual cycle/bleeding — — Partial Correlation (partial-r): -0.0068 [-0.066, 0.0525] sex, age, birth date, deprivation index, 16 PCs —
PPM011499 PSS007790|
African Ancestry|
1,471 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: Irregular menstrual cycle/bleeding — — Partial Correlation (partial-r): -0.0312 [-0.0825, 0.0202] sex, age, birth date, deprivation index, 16 PCs —
PPM011500 PSS008894|
African Ancestry|
1,972 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: Irregular menstrual cycle/bleeding — — Partial Correlation (partial-r): 0.0036 [-0.0408, 0.0479] sex, age, birth date, deprivation index, 16 PCs —
PPM011494 PSS009117|
European Ancestry|
2,376 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: Irregular menstrual cycle/bleeding — — Partial Correlation (partial-r): 0.0467 [0.0064, 0.0869] 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
PSS008006 — — 1,113 individuals — East Asian China (East Asia) UKB —
PSS007790 — — 1,471 individuals — African American or Afro-Caribbean Carribean UKB —
PSS009343 — — 10,063 individuals — European UK (+ Ireland) UKB —
PSS008445 — — 441 individuals — Greater Middle Eastern (Middle Eastern, North African or Persian) Iran (Middle East) UKB —
PSS008894 — — 1,972 individuals — African unspecified Nigeria (West Africa) UKB —
PSS008671 — — 3,394 individuals — European Italy (South Europe) UKB —
PSS009117 — — 2,376 individuals — European Poland (NE Europe) UKB —
PSS008225 — — 2,690 individuals — South Asian India (South Asia) UKB —