Polygenic Score (PGS) ID: PGS002079

Predicted Trait
Reported Trait Irregular menstrual cycle/bleeding
Mapped Trait(s) anomaly of puberty or/and menstrual cycle (MONDO_0015860)
Additional Trait Information genitourinary
Released in PGS Catalog: Jan. 10, 2022
Download Score FTP directory
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 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