Trait: anomaly of puberty or/and menstrual cycle

Trait Information
Identifier MONDO_0015860
Trait category
Other disease
Mapped term Orphanet:180208

Associated Polygenic Score(s)

Filter PGS by Participant Ancestry
Individuals included in:
G - Source of Variant Associations (GWAS)
D - Score Development/Training
E - PGS Evaluation
List of ancestries includes:
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Multi-ancestry (including European)
Multi-ancestry (excluding European)
African
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Additional Asian Ancestries
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Hispanic or Latin American
Additional Diverse Ancestries
Not Reported
Polygenic Score ID & Name PGS Publication ID (PGP) Reported Trait Mapped Trait(s) (Ontology) Number of Variants Ancestry distribution Scoring File (FTP Link)
PGS002079
(portability-ldpred2_626.1)
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Irregular menstrual cycle/bleeding anomaly of puberty or/and menstrual cycle 719,789
-
 https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS002079/ScoringFiles/PGS002079.txt.gz

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) 		Evaluated Score 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 PGS002079
(portability-ldpred2_626.1)
 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 PGS002079
(portability-ldpred2_626.1)
 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 PGS002079
(portability-ldpred2_626.1)
 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 PGS002079
(portability-ldpred2_626.1)
 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 PGS002079
(portability-ldpred2_626.1)
 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 PGS002079
(portability-ldpred2_626.1)
 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 PGS002079
(portability-ldpred2_626.1)
 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 PGS002079
(portability-ldpred2_626.1)
 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 —