Polygenic Score (PGS) ID: PGS002077

Predicted Trait
Reported Trait Endometriosis
Mapped Trait(s) endometriosis (EFO_0001065)
Additional Trait Information genitourinary
Released in PGS Catalog: Jan. 10, 2022
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Score Details

Score Construction
PGS Name portability-ldpred2_615
Development Method
Name LDpred2 (bigsnpr)
Parameters LDpred2-auto using HapMap3 variants
Variants
Original Genome Build GRCh37
Number of Variants 534,802
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
PPM011477 PSS009341|
European Ancestry|
10,566 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: Endometriosis — — Partial Correlation (partial-r): 0.0252 [0.0061, 0.0442] sex, age, birth date, deprivation index, 16 PCs —
PPM011478 PSS009115|
European Ancestry|
2,514 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: Endometriosis — — Partial Correlation (partial-r): 0.0048 [-0.0345, 0.044] sex, age, birth date, deprivation index, 16 PCs —
PPM011479 PSS008669|
European Ancestry|
3,593 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: Endometriosis — — Partial Correlation (partial-r): 0.0127 [-0.0201, 0.0455] sex, age, birth date, deprivation index, 16 PCs —
PPM011480 PSS008443|
Greater Middle Eastern Ancestry|
468 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: Endometriosis — — Partial Correlation (partial-r): 0.0933 sex, age, birth date, deprivation index, 16 PCs —
PPM011481 PSS008223|
South Asian Ancestry|
2,826 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: Endometriosis — — Partial Correlation (partial-r): 0.0077 [-0.0293, 0.0447] sex, age, birth date, deprivation index, 16 PCs —
PPM011482 PSS008004|
East Asian Ancestry|
1,175 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: Endometriosis — — Partial Correlation (partial-r): -0.0422 [-0.0996, 0.0155] sex, age, birth date, deprivation index, 16 PCs —
PPM011483 PSS007788|
African Ancestry|
1,515 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: Endometriosis — — Partial Correlation (partial-r): -0.0013 [-0.052, 0.0494] sex, age, birth date, deprivation index, 16 PCs —
PPM011484 PSS008892|
African Ancestry|
2,021 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: Endometriosis — — Partial Correlation (partial-r): 0.002 [-0.0418, 0.0458] 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
PSS008004 — — 1,175 individuals — East Asian China (East Asia) UKB —
PSS007788 — — 1,515 individuals — African American or Afro-Caribbean Carribean UKB —
PSS008669 — — 3,593 individuals — European Italy (South Europe) UKB —
PSS009115 — — 2,514 individuals — European Poland (NE Europe) UKB —
PSS008443 — — 468 individuals — Greater Middle Eastern (Middle Eastern, North African or Persian) Iran (Middle East) UKB —
PSS008892 — — 2,021 individuals — African unspecified Nigeria (West Africa) UKB —
PSS009341 — — 10,566 individuals — European UK (+ Ireland) UKB —
PSS008223 — — 2,826 individuals — South Asian India (South Asia) UKB —