Polygenic Score (PGS) ID: PGS001866

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-PLR_615
Development Method
Name Penalized regression (bigstatsr)
Parameters HapMap3 variants
Variants
Original Genome Build GRCh37
Number of Variants 399
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
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
391,124 individuals European UK (+ Ireland) UKB

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
PPM009817 PSS009341|
European Ancestry|
10,566 individuals
PGP000263 |
Privé F et al. Am J Hum Genet (2022)
Reported Trait: Endometriosis Partial Correlation (partial-r): 0.0219 [0.0028, 0.041] sex, age, birth date, deprivation index, 16 PCs
PPM009818 PSS009115|
European Ancestry|
2,514 individuals
PGP000263 |
Privé F et al. Am J Hum Genet (2022)
Reported Trait: Endometriosis Partial Correlation (partial-r): 0.0355 [-0.0037, 0.0747] sex, age, birth date, deprivation index, 16 PCs
PPM009819 PSS008669|
European Ancestry|
3,593 individuals
PGP000263 |
Privé F et al. Am J Hum Genet (2022)
Reported Trait: Endometriosis Partial Correlation (partial-r): 0.0028 [-0.03, 0.0356] sex, age, birth date, deprivation index, 16 PCs
PPM009820 PSS008443|
Greater Middle Eastern Ancestry|
468 individuals
PGP000263 |
Privé F et al. Am J Hum Genet (2022)
Reported Trait: Endometriosis Partial Correlation (partial-r): 0.0366 [-0.0562, 0.1287] sex, age, birth date, deprivation index, 16 PCs
PPM009821 PSS008223|
South Asian Ancestry|
2,826 individuals
PGP000263 |
Privé F et al. Am J Hum Genet (2022)
Reported Trait: Endometriosis Partial Correlation (partial-r): 0.0358 [-0.0012, 0.0727] sex, age, birth date, deprivation index, 16 PCs
PPM009822 PSS008004|
East Asian Ancestry|
1,175 individuals
PGP000263 |
Privé F et al. Am J Hum Genet (2022)
Reported Trait: Endometriosis Partial Correlation (partial-r): 0.0619 [0.0042, 0.1191] sex, age, birth date, deprivation index, 16 PCs
PPM009823 PSS007788|
African Ancestry|
1,515 individuals
PGP000263 |
Privé F et al. Am J Hum Genet (2022)
Reported Trait: Endometriosis Partial Correlation (partial-r): 0.0248 [-0.0259, 0.0754] sex, age, birth date, deprivation index, 16 PCs
PPM009824 PSS008892|
African Ancestry|
2,021 individuals
PGP000263 |
Privé F et al. Am J Hum Genet (2022)
Reported Trait: Endometriosis Partial Correlation (partial-r): 0.024 [-0.0199, 0.0677] 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