Polygenic Score (PGS) ID: PGS001182

Predicted Trait
Reported Trait Estradiol [> 212 pmol/L]
Mapped Trait(s) estradiol measurement (EFO_0004697)
Additional Trait Information https://biobankengine.stanford.edu/RIVAS_HG19/snpnet/BIN10030800
Released in PGS Catalog: Oct. 21, 2021
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 GBE_BIN10030800
Development Method
Name snpnet
Parameters NR
Variants
Original Genome Build GRCh37
Number of Variants 351
Effect Weight Type NR
PGS Source
PGS Catalog Publication (PGP) ID PGP000244
Citation (link to publication) Tanigawa Y et al. PLoS Genet (2022)
Ancestry Distribution
Score Development/Training
European: 100%
239,637 individuals (100%)
PGS Evaluation
European: 40%
African: 20%
East Asian: 20%
South Asian: 20%
5 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
—
[
  • 31,042 cases
  • , 208,595 controls
]
 European UKB — — — white British ancestry —

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
PPM008599 PSS003617|
African Ancestry|
5,634 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: Oestradiol > 212 pmol/L — AUROC: 0.84561 [0.83153, 0.85969] R²: 0.36666
Incremental AUROC (full-covars): 0.0004
PGS R2 (no covariates): 0.00269
PGS AUROC (no covariates): 0.52894 [0.51075, 0.54713]		 age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM008600 PSS003618|
East Asian Ancestry|
1,519 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: Oestradiol > 212 pmol/L — AUROC: 0.87744 [0.85387, 0.90101] R²: 0.4381
Incremental AUROC (full-covars): 0.00067
PGS R2 (no covariates): 0.00244
PGS AUROC (no covariates): 0.52764 [0.49274, 0.56254]		 age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM008601 PSS003619|
European Ancestry|
22,152 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: Oestradiol > 212 pmol/L — AUROC: 0.86243 [0.85486, 0.87001] R²: 0.40572
Incremental AUROC (full-covars): 0.00045
PGS R2 (no covariates): 0.00134
PGS AUROC (no covariates): 0.52174 [0.51159, 0.5319]		 age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM008602 PSS003620|
South Asian Ancestry|
6,943 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: Oestradiol > 212 pmol/L — AUROC: 0.84655 [0.8301, 0.86301] R²: 0.36479
Incremental AUROC (full-covars): -0.00035
PGS R2 (no covariates): 1e-05
PGS AUROC (no covariates): 0.50081 [0.48154, 0.52008]		 age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM008603 PSS003621|
European Ancestry|
59,957 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: Oestradiol > 212 pmol/L — AUROC: 0.85144 [0.84586, 0.85701] R²: 0.36546
Incremental AUROC (full-covars): 0.00059
PGS R2 (no covariates): 0.00121
PGS AUROC (no covariates): 0.52103 [0.51414, 0.52793]		 age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method

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
PSS003617 — —
[
  • 1,208 cases
  • , 4,426 controls
]
 — African unspecified — UKB —
PSS003618 — —
[
  • 309 cases
  • , 1,210 controls
]
 — East Asian — UKB —
PSS003619 — —
[
  • 3,703 cases
  • , 18,449 controls
]
 — European non-white British ancestry UKB —
PSS003620 — —
[
  • 1,023 cases
  • , 5,920 controls
]
 — South Asian — UKB —
PSS003621 — —
[
  • 7,653 cases
  • , 52,304 controls
]
 — European white British ancestry UKB Testing cohort (heldout set)