Polygenic Score (PGS) ID: PGS001015

Predicted Trait
Reported Trait Enlarged prostate
Mapped Trait(s) prostate disease (EFO_0009602)
Additional Trait Information https://biobankengine.stanford.edu/RIVAS_HG19/snpnet/HC85
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_HC85
Development Method
Name snpnet
Parameters NR
Variants
Original Genome Build GRCh37
Number of Variants 449
Effect Weight Type NR
PGS Source
PGS Catalog Publication (PGP) ID PGP000244
Citation (link to publication) Tanigawa Y et al. medRxiv (2021) Preprint
Ancestry Distribution
Score Development/Training
European: 100%
269,704 individuals (100%)
PGS Evaluation
European: 40%
African: 20%
East Asian: 20%
South Asian: 20%
5 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
[
  • 4,619 cases
  • , 265,085 controls
]
European white British ancestry 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
PPM007838 PSS004657|
African Ancestry|
6,497 individuals
PGP000244 |
Tanigawa Y et al. medRxiv (2021)
|Pre
Reported Trait: Enlarged prostate AUROC: 0.93105 [0.91258, 0.94952] : 0.30098
Incremental AUROC (full-covars): 0.00141
PGS R2 (no covariates): 0.00292
PGS AUROC (no covariates): 0.54724 [0.47568, 0.6188]
age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM007839 PSS004658|
East Asian Ancestry|
1,704 individuals
PGP000244 |
Tanigawa Y et al. medRxiv (2021)
|Pre
Reported Trait: Enlarged prostate AUROC: 0.94421 [0.91689, 0.97153] : 0.32389
Incremental AUROC (full-covars): -0.00334
PGS R2 (no covariates): 2e-05
PGS AUROC (no covariates): 0.51196 [0.35247, 0.67145]
age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM007840 PSS004659|
European Ancestry|
24,905 individuals
PGP000244 |
Tanigawa Y et al. medRxiv (2021)
|Pre
Reported Trait: Enlarged prostate AUROC: 0.90067 [0.89167, 0.90966] : 0.26226
Incremental AUROC (full-covars): 0.00374
PGS R2 (no covariates): 0.01025
PGS AUROC (no covariates): 0.58554 [0.55363, 0.61744]
age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM007841 PSS004660|
South Asian Ancestry|
7,831 individuals
PGP000244 |
Tanigawa Y et al. medRxiv (2021)
|Pre
Reported Trait: Enlarged prostate AUROC: 0.89677 [0.87594, 0.9176] : 0.24889
Incremental AUROC (full-covars): -0.00207
PGS R2 (no covariates): 0.00055
PGS AUROC (no covariates): 0.48167 [0.42901, 0.53433]
age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM007842 PSS004661|
European Ancestry|
67,425 individuals
PGP000244 |
Tanigawa Y et al. medRxiv (2021)
|Pre
Reported Trait: Enlarged prostate AUROC: 0.87353 [0.8676, 0.87947] : 0.22935
Incremental AUROC (full-covars): 0.00218
PGS R2 (no covariates): 0.00233
PGS AUROC (no covariates): 0.54102 [0.52363, 0.5584]
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
PSS004657
[
  • 54 cases
  • , 6,443 controls
]
African unspecified UKB
PSS004658
[
  • 14 cases
  • , 1,690 controls
]
East Asian UKB
PSS004659
[
  • 346 cases
  • , 24,559 controls
]
European non-white British ancestry UKB
PSS004660
[
  • 102 cases
  • , 7,729 controls
]
South Asian UKB
PSS004661
[
  • 1,111 cases
  • , 66,314 controls
]
European white British ancestry UKB Testing cohort (heldout set)