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
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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. PLoS Genet (2022)
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
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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
—
[
  • 4,619 cases
  • , 265,085 controls
]
EuropeanUKB———white British ancestry—
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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.

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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
PPM007838PSS004657|
African Ancestry|
6,497 individuals
PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
Reported Trait: Enlarged prostate—AUROC: 0.93105 [0.91258, 0.94952]R²: 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 PCsFull Model & PGS R2 is estimated using Nagelkerke's method
PPM007839PSS004658|
East Asian Ancestry|
1,704 individuals
PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
Reported Trait: Enlarged prostate—AUROC: 0.94421 [0.91689, 0.97153]R²: 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 PCsFull Model & PGS R2 is estimated using Nagelkerke's method
PPM007840PSS004659|
European Ancestry|
24,905 individuals
PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
Reported Trait: Enlarged prostate—AUROC: 0.90067 [0.89167, 0.90966]R²: 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 PCsFull Model & PGS R2 is estimated using Nagelkerke's method
PPM007841PSS004660|
South Asian Ancestry|
7,831 individuals
PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
Reported Trait: Enlarged prostate—AUROC: 0.89677 [0.87594, 0.9176]R²: 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 PCsFull Model & PGS R2 is estimated using Nagelkerke's method
PPM007842PSS004661|
European Ancestry|
67,425 individuals
PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
Reported Trait: Enlarged prostate—AUROC: 0.87353 [0.8676, 0.87947]R²: 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 PCsFull Model & PGS R2 is estimated using Nagelkerke's method
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Evaluated Samples

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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
]
—Europeannon-white British ancestryUKB—
PSS004660——
[
  • 102 cases
  • , 7,729 controls
]
—South Asian—UKB—
PSS004661——
[
  • 1,111 cases
  • , 66,314 controls
]
—Europeanwhite British ancestryUKBTesting cohort (heldout set)
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