Polygenic Score (PGS) ID: PGS001338

Predicted Trait
Reported Trait Hyperplasia of prostate (time-to-event)
Mapped Trait(s) benign prostatic hyperplasia (EFO_0000284)
Additional Trait Information https://biobankengine.stanford.edu/RIVAS_HG19/snpnet/HC1322
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_HC1322
Development Method
Name snpnet
Parameters NR
Variants
Original Genome Build GRCh37
Number of Variants 1,223
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
[
  • 14,355 cases
  • , 255,349 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
PPM009176 PSS004258|
African Ancestry|
6,497 individuals
PGP000244 |
Tanigawa Y et al. medRxiv (2021)
|Pre
Reported Trait: TTE hyperplasia of prostate AUROC: 0.91126 [0.89869, 0.92382] : 0.34787
Incremental AUROC (full-covars): 0.00071
PGS R2 (no covariates): 0.00242
PGS AUROC (no covariates): 0.53731 [0.49821, 0.57641]
age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM009177 PSS004259|
East Asian Ancestry|
1,704 individuals
PGP000244 |
Tanigawa Y et al. medRxiv (2021)
|Pre
Reported Trait: TTE hyperplasia of prostate AUROC: 0.94551 [0.92698, 0.96403] : 0.41698
Incremental AUROC (full-covars): 0.00046
PGS R2 (no covariates): 0.00828
PGS AUROC (no covariates): 0.58436 [0.49628, 0.67245]
age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM009178 PSS004260|
European Ancestry|
24,905 individuals
PGP000244 |
Tanigawa Y et al. medRxiv (2021)
|Pre
Reported Trait: TTE hyperplasia of prostate AUROC: 0.89905 [0.89319, 0.90491] : 0.34121
Incremental AUROC (full-covars): 0.00211
PGS R2 (no covariates): 0.00524
PGS AUROC (no covariates): 0.55441 [0.53657, 0.57225]
age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM009179 PSS004261|
South Asian Ancestry|
7,831 individuals
PGP000244 |
Tanigawa Y et al. medRxiv (2021)
|Pre
Reported Trait: TTE hyperplasia of prostate AUROC: 0.87601 [0.86407, 0.88795] : 0.30354
Incremental AUROC (full-covars): 0.00252
PGS R2 (no covariates): 0.00385
PGS AUROC (no covariates): 0.54159 [0.51313, 0.57004]
age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM009180 PSS004262|
European Ancestry|
67,425 individuals
PGP000244 |
Tanigawa Y et al. medRxiv (2021)
|Pre
Reported Trait: TTE hyperplasia of prostate AUROC: 0.88092 [0.87739, 0.88444] : 0.32433
Incremental AUROC (full-covars): 0.00471
PGS R2 (no covariates): 0.0067
PGS AUROC (no covariates): 0.55724 [0.54752, 0.56697]
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
PSS004258
[
  • 224 cases
  • , 6,273 controls
]
African unspecified UKB
PSS004259
[
  • 43 cases
  • , 1,661 controls
]
East Asian UKB
PSS004260
[
  • 1,093 cases
  • , 23,812 controls
]
European non-white British ancestry UKB
PSS004261
[
  • 408 cases
  • , 7,423 controls
]
South Asian UKB
PSS004262
[
  • 3,588 cases
  • , 63,837 controls
]
European white British ancestry UKB Testing cohort (heldout set)