Polygenic Score (PGS) ID: PGS001291

Predicted Trait
Reported Trait Prostate cancer
Mapped Trait(s) prostate carcinoma (EFO_0001663)
Additional Trait Information https://biobankengine.stanford.edu/RIVAS_HG19/snpnet/cancer1044
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_cancer1044
Development Method
Name snpnet
Parameters NR
Variants
Original Genome Build GRCh37
Number of Variants 948
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
[
  • 6,278 cases
  • , 263,426 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
PPM008953 PSS007636|
African Ancestry|
6,497 individuals
PGP000244 |
Tanigawa Y et al. medRxiv (2021)
|Pre
Reported Trait: Prostate cancer AUROC: 0.92615 [0.91516, 0.93714] : 0.36445
Incremental AUROC (full-covars): 0.0009
PGS R2 (no covariates): 0.00433
PGS AUROC (no covariates): 0.55467 [0.51548, 0.59387]
age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM008954 PSS007637|
East Asian Ancestry|
1,704 individuals
PGP000244 |
Tanigawa Y et al. medRxiv (2021)
|Pre
Reported Trait: Prostate cancer AUROC: 0.97011 [0.94971, 0.99051] : 0.40156
Incremental AUROC (full-covars): 0.00138
PGS R2 (no covariates): 0.01286
PGS AUROC (no covariates): 0.63402 [0.52345, 0.74459]
age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM008955 PSS007638|
European Ancestry|
24,905 individuals
PGP000244 |
Tanigawa Y et al. medRxiv (2021)
|Pre
Reported Trait: Prostate cancer AUROC: 0.91101 [0.90322, 0.91879] : 0.29589
Incremental AUROC (full-covars): 0.01454
PGS R2 (no covariates): 0.03164
PGS AUROC (no covariates): 0.65437 [0.62906, 0.67968]
age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM008956 PSS007639|
South Asian Ancestry|
7,831 individuals
PGP000244 |
Tanigawa Y et al. medRxiv (2021)
|Pre
Reported Trait: Prostate cancer AUROC: 0.9026 [0.88127, 0.92393] : 0.25031
Incremental AUROC (full-covars): 0.01068
PGS R2 (no covariates): 0.02013
PGS AUROC (no covariates): 0.62511 [0.56383, 0.6864]
age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM008957 PSS007640|
European Ancestry|
67,425 individuals
PGP000244 |
Tanigawa Y et al. medRxiv (2021)
|Pre
Reported Trait: Prostate cancer AUROC: 0.8892 [0.88431, 0.89409] : 0.27234
Incremental AUROC (full-covars): 0.01941
PGS R2 (no covariates): 0.02942
PGS AUROC (no covariates): 0.63978 [0.62584, 0.65373]
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
PSS007636
[
  • 199 cases
  • , 6,298 controls
]
African unspecified UKB
PSS007637
[
  • 9 cases
  • , 1,695 controls
]
East Asian UKB
PSS007638
[
  • 441 cases
  • , 24,464 controls
]
European non-white British ancestry UKB
PSS007639
[
  • 80 cases
  • , 7,751 controls
]
South Asian UKB
PSS007640
[
  • 1,563 cases
  • , 65,862 controls
]
European white British ancestry UKB Testing cohort (heldout set)