Polygenic Score (PGS) ID: PGS001292

Predicted Trait
Reported Trait Family history of prostate cancer
Mapped Trait(s) family history of prostate cancer (EFO_0600083)
Additional Trait Information https://biobankengine.stanford.edu/RIVAS_HG19/snpnet/FH1044
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_FH1044
Development Method
Name snpnet
Parameters NR
Variants
Original Genome Build GRCh37
Number of Variants 602
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
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
—
[
  • 27,466 cases
  • , 242,238 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
PPM008958 PSS004039|
African Ancestry|
6,497 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: Prostate cancer (FH) — AUROC: 0.61052 [0.58828, 0.63276] R²: 0.03568
Incremental AUROC (full-covars): -0.00159
PGS R2 (no covariates): 0.00029
PGS AUROC (no covariates): 0.5142 [0.49179, 0.53661]		 age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM008959 PSS004040|
East Asian Ancestry|
1,704 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: Prostate cancer (FH) — AUROC: 0.62093 [0.55962, 0.68225] R²: 0.02796
Incremental AUROC (full-covars): -0.01226
PGS R2 (no covariates): 0.00143
PGS AUROC (no covariates): 0.48253 [0.41865, 0.5464]		 age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM008960 PSS004041|
European Ancestry|
24,905 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: Prostate cancer (FH) — AUROC: 0.56572 [0.5538, 0.57764] R²: 0.01155
Incremental AUROC (full-covars): 0.01702
PGS R2 (no covariates): 0.00547
PGS AUROC (no covariates): 0.54869 [0.53677, 0.56062]		 age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM008961 PSS004042|
South Asian Ancestry|
7,831 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: Prostate cancer (FH) — AUROC: 0.6064 [0.57694, 0.63587] R²: 0.02296
Incremental AUROC (full-covars): 0.00822
PGS R2 (no covariates): 0.00335
PGS AUROC (no covariates): 0.54379 [0.5154, 0.57217]		 age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM008962 PSS004043|
European Ancestry|
67,425 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: Prostate cancer (FH) — AUROC: 0.58464 [0.57731, 0.59197] R²: 0.01828
Incremental AUROC (full-covars): 0.01195
PGS R2 (no covariates): 0.00542
PGS AUROC (no covariates): 0.54716 [0.53996, 0.55435]		 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
PSS004039 — —
[
  • 769 cases
  • , 5,728 controls
]
 — African unspecified — UKB —
PSS004040 — —
[
  • 79 cases
  • , 1,625 controls
]
 — East Asian — UKB —
PSS004041 — —
[
  • 2,572 cases
  • , 22,333 controls
]
 — European non-white British ancestry UKB —
PSS004042 — —
[
  • 413 cases
  • , 7,418 controls
]
 — South Asian — UKB —
PSS004043 — —
[
  • 6,888 cases
  • , 60,537 controls
]
 — European white British ancestry UKB Testing cohort (heldout set)