Polygenic Score (PGS) ID: PGS001164

Predicted Trait
Reported Trait Testicular cancer
Mapped Trait(s) testicular carcinoma (EFO_0005088)
Additional Trait Information https://biobankengine.stanford.edu/RIVAS_HG19/snpnet/cancer1045
Released in PGS Catalog: Oct. 21, 2021
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Score Details

Score Construction
PGS Name GBE_cancer1045
Development Method
Name snpnet
Parameters NR
Variants
Original Genome Build GRCh37
Number of Variants 280
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: 66.7%
South Asian: 33.3%
3 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
—
[
  • 554 cases
  • , 269,150 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
PPM008542 PSS007643|
European Ancestry|
24,905 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: Testicular cancer — AUROC: 0.89735 [0.86792, 0.92679] R²: 0.1704
Incremental AUROC (full-covars): 0.01226
PGS R2 (no covariates): 0.01529
PGS AUROC (no covariates): 0.62484 [0.5376, 0.71208]		 age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM008543 PSS007644|
South Asian Ancestry|
7,831 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: Testicular cancer — AUROC: 0.9816 [0.96678, 0.99641] R²: 0.29699
Incremental AUROC (full-covars): 0.00299
PGS R2 (no covariates): 0.00616
PGS AUROC (no covariates): 0.386 [0.0998, 0.67219]		 age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM008544 PSS007645|
European Ancestry|
67,425 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: Testicular cancer — AUROC: 0.83915 [0.8185, 0.85981] R²: 0.1291
Incremental AUROC (full-covars): 0.03126
PGS R2 (no covariates): 0.01573
PGS AUROC (no covariates): 0.62956 [0.58302, 0.67611]		 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
PSS007644 — —
[
  • 5 cases
  • , 7,826 controls
]
 — South Asian — UKB —
PSS007645 — —
[
  • 135 cases
  • , 67,290 controls
]
 — European white British ancestry UKB Testing cohort (heldout set)
PSS007643 — —
[
  • 36 cases
  • , 24,869 controls
]
 — European non-white British ancestry UKB —