Polygenic Score (PGS) ID: PGS001111

Predicted Trait
Reported Trait Male genital tract cancer
Mapped Trait(s) male reproductive organ cancer (EFO_0007355)
Additional Trait Information https://biobankengine.stanford.edu/RIVAS_HG19/snpnet/cancer1038
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_cancer1038
Development Method
Name snpnet
Parameters NR
Variants
Original Genome Build GRCh37
Number of Variants 313
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
—
[
  • 3,029 cases
  • , 266,675 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
PPM008293 PSS007626|
African Ancestry|
6,497 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: Male genital tract cancer — AUROC: 0.94061 [0.92454, 0.95668] R²: 0.33303
Incremental AUROC (full-covars): 0.00101
PGS R2 (no covariates): 0.00403
PGS AUROC (no covariates): 0.56122 [0.49463, 0.62782]		 age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM008294 PSS007627|
East Asian Ancestry|
1,704 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: Male genital tract cancer — AUROC: 0.87441 [0.81711, 0.93171] R²: 0.13571
Incremental AUROC (full-covars): 0.0
PGS R2 (no covariates): 0.0007
PGS AUROC (no covariates): 0.45176 [0.26684, 0.63669]		 age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM008295 PSS007628|
European Ancestry|
24,905 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: Male genital tract cancer — AUROC: 0.88352 [0.86817, 0.89886] R²: 0.21048
Incremental AUROC (full-covars): 0.00892
PGS R2 (no covariates): 0.01449
PGS AUROC (no covariates): 0.61572 [0.57768, 0.65376]		 age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM008296 PSS007629|
South Asian Ancestry|
7,831 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: Male genital tract cancer — AUROC: 0.85217 [0.80773, 0.89661] R²: 0.15181
Incremental AUROC (full-covars): 0.00129
PGS R2 (no covariates): 0.00325
PGS AUROC (no covariates): 0.54773 [0.44057, 0.65489]		 age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM008297 PSS007630|
European Ancestry|
67,425 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: Male genital tract cancer — AUROC: 0.8538 [0.84546, 0.86213] R²: 0.18861
Incremental AUROC (full-covars): 0.00805
PGS R2 (no covariates): 0.00804
PGS AUROC (no covariates): 0.58084 [0.56034, 0.60134]		 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
PSS007626 — —
[
  • 68 cases
  • , 6,429 controls
]
 — African unspecified — UKB —
PSS007627 — —
[
  • 4 cases
  • , 1,700 controls
]
 — East Asian — UKB —
PSS007628 — —
[
  • 199 cases
  • , 24,706 controls
]
 — European non-white British ancestry UKB —
PSS007629 — —
[
  • 32 cases
  • , 7,799 controls
]
 — South Asian — UKB —
PSS007630 — —
[
  • 765 cases
  • , 66,660 controls
]
 — European white British ancestry UKB Testing cohort (heldout set)