Polygenic Score (PGS) ID: PGS000579

Predicted Trait
Reported Trait Prostate cancer
Mapped Trait(s) prostate carcinoma (EFO_0001663)
Additional Trait Information PheCode 185
Released in PGS Catalog: Dec. 15, 2020
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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 PRSWEB_PHECODE185_GWAS-Catalog-r2019-05-03-X185_PT_MGI_20200608
Development Method
Name Pruning and Thresholding (P+T)
Parameters LD Clumping (MAF >= 1%, r^2 <= 0.1) & P<=2.51e-07
Variants
Original Genome Build GRCh37
Number of Variants 122
Effect Weight Type NR
PGS Source
PGS Catalog Publication (PGP) ID PGP000118
Citation (link to publication) Fritsche LG et al. Am J Hum Genet (2020)
Ancestry Distribution
Source of Variant
Associations (GWAS)
European: 100%
644,688 individuals (100%)
Score Development/Training
European: 100%
5,650 individuals (100%)
PGS Evaluation
European: 100%
1 Sample Sets

Development Samples

Source of Variant Associations (GWAS)
Study Identifiers Sample Numbers Sample Ancestry Cohort(s)
GWAS Catalog: GCST000152
Europe PMC: 18264097
 3,748 individuals European NR
GWAS Catalog: GCST000153
Europe PMC: 18264098
 23,226 individuals European NR
GWAS Catalog: GCST000154
Europe PMC: 18264096
 2,329 individuals European NR
GWAS Catalog: GCST000489
Europe PMC: 19767754
 37,350 individuals European NR
GWAS Catalog: GCST001147
Europe PMC: 21743057
 7,240 individuals European NR
GWAS Catalog: GCST001148
Europe PMC: 21743467
 13,560 individuals European NR
GWAS Catalog: GCST001719
Europe PMC: 23104005
 59,585 individuals European NR
GWAS Catalog: GCST001942
Europe PMC: 23535732
 22,548 individuals European NR
GWAS Catalog: GCST002413
Europe PMC: 24740154
 5,051 individuals European NR
GWAS Catalog: GCST002890
Europe PMC: 25939597
 7,541 individuals European NR
GWAS Catalog: GCST003586
Europe PMC: 27262462
 3,893 individuals European NR
GWAS Catalog: GCST006085
Europe PMC: 29892016
 140,254 individuals European NR
GWAS Catalog: GCST000019
Europe PMC: 17401366
 4,517 individuals European NR
GWAS Catalog: GCST000050
Europe PMC: 17603485
 12,791 individuals European NR
GWAS Catalog: GCST000307
Europe PMC: 19117981
 2,834 individuals European NR
GWAS Catalog: GCST000017
Europe PMC: 17401363
 2,329 individuals European NR
GWAS Catalog: GCST007506
Europe PMC: 30410027
 295,892 individuals European NR
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
Europe PMC: 32991828
[
  • 1,242 cases
  • , 4,408 controls
]
 European MGI PheCode:185; ICD9CM:185, 233.4, V10.46; ICD10CM:C61, D07.5 — — — —

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
PPM001264 PSS000552|
European Ancestry|
5,607 individuals
 PGP000118 |
Fritsche LG et al. Am J Hum Genet (2020)
 Reported Trait: Cancer of prostate OR: 1.747 [1.626, 1.876]
β: 0.558 (0.0364)		 AUROC: 0.646 [0.627, 0.664] Nagelkerke's Pseudo-R²: 0.0675
Brier score: 0.147
Odds Ratio (OR, top 1% vs. Rest): 3.53 [2.26, 5.51]		 age, sex, batch PCs 1-4 Cancer PRSweb PheWAS Results: PRSWEB_PHECODE185_GWAS-Catalog-r2019-05-03-X185_PT_MGI_20200608

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
PSS000552 PheCode:185; ICD9CM:185, 233.4, V10.46; ICD10CM:C61, D07.5 —
[
  • 1,190 cases
  • , 4,417 controls
]
 — European — MGI —