Polygenic Score (PGS) ID: PGS000579

Predicted Trait
Reported Trait Cancer of prostate
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
Variants
Original Genome Build GRCh37
Number of Variants 122
Development Method
Name P&T
Parameters LD Clumping (MAF >= 1%, r^2 <= 0.1) & P<=2.51e-07
PGS Source
PGS Catalog Publication (PGP) ID PGP000118
Citation (link to publication) Fritsche LG et al. Am J Hum Genet (2020)

Contributing Samples

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

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 ID)
PGS Sample Set ID
(PSS ID)
Performance Source Trait PGS Effect Sizes
(per SD change)
PGS Classification Metrics Other Metrics Covariates Included in the Model PGS Performance: Other Relevant Information
PPM001264 PSS000552 PGP000118 Fritsche LG et al. (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 ID)
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