Polygenic Score (PGS) ID: PGS000588

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
Download Score FTP directory
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_Pca-PRACTICAL_LASSOSUM_UKB_20200608
Variants
Original Genome Build GRCh37
Number of Variants 178,259
Development Method
Name Lassosum
Parameters s=0.9;Lambda=0.005456
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
EuropePMC: 29892016
[
  • 79,148 cases
  • , 61,106 controls
]
 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; ICD9:185, 233.4; ICD10:C61, D07.5 —
[
  • 2,962 cases
  • , 29,160 controls
]
 — European — UKB —

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
PPM001273 PSS000573 PGP000118 Fritsche LG et al. (2020) Reported Trait: Cancer of prostate OR: 2.127 [2.043, 2.215]
β: 0.755 (0.0206)		 AUROC: 0.699 [0.69, 0.71] Nagelkerke's Pseudo-R²: 0.0943
Brier score: 0.0794
Odds Ratio (OR, top 1% vs. Rest): 5.88 [4.85, 7.14]		 age, sex, batch PCs 1-4 Cancer PRSweb PheWAS Results: PRSWEB_PHECODE185_Pca-PRACTICAL_LASSOSUM_UKB_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
PSS000573 PheCode:185; ICD9:185, 233.4; ICD10:C61, D07.5 —
[
  • 3,012 cases
  • , 29,652 controls
]
 — European — UKB —