Polygenic Score (PGS) ID: PGS000590

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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Score Details

Score Construction
PGS Name PRSWEB_PHECODE185_UKBB-SAIGE-HRC-X185_PRS-CS_MGI_20200608
Variants
Original Genome Build GRCh37
Number of Variants 1,119,236
Development Method
Name PRS-CS
Parameters Parameters = auto; LD reference (eur)
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: 32424355
[
  • 6,743 cases
  • , 169,185 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; 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
PPM001275 PSS000552 PGP000118 Fritsche LG et al. (2020) Reported Trait: Cancer of prostate OR: 1.516 [1.415, 1.624]
β: 0.416 (0.0353)		 AUROC: 0.614 [0.595, 0.633] Nagelkerke's Pseudo-R²: 0.0395
Brier score: 0.15
Odds Ratio (OR, top 1% vs. Rest): 2.32 [1.42, 3.78]		 age, sex, batch PCs 1-4 Cancer PRSweb PheWAS Results: PRSWEB_PHECODE185_UKBB-SAIGE-HRC-X185_PRS-CS_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 —