Polygenic Score (PGS) ID: PGS000333

Predicted Trait
Reported Trait Prostate cancer
Mapped Trait(s) prostate carcinoma (EFO_0001663)
Released in PGS Catalog: Sept. 18, 2020
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Score Details

Score Construction
PGS Name PRS_PC
Development Method
Name LDpred
Parameters ρ = 0.01; LD radius = 4000; LD reference panel = 2,690 Finnish individuals [autosomal variants only]
Variants
Original Genome Build hg19
Number of Variants 6,606,785
Effect Weight Type NR
PGS Source
PGS Catalog Publication (PGP) ID PGP000100
Citation (link to publication) Mars N et al. Nat Med (2020)
Ancestry Distribution
Source of Variant
Associations (GWAS)
European: 100%
140,254 individuals (100%)
Score Development/Training
European: 100%
21,813 individuals (100%)
PGS Evaluation
European: 66.7%
Multi-ancestry (including European): 33.3%
  • European
  • African
  • Additional Asian Ancestries
  • Not Reported
3 Sample Sets

Development Samples

Source of Variant Associations (GWAS)
Study Identifiers Sample Numbers Sample Ancestry Cohort(s)
GWAS Catalog: GCST006085
Europe PMC: 29892016
 140,254 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
— 21,813 individuals,
47.3 % Male samples
 European
(Finnish)		 FINRISK National registries were used to assess disease incidence. Follow-up ended at first-ever diagnosis of the disease of interest, death or at the end of follow-up on December 31, 2018, whichever came first. Disease endpoints are defined in Table S9. Mean (Age At Baseline) = 48.0 years — — Used to select optimal threshold of ρ for all subsequent analyses. FINRISK surveys from 1992, 1997, 2002 and 2007

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
PPM000900 PSS000447|
European Ancestry|
48,851 individuals
 PGP000100 |
Mars N et al. Nat Med (2020)
 Reported Trait: Incident prostate cancer — C-index: 0.866 — age, family history, history of benign prostate hyperplasia, genotyping array/batch, 10 ancestry PCs 10-year risk
PPM000895 PSS000447|
European Ancestry|
48,851 individuals
 PGP000100 |
Mars N et al. Nat Med (2020)
 Reported Trait: Incident prostate cancer — C-index: 0.857 — age, genotyping array/batch, 10 ancestry PCs 10-year risk
PPM000890 PSS000446|
European Ancestry|
59,126 individuals
 PGP000100 |
Mars N et al. Nat Med (2020)
 Reported Trait: Prostate cancer (incident and prevalent cases) HR: 1.83 [1.78, 1.9] — — genotyping array/batch, 10 ancestry PCs —
PPM014914 PSS009926|
Multi-ancestry (including European)|
91,106 individuals
 PGP000356 |
Varma A et al. Cancer Med (2022)
|Ext.		 Reported Trait: Prostate cancer — AUROC: 0.788 [0.758, 0.819] — Age, father's history, body mass index (BMI), smoking status, glycated hemoglobin, C-reactive protein, insulin-like growth factor 1, number of sex partners, diabetes diagnosis, and diabetes medication —

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
PSS009926 The ICD-10 code used to define PCa was C61-malignant neoplasm of prostate, and the self-reported cancer code was 1044—prostate cancer. —
[
  • 624 cases
  • , 82,384 controls
]
,
100.0 % Male samples
 — European White UKB —
PSS009926 The ICD-10 code used to define PCa was C61-malignant neoplasm of prostate, and the self-reported cancer code was 1044—prostate cancer. —
[
  • 37 cases
  • , 2,239 controls
]
,
100.0 % Male samples
 — African unspecified Black UKB —
PSS009926 The ICD-10 code used to define PCa was C61-malignant neoplasm of prostate, and the self-reported cancer code was 1044—prostate cancer. —
[
  • 13 cases
  • , 3,377 controls
]
,
100.0 % Male samples
 — Asian unspecified — UKB —
PSS009926 The ICD-10 code used to define PCa was C61-malignant neoplasm of prostate, and the self-reported cancer code was 1044—prostate cancer. —
[
  • 13 cases
  • , 2,419 controls
]
,
100.0 % Male samples
 — Not reported — UKB —
PSS000446 National registries were used to assess disease incidence. Follow-up ended at first-ever diagnosis of the disease of interest, death or at the end of follow-up on December 31, 2018, whichever came first. Disease endpoints are defined in Table S9. —
[
  • 3,617 cases
  • , 55,509 controls
]
,
100.0 % Male samples
 — European
(Finnish)		 — FinnGen —
PSS000447 National registries were used to assess disease incidence. Follow-up ended at first-ever diagnosis of the disease of interest, death or at the end of follow-up on December 31, 2018, whichever came first. Disease endpoints are defined in Table S9. —
[
  • 1,172 cases
  • , 47,679 controls
]
 — European
(Finnish)		 — FinnGen —