Polygenic Score (PGS) ID: PGS000662

Predicted Trait
Reported Trait Prostate Cancer
Mapped Trait(s) prostate carcinoma (EFO_0001663)
Released in PGS Catalog: Jan. 7, 2021
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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 GRS.PCa.269
Development Method
Name Independent genome-wide significant variants identified by fine-mapping using JAM (Joint Analysis of Marginal summary statistics)
Parameters Population-specific betas were combined using an inverse Z-score-weighted fixed-effects meta-analysis to obtain multi-ancestry conditional betas.
Variants
Original Genome Build GRCh37
Number of Variants 269
Effect Weight Type beta
PGS Source
PGS Catalog Publication (PGP) ID PGP000122
Citation (link to publication) Conti DV et al. Nat Genet (2021)
Ancestry Distribution
Source of Variant
Associations (GWAS)
European: 75.8%
East Asian: 11.7%
Multi-ancestry (excluding European): 9.1%
  • African
Hispanic or Latin American: 3.4%
234,253 individuals (100%)
PGS Evaluation
European: 60%
African: 40%
5 Sample Sets

Development Samples

Source of Variant Associations (GWAS)
Study Identifiers Sample Numbers Sample Ancestry Cohort(s)
GWAS Catalog: GCST011049
Europe PMC: 33398198
177,526 individuals,
100.0 % Male samples
European 12 cohorts
  • AAPC
  • ,BBJ
  • ,BPC3
  • ,CAPS
  • ,ELLIPSE
  • ,GPS
  • ,MEC
  • ,PEGASUS_PCa
  • ,PRACTICAL
  • ,ProHealth
  • ,UKGPCS
  • ,iCOGS
GWAS Catalog: GCST011049
Europe PMC: 33398198
21,354 individuals,
100.0 % Male samples
African American or Afro-Caribbean, African unspecified 12 cohorts
  • AAPC
  • ,BBJ
  • ,BPC3
  • ,CAPS
  • ,ELLIPSE
  • ,GPS
  • ,MEC
  • ,PEGASUS_PCa
  • ,PRACTICAL
  • ,ProHealth
  • ,UKGPCS
  • ,iCOGS
GWAS Catalog: GCST011049
Europe PMC: 33398198
27,420 individuals,
100.0 % Male samples
East Asian 12 cohorts
  • AAPC
  • ,BBJ
  • ,BPC3
  • ,CAPS
  • ,ELLIPSE
  • ,GPS
  • ,MEC
  • ,PEGASUS_PCa
  • ,PRACTICAL
  • ,ProHealth
  • ,UKGPCS
  • ,iCOGS
GWAS Catalog: GCST011049
Europe PMC: 33398198
7,953 individuals,
100.0 % Male samples
Hispanic or Latin American 12 cohorts
  • AAPC
  • ,BBJ
  • ,BPC3
  • ,CAPS
  • ,ELLIPSE
  • ,GPS
  • ,MEC
  • ,PEGASUS_PCa
  • ,PRACTICAL
  • ,ProHealth
  • ,UKGPCS
  • ,iCOGS

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
PPM001366 PSS000595|
African Ancestry|
2,633 individuals
PGP000122 |
Conti DV et al. Nat Genet (2021)
Reported Trait: Prostate Cancer AUROC: 0.679 Odds ratio (OR, top 10% versus 40-60% GRS): 3.53 Age, 10 PCs, study
PPM001365 PSS000596|
European Ancestry|
199,969 individuals
PGP000122 |
Conti DV et al. Nat Genet (2021)
Reported Trait: Prostate Cancer AUROC: 0.833 Odds ratio (OR, top 10% versus 40-60% GRS): 4.17
Overall Net Reclassification Index (NRI [%]): 59.4
Age, 10 PCs
PPM001955 PSS000975|
African Ancestry|
524 individuals
PGP000168 |
Plym A et al. J Natl Cancer Inst (2021)
|Ext.
Reported Trait: Prevalent prostate cancer Odds ratio (OR, bottom 10% vs. middle 20%): 0.15 [0.01, 0.92] Age at blood collection, genotyping platform, PCs(1-2) Only 261 of the original 269 SNPs were available for analysis due to no imputation of the X chromosome.
PPM001954 PSS000975|
African Ancestry|
524 individuals
PGP000168 |
Plym A et al. J Natl Cancer Inst (2021)
|Ext.
Reported Trait: Prevalent prostate cancer Odds ratio (OR, top 10% vs. middle 20%): 3.81 [1.48, 10.19] Age at blood collection, genotyping platform, PCs(1-2) Only 261 of the original 269 SNPs were available for analysis due to no imputation of the X chromosome.
PPM001953 PSS000976|
European Ancestry|
12,472 individuals
PGP000168 |
Plym A et al. J Natl Cancer Inst (2021)
|Ext.
Reported Trait: Elevated prostate specific antigen OR: 1.54 Age at blood collection, genotyping platform, PCs(1-10) Only 261 of the original 269 SNPs were available for analysis due to no imputation of the X chromosome.
PPM001952 PSS000976|
European Ancestry|
12,472 individuals
PGP000168 |
Plym A et al. J Natl Cancer Inst (2021)
|Ext.
Reported Trait: Prevalent prostate cancer Odds ratio (OR, bottom 10% vs. middle 20%): 0.34 [0.25, 0.46] Age at blood collection, genotyping platform, PCs(1-10) Only 261 of the original 269 SNPs were available for analysis due to no imputation of the X chromosome.
PPM001951 PSS000976|
European Ancestry|
12,472 individuals
PGP000168 |
Plym A et al. J Natl Cancer Inst (2021)
|Ext.
Reported Trait: Prevalent prostate cancer OR: 2.04 Odds ratio (OR, top 10% vs. middle 20%): 3.89 [3.24, 4.68] Age at blood collection, genotyping platform, PCs(1-10) Only 261 of the original 269 SNPs were available for analysis due to no imputation of the X chromosome.
PPM001970 PSS000983|
European Ancestry|
81,094 individuals
PGP000173 |
Darst BF et al. Eur Urol (2021)
|Ext.
Reported Trait: Prostate cancer in carriers of rare pathogenic, likely pathogenic and/or deleterious germline variants OR: 2.62 [2.51, 2.74] Age, PCs (1-10) Only 267 SNPs from PGS000662 were utilised. 2 SNPs were not included as they were not present in the UK Biobank (UKB) data and had an imputation info score of > 0.50 (median info score = 0.99).

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
PSS000983 Cases were individuals with malignant prostate cancer. All individuals (cases and controls) were carriers of rare pathogenic, likely pathogenic and/or deleterious germline variants in ATM, BRCA2, CHEK2, and HOXB13 genes.
[
  • 3,568 cases
  • , 77,526 controls
]
,
100.0 % Male samples
European UKB
PSS000595
[
  • 1,586 cases
  • , 1,047 controls
]
,
100.0 % Male samples
African unspecified CAUG
PSS000596
[
  • 6,852 cases
  • , 193,117 controls
]
,
100.0 % Male samples
European UKB
PSS000975 Cases were defined as having a biopsy-confirmed prostate cancer documented by a pathology report or at least two prostate cancer-related billing codes any time before or within 6 months of the date of blood collection.
[
  • 67 cases
  • , 457 controls
]
,
100.0 % Male samples
African unspecified MGBB Formerly known as Partners healthcare Biobank (PHB)
PSS000976 Cases were defined as having a biopsy-confirmed prostate cancer documented by a pathology report or at least two prostate cancer-related billing codes any time before or within 6 months of the date of blood collection.
[
  • 1,554 cases
  • , 10,918 controls
]
,
100.0 % Male samples
European MGBB Formerly known as Partners healthcare Biobank (PHB)