Polygenic Score (PGS) ID: PGS003379

Predicted Trait
Reported Trait Prostate-specific antigen (PSA) levels
Mapped Trait(s) prostate specific antigen amount (OBA_2050200)
Additional Trait Information log(PSA) in men without prostate cancer
Released in PGS Catalog: June 1, 2023
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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 PSA_PGS_CSx
Development Method
Name PRS-CSx
Parameters PRS-CSx settings: phi=1e-04 meta=TRUE; Since PRS-CSx excludes chrX, these variants were selected using clumping (p-value<5E-08, LD r2<0.01) and added to score separately
Variants
Original Genome Build GRCh37
Number of Variants 1,071,278
Effect Weight Type NR
PGS Source
PGS Catalog Publication (PGP) ID PGP000412
Citation (link to publication) Kachuri L et al. Nat Med (2023)
Ancestry Distribution
Source of Variant
Associations (GWAS)
European: 89.6%
African: 3.7%
East Asian: 3.5%
Hispanic or Latin American: 3.2%
95,768 individuals (100%)
PGS Evaluation
African: 37.5%
European: 25%
Multi-ancestry (including European): 25%
  • European
  • African
  • Not Reported
East Asian: 12.5%
8 Sample Sets

Development Samples

Source of Variant Associations (GWAS)
Study Identifiers Sample Numbers Sample Ancestry Cohort(s)
— 85,824 individuals,
100.0 % Male samples
 European BioVU, GERA, MDC, PLCO, UKB
— 3,509 individuals,
100.0 % Male samples
 African American or Afro-Caribbean BioVU, GERA, PLCO
— 3,337 individuals,
100.0 % Male samples
 East Asian GERA, PLCO
— 3,098 individuals,
100.0 % Male samples
 Hispanic or Latin American GERA, PLCO

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
PPM016248 PSS010066|
European Ancestry|
5,725 individuals
 PGP000412 |
Kachuri L et al. Nat Med (2023)
 Reported Trait: Baseline/pre-randomization log(PSA) β: 0.194 — Partial R2 (%, variation explained by the PGS only): 8.6 Age at PSA measurement, within-population genetic ancestry PC1-PC10 Beta per SD increase in PGS; PGS converted to standardized z-score with mean=0 and SD=1; SNPs and weights specific for use in this cohort (1,058,173 SNPs)
PPM016249 PSS010073|
Multi-ancestry (including European)|
25,917 individuals
 PGP000412 |
Kachuri L et al. Nat Med (2023)
 Reported Trait: Baseline/pre-randomization log(PSA) β: 0.258 — Partial R2 (%, variation explained by the PGS only): 9.61 Age at PSA measurement, within-population genetic ancestry PC1-PC10, genetic ancestry proportions (AFR + EAS) Beta per SD increase in PGS; PGS converted to standardized z-score with mean=0 and SD=1; SNPs and weights specific for use in this cohort (1,071,278 SNPs)
PPM016250 PSS010072|
European Ancestry|
22,173 individuals
 PGP000412 |
Kachuri L et al. Nat Med (2023)
 Reported Trait: Baseline/pre-randomization log(PSA) β: 0.283 — Partial R2 (%, variation explained by the PGS only): 10.94 Age at PSA measurement, within-population genetic ancestry PC1-PC10 Beta per SD increase in PGS; PGS converted to standardized z-score with mean=0 and SD=1; SNPs and weights specific for use in this cohort (1,071,278 SNPs)
PPM016251 PSS010070|
African Ancestry|
2,936 individuals
 PGP000412 |
Kachuri L et al. Nat Med (2023)
 Reported Trait: Baseline/pre-randomization log(PSA) β: 0.134 — Partial R2 (%, variation explained by the PGS only): 3.11 Age at PSA measurement, within-population genetic ancestry PC1-PC10, genetic ancestry proportions (AFR) Beta per SD increase in PGS; PGS converted to standardized z-score with mean=0 and SD=1; SNPs and weights specific for use in this cohort (1,071,278 SNPs)
PPM016252 PSS010068|
African Ancestry|
1,173 individuals
 PGP000412 |
Kachuri L et al. Nat Med (2023)
 Reported Trait: Baseline/pre-randomization log(PSA) β: 0.098 — Partial R2 (%, variation explained by the PGS only): 1.64 Age at PSA measurement, within-population genetic ancestry PC1-PC10 Beta per SD increase in PGS; PGS converted to standardized z-score with mean=0 and SD=1; SNPs and weights specific for use in this cohort (1,071,278 SNPs)
PPM016247 PSS010067|
Multi-ancestry (including European)|
5,883 individuals
 PGP000412 |
Kachuri L et al. Nat Med (2023)
 Reported Trait: Baseline/pre-randomization log(PSA) β: 0.186 — Partial R2 (%, variation explained by the PGS only): 8.13 Age at PSA measurement, within-population genetic ancestry PC1-PC10, genetic ancestry proportions (AFR + EAS) Beta per SD increase in PGS; PGS converted to standardized z-score with mean=0 and SD=1; SNPs and weights specific for use in this cohort (1,058,173 SNPs)
PPM016253 PSS010069|
African Ancestry|
1,763 individuals
 PGP000412 |
Kachuri L et al. Nat Med (2023)
 Reported Trait: Baseline/pre-randomization log(PSA) β: 0.157 — Partial R2 (%, variation explained by the PGS only): 4.22 Age at PSA measurement, within-population genetic ancestry PC1-PC10 Beta per SD increase in PGS; PGS converted to standardized z-score with mean=0 and SD=1; SNPs and weights specific for use in this cohort (1,071,278 SNPs)
PPM016254 PSS010071|
East Asian Ancestry|
257 individuals
 PGP000412 |
Kachuri L et al. Nat Med (2023)
 Reported Trait: Baseline/pre-randomization log(PSA) β: 0.258 — Partial R2 (%, variation explained by the PGS only): 9.22 Age at PSA measurement, within-population genetic ancestry PC1-PC10 Beta per SD increase in PGS; PGS converted to standardized z-score with mean=0 and SD=1; SNPs and weights specific for use in this cohort (1,071,278 SNPs)

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
PSS010066 Baseline/pre-randomization PSA in men without prostate cancer — 5,725 individuals,
100.0 % Male samples
 — European
(Predominantly European)		 European (EUR) ancestry cluster based on SNPWEIGHTS score >=0.80; median EUR = 0.998; mean EUR = 0.991 PCPT Minimum enrollment age was 55 years with serum PSA <= 3 ng/mL
PSS010067 Baseline/pre-randomization PSA in men without prostate cancer — 5,883 individuals,
100.0 % Male samples
 — European, Not reported Multi-ancestry pooled sample PCPT Minimum enrollment age was 55 years with serum PSA <= 3 ng/mL
PSS010068 Baseline/pre-randomization PSA in men without prostate cancer — 1,173 individuals,
100.0 % Male samples
 — African American or Afro-Caribbean
(Predominantly West African)		 West African (AFR) ancestry cluster based on SNPWEIGHTS score >=0.80; median AFR = 0.855; mean AFR = 0.861 SELECT Minimum enrollment age was 50 years for African Americans and 55 years for all other men; serum PSA <= 4 ng/mL
PSS010069 Baseline/pre-randomization PSA in men without prostate cancer — 1,763 individuals,
100.0 % Male samples
 — African American or Afro-Caribbean
(West African admixed)		 0.20 < West African (AFR) ancestry score <0.80 based on SNPWEIGHTS; median AFR = 0.673; mean AFR = 0.602 SELECT Minimum enrollment age was 50 years for African Americans and 55 years for all other men; serum PSA <= 4 ng/mL
PSS010070 Baseline/pre-randomization PSA in men without prostate cancer — 2,936 individuals,
100.0 % Male samples
 — African American or Afro-Caribbean
(West African admixed)		 West African (AFR) ancestry score >0.20 based on SNPWEIGHTS; median AFR = 0.765; mean AFR = 0.705 SELECT Minimum enrollment age was 50 years for African Americans and 55 years for all other men; serum PSA <= 4 ng/mL
PSS010071 Baseline/pre-randomization PSA in men without prostate cancer — 257 individuals,
100.0 % Male samples
 — East Asian
(Predominantly East Asian)		 East Asian (EAS) ancestry cluster based on SNPWEIGHTS score >=0.80; median EAS = 0.978; mean EAS = 0.972 SELECT Minimum enrollment age was 50 years for African Americans and 55 years for all other men; serum PSA <= 4 ng/mL
PSS010072 Baseline/pre-randomization PSA in men without prostate cancer — 22,173 individuals,
100.0 % Male samples
 — European
(Predominantly European)		 European (EUR) ancestry cluster based on SNPWEIGHTS score >=0.80; median EUR = 0.995; mean EUR = 0.986 SELECT Minimum enrollment age was 50 years for African Americans and 55 years for all other men; serum PSA <= 4 ng/mL
PSS010073 Baseline/pre-randomization PSA in men without prostate cancer — 25,917 individuals,
100.0 % Male samples
 — European, African American or Afro-Caribbean Multi-ancestry pooled sample SELECT Minimum enrollment age was 50 years for African Americans and 55 years for all other men; serum PSA <= 4 ng/mL