PGS Publication: PGP000412

Publication Information (EuropePMC)
Title Genetically adjusted PSA levels for prostate cancer screening.
PubMed ID 37264206(Europe PMC)
doi 10.1038/s41591-023-02277-9
Publication Date June 1, 2023
Journal Nat Med
Author(s) Kachuri L, Hoffmann TJ, Jiang Y, Berndt SI, Shelley JP, Schaffer KR, Machiela MJ, Freedman ND, Huang WY, Li SA, Easterlin R, Goodman PJ, Till C, Thompson I, Lilja H, Van Den Eeden SK, Chanock SJ, Haiman CA, Conti DV, Klein RJ, Mosley JD, Graff RE, Witte JS.
Released in PGS Catalog: June 1, 2023

Associated Polygenic Score(s)

Filter PGS by Participant Ancestry
Individuals included in:
G - Source of Variant Associations (GWAS)
D - Score Development/Training
E - PGS Evaluation
List of ancestries includes:
Display options:
Ancestry legend
Multi-ancestry (including European)
Multi-ancestry (excluding European)
African
East Asian
South Asian
Additional Asian Ancestries
European
Greater Middle Eastern
Hispanic or Latin American
Additional Diverse Ancestries
Not Reported

PGS Developed By This Publication

Polygenic Score ID & Name PGS Publication ID (PGP) Reported Trait Mapped Trait(s) (Ontology) Number of Variants Ancestry distribution
GWAS
Dev
Eval
 Scoring File (FTP Link)
PGS003379
(PSA_PGS_CSx)
 PGP000412 |
Kachuri L et al. Nat Med (2023)
 Prostate-specific antigen (PSA) levels prostate specific antigen amount 1,071,278
-
 https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS003379/ScoringFiles/PGS003379.txt.gz
PGS003378
(PSA_PGS_128)
 PGP000412 |
Kachuri L et al. Nat Med (2023)
 Prostate-specific antigen (PSA) levels prostate specific antigen amount 128
-
 https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS003378/ScoringFiles/PGS003378.txt.gz

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) 		Evaluated Score 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
PPM016240 PGS003378
(PSA_PGS_128)
 PSS010066|
European Ancestry|
5,725 individuals
 PGP000412 |
Kachuri L et al. Nat Med (2023)
 Reported Trait: Baseline/pre-randomization log(PSA) β: 0.169 — Partial R2 (%, variation explained by the PGS only): 7.33 Age at PSA measurement, genetic ancestry PC1-PC10 computed within ancestry group Beta per SD increase in PGS; PGS converted to standardized z-score with mean=0 and SD=1
PPM016241 PGS003378
(PSA_PGS_128)
 PSS010073|
Multi-ancestry (including European)|
25,917 individuals
 PGP000412 |
Kachuri L et al. Nat Med (2023)
 Reported Trait: Baseline/pre-randomization log(PSA) β: 0.207 — Partial R2 (%, variation explained by the PGS only): 8.0 Age at PSA measurement, population-specific 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
PPM016242 PGS003378
(PSA_PGS_128)
 PSS010072|
European Ancestry|
22,173 individuals
 PGP000412 |
Kachuri L et al. Nat Med (2023)
 Reported Trait: Baseline/pre-randomization log(PSA) β: 0.213 — Partial R2 (%, variation explained by the PGS only): 8.78 Age at PSA measurement, genetic ancestry PC1-PC10 computed within ancestry group Beta per SD increase in PGS; PGS converted to standardized z-score with mean=0 and SD=1
PPM016243 PGS003378
(PSA_PGS_128)
 PSS010070|
African Ancestry|
2,936 individuals
 PGP000412 |
Kachuri L et al. Nat Med (2023)
 Reported Trait: Baseline/pre-randomization log(PSA) β: 0.154 — Partial R2 (%, variation explained by the PGS only): 3.36 Age at PSA measurement, population-specific 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
PPM016244 PGS003378
(PSA_PGS_128)
 PSS010068|
African Ancestry|
1,173 individuals
 PGP000412 |
Kachuri L et al. Nat Med (2023)
 Reported Trait: Baseline/pre-randomization log(PSA) β: 0.163 — Partial R2 (%, variation explained by the PGS only): 3.45 Age at PSA measurement, genetic ancestry PC1-PC10 computed within ancestry group Beta per SD increase in PGS; PGS converted to standardized z-score with mean=0 and SD=1
PPM016245 PGS003378
(PSA_PGS_128)
 PSS010069|
African Ancestry|
1,763 individuals
 PGP000412 |
Kachuri L et al. Nat Med (2023)
 Reported Trait: Baseline/pre-randomization log(PSA) β: 0.146 — Partial R2 (%, variation explained by the PGS only): 3.32 Age at PSA measurement, genetic ancestry PC1-PC10 computed within ancestry group Beta per SD increase in PGS; PGS converted to standardized z-score with mean=0 and SD=1
PPM016246 PGS003378
(PSA_PGS_128)
 PSS010071|
East Asian Ancestry|
257 individuals
 PGP000412 |
Kachuri L et al. Nat Med (2023)
 Reported Trait: Baseline/pre-randomization log(PSA) β: 0.136 — Partial R2 (%, variation explained by the PGS only): 2.45 Age at PSA measurement, genetic ancestry PC1-PC10 computed within ancestry group Beta per SD increase in PGS; PGS converted to standardized z-score with mean=0 and SD=1
PPM016248 PGS003379
(PSA_PGS_CSx)
 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 PGS003379
(PSA_PGS_CSx)
 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 PGS003379
(PSA_PGS_CSx)
 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 PGS003379
(PSA_PGS_CSx)
 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 PGS003379
(PSA_PGS_CSx)
 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)
PPM016239 PGS003378
(PSA_PGS_128)
 PSS010067|
Multi-ancestry (including European)|
5,883 individuals
 PGP000412 |
Kachuri L et al. Nat Med (2023)
 Reported Trait: Baseline/pre-randomization log(PSA) β: 0.168 — Partial R2 (%, variation explained by the PGS only): 7.16 Age at PSA measurement, population-specific 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
PPM016247 PGS003379
(PSA_PGS_CSx)
 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 PGS003379
(PSA_PGS_CSx)
 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 PGS003379
(PSA_PGS_CSx)
 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