PGS Publication: PGP000692

Publication Information (EuropePMC)
Title Genome-wide association study of prostate-specific antigen levels in 392,522 men identifies new loci and improves prediction across ancestry groups.
PubMed ID 39930085(Europe PMC)
doi 10.1038/s41588-024-02068-z
Publication Date Feb. 10, 2025
Journal Nat Genet
Author(s) Hoffmann TJ, Graff RE, Madduri RK, Rodriguez AA, Cario CL, Feng K, Jiang Y, Wang A, Klein RJ, Pierce BL, Eggener S, Tong L, Blot W, Long J, Goss LB, Darst BF, Rebbeck T, Lachance J, Andrews C, Adebiyi AO, Adusei B, Aisuodionoe-Shadrach OI, Fernandez PW, Jalloh M, Janivara R, Chen WC, Mensah JE, Agalliu I, Berndt SI, Shelley JP, Schaffer K, Machiela MJ, Freedman ND, Huang WY, Li SA, Goodman PJ, Till C, Thompson I, Lilja H, Ranatunga DK, Presti J, Van Den Eeden SK, Chanock SJ, Mosley JD, Conti DV, Haiman CA, Justice AC, Kachuri L, Witte JS.
Released in PGS Catalog: Feb. 26, 2025

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)
PGS005098
(psa2024_prs_318)
 PGP000692 |
Hoffmann TJ et al. Nat Genet (2025)
 Prostate specific antigen prostate specific antigen amount 318
-
 https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS005098/ScoringFiles/PGS005098.txt.gz
PGS005100
(psa2024_prs_disc)
 PGP000692 |
Hoffmann TJ et al. Nat Genet (2025)
 Prostate specific antigen prostate specific antigen amount 1,070,227
-
 https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS005100/ScoringFiles/PGS005100.txt.gz
PGS005099
(psa2024_prs_447)
 PGP000692 |
Hoffmann TJ et al. Nat Genet (2025)
 Prostate specific antigen prostate specific antigen amount 447
-
 https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS005099/ScoringFiles/PGS005099.txt.gz
PGS005101
(psa2024_prs_joint)
 PGP000692 |
Hoffmann TJ et al. Nat Genet (2025)
 Prostate specific antigen prostate specific antigen amount 1,070,230
-
 https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS005101/ScoringFiles/PGS005101.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
PPM022209 PGS005099
(psa2024_prs_447)
 PSS011850|
European Ancestry|
22,173 individuals
 PGP000692 |
Hoffmann TJ et al. Nat Genet (2025)
 Reported Trait: log(PSA) — — Partial R2: 0.109 age, ancestry pcs Partial r2: variation explained by the PGS only, but derived from a fully adjusted model that includes listed covariates
PPM022210 PGS005100
(psa2024_prs_disc)
 PSS011850|
European Ancestry|
22,173 individuals
 PGP000692 |
Hoffmann TJ et al. Nat Genet (2025)
 Reported Trait: log(PSA) — — Partial R2: 0.124 age, ancestry pcs Partial r2: variation explained by the PGS only, but derived from a fully adjusted model that includes listed covariates
PPM022211 PGS005101
(psa2024_prs_joint)
 PSS011850|
European Ancestry|
22,173 individuals
 PGP000692 |
Hoffmann TJ et al. Nat Genet (2025)
 Reported Trait: log(PSA) — — Partial R2: 0.139 age, ancestry pcs Partial r2: variation explained by the PGS only, but derived from a fully adjusted model that includes listed covariates
PPM022212 PGS005098
(psa2024_prs_318)
 PSS011848|
African Ancestry|
1,173 individuals
 PGP000692 |
Hoffmann TJ et al. Nat Genet (2025)
 Reported Trait: log(PSA) — — Partial R2: 0.065 age, ancestry pcs Partial r2: variation explained by the PGS only, but derived from a fully adjusted model that includes listed covariates
PPM022213 PGS005099
(psa2024_prs_447)
 PSS011848|
African Ancestry|
1,173 individuals
 PGP000692 |
Hoffmann TJ et al. Nat Genet (2025)
 Reported Trait: log(PSA) — — Partial R2: 0.07 age, ancestry pcs Partial r2: variation explained by the PGS only, but derived from a fully adjusted model that includes listed covariates
PPM022214 PGS005100
(psa2024_prs_disc)
 PSS011848|
African Ancestry|
1,173 individuals
 PGP000692 |
Hoffmann TJ et al. Nat Genet (2025)
 Reported Trait: log(PSA) — — Partial R2: 0.073 age, ancestry pcs Partial r2: variation explained by the PGS only, but derived from a fully adjusted model that includes listed covariates
PPM022215 PGS005101
(psa2024_prs_joint)
 PSS011848|
African Ancestry|
1,173 individuals
 PGP000692 |
Hoffmann TJ et al. Nat Genet (2025)
 Reported Trait: log(PSA) — — Partial R2: 0.072 age, ancestry pcs Partial r2: variation explained by the PGS only, but derived from a fully adjusted model that includes listed covariates
PPM022216 PGS005098
(psa2024_prs_318)
 PSS011849|
Additional Asian Ancestries|
257 individuals
 PGP000692 |
Hoffmann TJ et al. Nat Genet (2025)
 Reported Trait: log(PSA) — — Partial R2: 0.038 age, ancestry pcs Partial r2: variation explained by the PGS only, but derived from a fully adjusted model that includes listed covariates
PPM022217 PGS005099
(psa2024_prs_447)
 PSS011849|
Additional Asian Ancestries|
257 individuals
 PGP000692 |
Hoffmann TJ et al. Nat Genet (2025)
 Reported Trait: log(PSA) — — Partial R2: 0.035 age, ancestry pcs Partial r2: variation explained by the PGS only, but derived from a fully adjusted model that includes listed covariates
PPM022218 PGS005100
(psa2024_prs_disc)
 PSS011849|
Additional Asian Ancestries|
257 individuals
 PGP000692 |
Hoffmann TJ et al. Nat Genet (2025)
 Reported Trait: log(PSA) — — Partial R2: 0.086 age, ancestry pcs Partial r2: variation explained by the PGS only, but derived from a fully adjusted model that includes listed covariates
PPM022219 PGS005101
(psa2024_prs_joint)
 PSS011849|
Additional Asian Ancestries|
257 individuals
 PGP000692 |
Hoffmann TJ et al. Nat Genet (2025)
 Reported Trait: log(PSA) — — Partial R2: 0.107 age, ancestry pcs Partial r2: variation explained by the PGS only, but derived from a fully adjusted model that includes listed covariates
PPM022221 PGS005099
(psa2024_prs_447)
 PSS011846|
European Ancestry|
11,922 individuals
 PGP000692 |
Hoffmann TJ et al. Nat Genet (2025)
 Reported Trait: log(PSA) — — Partial R2: 0.113 age, ancestry pcs Partial r2: variation explained by the PGS only, but derived from a fully adjusted model that includes listed covariates
PPM022222 PGS005100
(psa2024_prs_disc)
 PSS011846|
European Ancestry|
11,922 individuals
 PGP000692 |
Hoffmann TJ et al. Nat Genet (2025)
 Reported Trait: log(PSA) — — Partial R2: 0.138 age, ancestry pcs Partial r2: variation explained by the PGS only, but derived from a fully adjusted model that includes listed covariates
PPM022223 PGS005101
(psa2024_prs_joint)
 PSS011846|
European Ancestry|
11,922 individuals
 PGP000692 |
Hoffmann TJ et al. Nat Genet (2025)
 Reported Trait: log(PSA) — — Partial R2: 0.147 age, ancestry pcs Partial r2: variation explained by the PGS only, but derived from a fully adjusted model that includes listed covariates
PPM022224 PGS005098
(psa2024_prs_318)
 PSS011844|
African Ancestry|
2,469 individuals
 PGP000692 |
Hoffmann TJ et al. Nat Genet (2025)
 Reported Trait: log(PSA) — — Partial R2: 0.049 age, ancestry pcs Partial r2: variation explained by the PGS only, but derived from a fully adjusted model that includes listed covariates
PPM022225 PGS005099
(psa2024_prs_447)
 PSS011844|
African Ancestry|
2,469 individuals
 PGP000692 |
Hoffmann TJ et al. Nat Genet (2025)
 Reported Trait: log(PSA) — — Partial R2: 0.053 age, ancestry pcs Partial r2: variation explained by the PGS only, but derived from a fully adjusted model that includes listed covariates
PPM022226 PGS005100
(psa2024_prs_disc)
 PSS011844|
African Ancestry|
2,469 individuals
 PGP000692 |
Hoffmann TJ et al. Nat Genet (2025)
 Reported Trait: log(PSA) — — Partial R2: 0.055 age, ancestry pcs Partial r2: variation explained by the PGS only, but derived from a fully adjusted model that includes listed covariates
PPM022227 PGS005101
(psa2024_prs_joint)
 PSS011844|
African Ancestry|
2,469 individuals
 PGP000692 |
Hoffmann TJ et al. Nat Genet (2025)
 Reported Trait: log(PSA) — — Partial R2: 0.058 age, ancestry pcs Partial r2: variation explained by the PGS only, but derived from a fully adjusted model that includes listed covariates
PPM022228 PGS005098
(psa2024_prs_318)
 PSS011847|
Additional Diverse Ancestries|
1,783 individuals
 PGP000692 |
Hoffmann TJ et al. Nat Genet (2025)
 Reported Trait: log(PSA) — — Partial R2: 0.073 age, ancestry pcs Partial r2: variation explained by the PGS only, but derived from a fully adjusted model that includes listed covariates
PPM022229 PGS005099
(psa2024_prs_447)
 PSS011847|
Additional Diverse Ancestries|
1,783 individuals
 PGP000692 |
Hoffmann TJ et al. Nat Genet (2025)
 Reported Trait: log(PSA) — — Partial R2: 0.086 age, ancestry pcs Partial r2: variation explained by the PGS only, but derived from a fully adjusted model that includes listed covariates
PPM022230 PGS005100
(psa2024_prs_disc)
 PSS011847|
Additional Diverse Ancestries|
1,783 individuals
 PGP000692 |
Hoffmann TJ et al. Nat Genet (2025)
 Reported Trait: log(PSA) — — Partial R2: 0.133 age, ancestry pcs Partial r2: variation explained by the PGS only, but derived from a fully adjusted model that includes listed covariates
PPM022231 PGS005101
(psa2024_prs_joint)
 PSS011847|
Additional Diverse Ancestries|
1,783 individuals
 PGP000692 |
Hoffmann TJ et al. Nat Genet (2025)
 Reported Trait: log(PSA) — — Partial R2: 0.14 age, ancestry pcs Partial r2: variation explained by the PGS only, but derived from a fully adjusted model that includes listed covariates
PPM022232 PGS005098
(psa2024_prs_318)
 PSS011845|
Hispanic or Latin American Ancestry|
1,336 individuals
 PGP000692 |
Hoffmann TJ et al. Nat Genet (2025)
 Reported Trait: log(PSA) — — Partial R2: 0.08 age, ancestry pcs Partial r2: variation explained by the PGS only, but derived from a fully adjusted model that includes listed covariates
PPM022233 PGS005099
(psa2024_prs_447)
 PSS011845|
Hispanic or Latin American Ancestry|
1,336 individuals
 PGP000692 |
Hoffmann TJ et al. Nat Genet (2025)
 Reported Trait: log(PSA) — — Partial R2: 0.096 age, ancestry pcs Partial r2: variation explained by the PGS only, but derived from a fully adjusted model that includes listed covariates
PPM022234 PGS005100
(psa2024_prs_disc)
 PSS011845|
Hispanic or Latin American Ancestry|
1,336 individuals
 PGP000692 |
Hoffmann TJ et al. Nat Genet (2025)
 Reported Trait: log(PSA) — — Partial R2: 0.135 age, ancestry pcs Partial r2: variation explained by the PGS only, but derived from a fully adjusted model that includes listed covariates
PPM022235 PGS005101
(psa2024_prs_joint)
 PSS011845|
Hispanic or Latin American Ancestry|
1,336 individuals
 PGP000692 |
Hoffmann TJ et al. Nat Genet (2025)
 Reported Trait: log(PSA) — — Partial R2: 0.135 age, ancestry pcs Partial r2: variation explained by the PGS only, but derived from a fully adjusted model that includes listed covariates
PPM022208 PGS005098
(psa2024_prs_318)
 PSS011850|
European Ancestry|
22,173 individuals
 PGP000692 |
Hoffmann TJ et al. Nat Genet (2025)
 Reported Trait: log(PSA) — — Partial R2: 0.095 age, ancestry pcs Partial r2: variation explained by the PGS only, but derived from a fully adjusted model that includes listed covariates
PPM022220 PGS005098
(psa2024_prs_318)
 PSS011846|
European Ancestry|
11,922 individuals
 PGP000692 |
Hoffmann TJ et al. Nat Genet (2025)
 Reported Trait: log(PSA) — — Partial R2: 0.096 age, ancestry pcs Partial r2: variation explained by the PGS only, but derived from a fully adjusted model that includes listed covariates

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
PSS011844 Prostate specific antigen — 2,469 individuals,
100.0 % Male samples
 — African unspecified — AllofUs —
PSS011845 Prostate specific antigen — 1,336 individuals,
100.0 % Male samples
 — Hispanic or Latin American — AllofUs —
PSS011846 Prostate specific antigen — 11,922 individuals,
100.0 % Male samples
 — European — AllofUs —
PSS011847 Prostate specific antigen — 1,783 individuals,
100.0 % Male samples
 — Other — AllofUs —
PSS011848 Prostate specific antigen — 1,173 individuals,
100.0 % Male samples
 — African unspecified — SELECT —
PSS011849 Prostate specific antigen — 257 individuals,
100.0 % Male samples
 — Asian unspecified — SELECT —
PSS011850 Prostate specific antigen — 22,173 individuals,
100.0 % Male samples
 — European — SELECT —