Polygenic Score (PGS) ID: PGS005238

Predicted Trait
Reported Trait Prostate carcinoma
Mapped Trait(s) prostate carcinoma (EFO_0001663)
Released in PGS Catalog: Oct. 6, 2025
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Terms and Licenses
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Score Details

Score Construction
PGS Name LDpred2
Development Method
Name LDpred2
Parameters LDpred2 estimates the posterior mean effect size of each SNP, while accounting for the effect estimates of other correlated SNPs. This method employs a point-normal prior, selecting only a subset of SNPs with non-zero estimated effects for inclusion in the PGS. LDpred2 involves three key hyperparameters: the fraction of causal SNPs, SNP-based heritability, and sparsity (True or False). Settings were selected based on their ability to produce the highest receiver operating characteristic curve (AUC) in the UKB tuning data, with final settings of 0.018 for the fraction of causal SNPs, 0.0866 for SNP-based heritability (70% of the LDSC estimate), and no sparsity, yielding an AUC of 0.7 in the UKB tuning data.
Variants
Original Genome Build GRCh37
Number of Variants 964,607
Effect Weight Type beta
PGS Source
PGS Catalog Publication (PGP) ID PGP000741
Citation (link to publication) Tanha HM et al. HGG Adv (2025)
Ancestry Distribution
Source of Variant
Associations (GWAS)
European: 75.8%
East Asian: 11.7%
African: 9.1%
Hispanic or Latin American: 3.4%
234,253 individuals (100%)
Score Development/Training
European: 100%
10,000 individuals (100%)
PGS Evaluation
European: 60%
African: 20%
South Asian: 20%
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 European NR
GWAS Catalog: GCST011049
Europe PMC: 33398198
 21,354 individuals African American or Afro-Caribbean,African unspecified NR
GWAS Catalog: GCST011049
Europe PMC: 33398198
 27,420 individuals East Asian NR
GWAS Catalog: GCST011049
Europe PMC: 33398198
 7,953 individuals Hispanic or Latin American 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
—
[
  • 678 cases
  • , 9,322 controls
]
,
100.0 % Male samples
 European UKB Linked cancer registry records were used to identify participants diagnosed with malignant neoplasm of the prostate (ICD-10 code: C61; ICD-9 code: 185). — PC1-PC4 values ±3s.d. from the 1000G European cluster —

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
PPM022676 PSS012055|
African Ancestry|
3,193 individuals
 PGP000741 |
Tanha HM et al. HGG Adv (2025)
 Reported Trait: 5-year incident prostate cancer — AUROC: 0.592 [0.533, 0.651] — - —
PPM022671 PSS012056|
European Ancestry|
184,010 individuals
 PGP000741 |
Tanha HM et al. HGG Adv (2025)
 Reported Trait: 5-year incident prostate cancer — AUROC: 0.698 [0.689, 0.707] — - —
PPM022681 PSS012057|
South Asian Ancestry|
5,097 individuals
 PGP000741 |
Tanha HM et al. HGG Adv (2025)
 Reported Trait: 5-year incident prostate cancer — AUROC: 0.742 [0.664, 0.82] — - —
PPM022686 PSS012054|
European Ancestry|
6,791 individuals
 PGP000741 |
Tanha HM et al. HGG Adv (2025)
 Reported Trait: 5-year incident prostate cancer — AUROC: 0.702 [0.67, 0.733] — - —
PPM022691 PSS012053|
European Ancestry|
1,809 individuals
 PGP000741 |
Tanha HM et al. HGG Adv (2025)
 Reported Trait: 5-year incident prostate cancer — AUROC: 0.717 [0.687, 0.747] — - —
PPM022696 PSS012056|
European Ancestry|
184,010 individuals
 PGP000741 |
Tanha HM et al. HGG Adv (2025)
 Reported Trait: 5-year incident prostate cancer — AUROC: 0.789 [0.782, 0.796] — Age-specific absolute risk adjusted by PGS relative risk —
PPM022701 PSS012057|
South Asian Ancestry|
5,097 individuals
 PGP000741 |
Tanha HM et al. HGG Adv (2025)
 Reported Trait: 5-year incident prostate cancer — AUROC: 0.842 [0.79, 0.894] — Age-specific absolute risk adjusted by PGS relative risk —
PPM022706 PSS012055|
African Ancestry|
3,193 individuals
 PGP000741 |
Tanha HM et al. HGG Adv (2025)
 Reported Trait: 5-year incident prostate cancer — AUROC: 0.798 [0.759, 0.838] — Age-specific absolute risk adjusted by PGS relative risk —
PPM022716 PSS012053|
European Ancestry|
1,809 individuals
 PGP000741 |
Tanha HM et al. HGG Adv (2025)
 Reported Trait: 5-year incident prostate cancer — AUROC: 0.725 [0.696, 0.754] — Age-specific absolute risk adjusted by PGS relative risk —
PPM022711 PSS012054|
European Ancestry|
6,791 individuals
 PGP000741 |
Tanha HM et al. HGG Adv (2025)
 Reported Trait: 5-year incident prostate cancer — AUROC: 0.741 [0.714, 0.768] — Age-specific absolute risk adjusted by PGS relative risk —

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
PSS012053 Linked cancer registry records were used to identify participants diagnosed with incident malignant neoplasm of the prostate (ICD-10 code: C61; ICD-9 code: 185) within five years of prediction baseline. —
[
  • 327 cases
  • , 1,482 controls
]
,
100.0 % Male samples
 European PC1-PC4 values ±3s.d. from the 1000G European cluster MCCS MCCS had a case/sub-cohort design, leading to a higher proportion of cases
PSS012054 Linked cancer registry records were used to identify participants diagnosed with incident malignant neoplasm of the prostate (ICD-10 code: C61; ICD-9 code: 185) within five years of prediction baseline. —
[
  • 269 cases
  • , 6,522 controls
]
,
100.0 % Male samples
 European PC1-PC4 values ±3s.d. from the 1000G European cluster QSKIN —
PSS012055 Linked cancer registry records were used to identify participants diagnosed with incident malignant neoplasm of the prostate (ICD-10 code: C61; ICD-9 code: 185) within five years of prediction baseline. —
[
  • 82 cases
  • , 3,111 controls
]
,
100.0 % Male samples
 African American or Afro-Caribbean AFR individuals were identified by PC1-PC4 from 1000G and k-means clustering. UKB —
PSS012056 Linked cancer registry records were used to identify participants diagnosed with incident malignant neoplasm of the prostate (ICD-10 code: C61; ICD-9 code: 185) within five years of prediction baseline. —
[
  • 3,133 cases
  • , 180,877 controls
]
,
100.0 % Male samples
 European EUR individuals were identified by PC1-PC4 from 1000G and k-means clustering. UKB —
PSS012057 Linked cancer registry records were used to identify participants diagnosed with incident malignant neoplasm of the prostate (ICD-10 code: C61; ICD-9 code: 185) within five years of prediction baseline. —
[
  • 30 cases
  • , 5,067 controls
]
,
100.0 % Male samples
 South Asian SAS individuals were identified by PC1-PC4 from 1000G and k-means clustering. UKB —