Polygenic Score (PGS) ID: PGS000751

Predicted Trait
Reported Trait Prostate cancer
Mapped Trait(s) prostate carcinoma (EFO_0001663)
Released in PGS Catalog: March 22, 2021
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Score Details

Score Construction
PGS Name PRS_PrCa_EuropeanWeighted
Development Method
Name Known prostate cancer risk alleles
Parameters p < 5e-2, MAF  ≥  0.001, r^2  ≥  0.3
Variants
Original Genome Build NR
Number of Variants 178
Effect Weight Type log(OR)
PGS Source
PGS Catalog Publication (PGP) ID PGP000156
Citation (link to publication) Du Z et al. Int J Cancer (2019)
Ancestry Distribution
Source of Variant
Associations (GWAS)
European: 93.5%
African: 2.9%
Multi-ancestry (excluding European): 1.9%
  • African
East Asian: 1.7%
436,934 individuals (100%)
PGS Evaluation
Hispanic or Latin American: 100%
1 Sample Sets

Development Samples

Source of Variant Associations (GWAS)
Study Identifiers Sample Numbers Sample Ancestry Cohort(s)
GWAS Catalog: GCST006085
Europe PMC: 29892016
140,254 individuals European 48 cohorts
  • AHS
  • ,ATBC
  • ,Aarhus
  • ,CCI
  • ,COH
  • ,CONOR
  • ,COSM
  • ,CPCS
  • ,CPSII
  • ,CeRePP
  • ,EPIC
  • ,ERSPC
  • ,ESTHER
  • ,FHCRC
  • ,Gene-PARE
  • ,HPFS
  • ,IMPACT
  • ,IPO-Porto
  • ,KULEUVEN
  • ,LAAPC
  • ,MCC-Spain
  • ,MCCS
  • ,MDACCS
  • ,MEC
  • ,MOF
  • ,PASS
  • ,PCMUS
  • ,PCPT
  • ,PHS
  • ,PLCO
  • ,PRAGGA
  • ,PROCAP
  • ,PROFILE
  • ,PROGRESS
  • ,Poland
  • ,ProMPT
  • ,ProtecT
  • ,QLD
  • ,RAPPER
  • ,SEARCH
  • ,SELECT
  • ,SFPCS
  • ,SPAG
  • ,STHLM2
  • ,TAMPERE
  • ,UKGPCS
  • ,ULM
  • ,WUGS
Europe PMC: 29892050
[
  • 82,591 cases
  • , 61,213 controls
]
,
100.0 % Male samples
European 7 cohorts
  • BPC4
  • ,CAPS
  • ,CRUK-CRI
  • ,OncoArray_Prostate
  • ,PEGASUS
  • ,PRACTICAL
  • ,iCOGS
GWAS Catalog: GCST004982
Europe PMC: 29117387
8,298 individuals African unspecified, African American or Afro-Caribbean 30 cohorts
  • BioVu
  • ,CPDR
  • ,CPSII
  • ,CaP Genes
  • ,CeRePP
  • ,DCPC
  • ,EPICAP
  • ,GECAP
  • ,Ghana
  • ,IPCG
  • ,KCPCS
  • ,LAAPC
  • ,MDA
  • ,MEC
  • ,MOFFITT
  • ,NCPCS
  • ,NMHS
  • ,PCBP
  • ,PCPT
  • ,PCaP
  • ,PLCO
  • ,ProHealth
  • ,SABOR
  • ,SCCS
  • ,SCPCS
  • ,SELECT
  • ,SFPCS
  • ,UKGPCS
  • ,WFPCS
  • ,WUGS
GWAS Catalog: GCST004982
Europe PMC: 29117387
932 individuals Sub-Saharan African 30 cohorts
  • BioVu
  • ,CPDR
  • ,CPSII
  • ,CaP Genes
  • ,CeRePP
  • ,DCPC
  • ,EPICAP
  • ,GECAP
  • ,Ghana
  • ,IPCG
  • ,KCPCS
  • ,LAAPC
  • ,MDA
  • ,MEC
  • ,MOFFITT
  • ,NCPCS
  • ,NMHS
  • ,PCBP
  • ,PCPT
  • ,PCaP
  • ,PLCO
  • ,ProHealth
  • ,SABOR
  • ,SCCS
  • ,SCPCS
  • ,SELECT
  • ,SFPCS
  • ,UKGPCS
  • ,WFPCS
  • ,WUGS
GWAS Catalog: GCST004982
Europe PMC: 29117387
11,782 individuals African American or Afro-Caribbean 30 cohorts
  • BioVu
  • ,CPDR
  • ,CPSII
  • ,CaP Genes
  • ,CeRePP
  • ,DCPC
  • ,EPICAP
  • ,GECAP
  • ,Ghana
  • ,IPCG
  • ,KCPCS
  • ,LAAPC
  • ,MDA
  • ,MEC
  • ,MOFFITT
  • ,NCPCS
  • ,NMHS
  • ,PCBP
  • ,PCPT
  • ,PCaP
  • ,PLCO
  • ,ProHealth
  • ,SABOR
  • ,SCCS
  • ,SCPCS
  • ,SELECT
  • ,SFPCS
  • ,UKGPCS
  • ,WFPCS
  • ,WUGS
GWAS Catalog: GCST003148
Europe PMC: 26443449
7,394 individuals East Asian BBJ, O-MRC
Europe PMC: 30397198
[
  • 71,535 cases
  • , 52,935 controls
]
,
100.0 % Male samples
European ELLIPSE, PRACTICAL, 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
PPM001907 PSS000953|
Hispanic or Latin American Ancestry|
4,324 individuals
PGP000156 |
Du Z et al. Int J Cancer (2019)
Reported Trait: Prostate cancer Odds ratio (OR, top 10% vs. middle 50%): 3.1 [2.55, 3.76] Age, study, PCs(1-10) Only 176 variants of the original 181 variants were utilised as 5 variants did not meet a MAF  ≥  0.001 and imputation r^2  ≥ 0.3 in Latino men.
PPM001908 PSS000953|
Hispanic or Latin American Ancestry|
4,324 individuals
PGP000156 |
Du Z et al. Int J Cancer (2019)
Reported Trait: Prostate cancer Odds ratio (OR, top 1% vs. middle 50%): 4.02 [2.46, 6.55] Age, study, PCs(1-10) Only 176 variants of the original 181 variants were utilised as 5 variants did not meet a MAF  ≥  0.001 and imputation r^2  ≥ 0.3 in Latino men.
PPM001909 PSS000953|
Hispanic or Latin American Ancestry|
4,324 individuals
PGP000156 |
Du Z et al. Int J Cancer (2019)
Reported Trait: Prostate cancer Odds ratio (OR, bottom 10% vs. middle 50%): 0.38 [0.28, 0.51] Age, study, PCs(1-10) Only 176 variants of the original 181 variants were utilised as 5 variants did not meet a MAF  ≥  0.001 and imputation r^2  ≥ 0.3 in Latino men.
PPM001910 PSS000953|
Hispanic or Latin American Ancestry|
4,324 individuals
PGP000156 |
Du Z et al. Int J Cancer (2019)
Reported Trait: Prostate cancer Odds ratio (OR, bottom 1% vs. middle 50%): 0.25 [0.09, 0.67] Age, study, PCs(1-10) Only 176 variants of the original 181 variants were utilised as 5 variants did not meet a MAF  ≥  0.001 and imputation r^2  ≥ 0.3 in Latino men.

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
PSS000953 In set 1 (1034 cases), prostate cancer cases were identified by linking with the cancer registries in Hawaii and California. In set 2 (1192 cases) cases were indiviuals with prostate cancer determined by cancer diagnosis, enrollment in prostate cancer studies at University of Texas M.D. Ancerson Cancer Centre or by biposy confirmation.
[
  • 2,226 cases
  • , 2,098 controls
]
,
100.0 % Male samples
Hispanic or Latin American LAAPC, MDA, MEC, SABOR