Polygenic Score (PGS) ID: PGS000795

Predicted Trait
Reported Trait Prostate cancer
Mapped Trait(s) prostate carcinoma (EFO_0001663)
Released in PGS Catalog: May 28, 2021
Download Score FTP directory
Terms and Licenses
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 CC_Prostate_IV
Development Method
Name 161 variants from Graff et al (PGS000084) with inverse variant weights
Parameters NR
Variants
Original Genome Build GRCh37
Number of Variants 161
Effect Weight Type Inverse-Variance weighting
PGS Source
PGS Catalog Publication (PGP) ID PGP000186
Citation (link to publication) Kachuri L et al. Nat Commun (2020)
Ancestry Distribution
Source of Variant
Associations (GWAS)
European: 93.4%
African: 2.8%
East Asian: 2.5%
Hispanic or Latin American: 1.2%
Not Reported: 0.1%
461,661 individuals (100%)
PGS Evaluation
European: 100%
1 Sample Sets

Development Samples

Source of Variant Associations (GWAS)
Study Identifiers Sample Numbers Sample Ancestry Cohort(s)
GWAS Catalog: GCST002606
Europe PMC: 25217961
67,543 individuals European 46 cohorts
  • ATBC
  • ,BBJ
  • ,CAPS
  • ,CPCS
  • ,CPSII
  • ,CaP Genes
  • ,DCPC
  • ,EOPCS
  • ,EPIC
  • ,EPIC-Norfolk
  • ,ESTHER
  • ,FHCRC
  • ,GECAP
  • ,Ghana Prostate
  • ,HPFS
  • ,IPCG
  • ,IPO-Porto
  • ,JAPC
  • ,KCPCS
  • ,LAAPC
  • ,LAPC
  • ,MAYO
  • ,MCCS
  • ,MDA
  • ,MEC
  • ,MOFFITT
  • ,NCPCS
  • ,PCBP
  • ,PCMUS
  • ,PEGASUS
  • ,PHS
  • ,PLCO
  • ,PPF-UNIS
  • ,Poland
  • ,ProMPT
  • ,ProtecT
  • ,QLD
  • ,RFPCS
  • ,SCCS
  • ,SEARCH
  • ,SELECT
  • ,STHLM1
  • ,TAMPERE
  • ,UKGPCS
  • ,ULM
  • ,UTAH
GWAS Catalog: GCST002606
Europe PMC: 25217961
6,954 individuals East Asian 46 cohorts
  • ATBC
  • ,BBJ
  • ,CAPS
  • ,CPCS
  • ,CPSII
  • ,CaP Genes
  • ,DCPC
  • ,EOPCS
  • ,EPIC
  • ,EPIC-Norfolk
  • ,ESTHER
  • ,FHCRC
  • ,GECAP
  • ,Ghana Prostate
  • ,HPFS
  • ,IPCG
  • ,IPO-Porto
  • ,JAPC
  • ,KCPCS
  • ,LAAPC
  • ,LAPC
  • ,MAYO
  • ,MCCS
  • ,MDA
  • ,MEC
  • ,MOFFITT
  • ,NCPCS
  • ,PCBP
  • ,PCMUS
  • ,PEGASUS
  • ,PHS
  • ,PLCO
  • ,PPF-UNIS
  • ,Poland
  • ,ProMPT
  • ,ProtecT
  • ,QLD
  • ,RFPCS
  • ,SCCS
  • ,SEARCH
  • ,SELECT
  • ,STHLM1
  • ,TAMPERE
  • ,UKGPCS
  • ,ULM
  • ,UTAH
GWAS Catalog: GCST002606
Europe PMC: 25217961
10,463 individuals Sub-Saharan African, African American or Afro-Caribbean 46 cohorts
  • ATBC
  • ,BBJ
  • ,CAPS
  • ,CPCS
  • ,CPSII
  • ,CaP Genes
  • ,DCPC
  • ,EOPCS
  • ,EPIC
  • ,EPIC-Norfolk
  • ,ESTHER
  • ,FHCRC
  • ,GECAP
  • ,Ghana Prostate
  • ,HPFS
  • ,IPCG
  • ,IPO-Porto
  • ,JAPC
  • ,KCPCS
  • ,LAAPC
  • ,LAPC
  • ,MAYO
  • ,MCCS
  • ,MDA
  • ,MEC
  • ,MOFFITT
  • ,NCPCS
  • ,PCBP
  • ,PCMUS
  • ,PEGASUS
  • ,PHS
  • ,PLCO
  • ,PPF-UNIS
  • ,Poland
  • ,ProMPT
  • ,ProtecT
  • ,QLD
  • ,RFPCS
  • ,SCCS
  • ,SEARCH
  • ,SELECT
  • ,STHLM1
  • ,TAMPERE
  • ,UKGPCS
  • ,ULM
  • ,UTAH
GWAS Catalog: GCST002606
Europe PMC: 25217961
2,080 individuals Hispanic or Latin American 46 cohorts
  • ATBC
  • ,BBJ
  • ,CAPS
  • ,CPCS
  • ,CPSII
  • ,CaP Genes
  • ,DCPC
  • ,EOPCS
  • ,EPIC
  • ,EPIC-Norfolk
  • ,ESTHER
  • ,FHCRC
  • ,GECAP
  • ,Ghana Prostate
  • ,HPFS
  • ,IPCG
  • ,IPO-Porto
  • ,JAPC
  • ,KCPCS
  • ,LAAPC
  • ,LAPC
  • ,MAYO
  • ,MCCS
  • ,MDA
  • ,MEC
  • ,MOFFITT
  • ,NCPCS
  • ,PCBP
  • ,PCMUS
  • ,PEGASUS
  • ,PHS
  • ,PLCO
  • ,PPF-UNIS
  • ,Poland
  • ,ProMPT
  • ,ProtecT
  • ,QLD
  • ,RFPCS
  • ,SCCS
  • ,SEARCH
  • ,SELECT
  • ,STHLM1
  • ,TAMPERE
  • ,UKGPCS
  • ,ULM
  • ,UTAH
GWAS Catalog: GCST002890
Europe PMC: 25939597
7,541 individuals European PLCO
GWAS Catalog: GCST000152
Europe PMC: 18264097
3,748 individuals European ProtecT, UKGPCS
GWAS Catalog: GCST001942
Europe PMC: 23535732
22,548 individuals European BPC3, CAPS, CGEMS
GWAS Catalog: GCST003587
Europe PMC: 27197191
123,671 individuals European GAME-ON, GECCO
GWAS Catalog: GCST002944
Europe PMC: 26034056
3,226 individuals East Asian CMHS, GERA, ProHealth, RPGEH
GWAS Catalog: GCST002944
Europe PMC: 26034056
2,251 individuals African American or Afro-Caribbean CMHS, GERA, ProHealth, RPGEH
GWAS Catalog: GCST002944
Europe PMC: 26034056
37,272 individuals European CMHS, GERA, ProHealth, RPGEH
GWAS Catalog: GCST002944
Europe PMC: 26034056
3,629 individuals Hispanic or Latin American CMHS, GERA, ProHealth, RPGEH
GWAS Catalog: GCST002421
Europe PMC: 24753544
2,950 individuals European ProtecT
GWAS Catalog: GCST001148
Europe PMC: 21743467
13,560 individuals European CGEMS, ProtecT, UKGPCS
GWAS Catalog: GCST002413
Europe PMC: 24740154
5,051 individuals European Illumina iControlDB, dbGAP
Europe PMC: 26881390
[
  • 495 cases
  • , 640 controls
]
,
100.0 % Male samples
East Asian
(Han Chinese)
CHIPGECS
GWAS Catalog: GCST001338
Europe PMC: 22130093
545 individuals Not reported NR
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
  • ,STHM2
  • ,TAMPERE
  • ,UKGPCS
  • ,ULM
  • ,WUGS
GWAS Catalog: GCST001147
Europe PMC: 21743057
7,240 individuals European 7 cohorts
  • ATBC
  • ,CPSII
  • ,EPIC
  • ,HPFS
  • ,MEC
  • ,PHS
  • ,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
PPM002066 PSS001023|
European Ancestry|
184,225 individuals
PGP000186 |
Kachuri L et al. Nat Commun (2020)
Reported Trait: Incident prostate cancer HR: 1.77 [1.72, 1.82] AUROC: 0.769
C-index: 0.768 (0.004)
: 0.51 Age at assessment, family history of prostate cancer, genotyping array, PCs(1-15), family history of prostate cancer C-index calculated as a weighted average between 1 and 5 years and AUC at 5 years.
PPM002069 PSS001023|
European Ancestry|
184,225 individuals
PGP000186 |
Kachuri L et al. Nat Commun (2020)
Reported Trait: Incident prostate cancer AUROC: 0.766
C-index: 0.763 (0.004)
: 0.496 Age, genotyping array, PCs(1-15) C-index calculated as a weighted average between 1 and 5 years and AUC at 5 years.

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
PSS001023 Individuals with at least one recorded incident diagnosis of a borderline, in situ, or malignant primary cancer were defined as cases.
[
  • 4,740 cases
  • , 179,485 controls
]
,
100.0 % Male samples
European UKB