Polygenic Score (PGS) ID: PGS000881

Predicted Trait
Reported Trait Prostate cancer
Mapped Trait(s) prostate carcinoma (EFO_0001663)
Released in PGS Catalog: Aug. 26, 2021
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Score Details

Score Construction
PGS Name GRS72_PCa
Development Method
Name Variants associated with prostate cancer
Parameters NR
Variants
Original Genome Build NR
Number of Variants 72
Effect Weight Type log(OR)
PGS Source
PGS Catalog Publication (PGP) ID PGP000227
Citation (link to publication) Xu J et al. Prostate (2021)
Ancestry Distribution
Source of Variant
Associations (GWAS)
European: 92.4%
Multi-ancestry (excluding European): 2.8%
  • African
East Asian: 2.7%
Hispanic or Latin American: 1.5%
African: 0.6%
374,196 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
  • ,STHM
  • ,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
  • ,STHM
  • ,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
  • ,STHM
  • ,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
  • ,STHM
  • ,TAMPERE
  • ,UKGPCS
  • ,ULM
  • ,UTAH
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
  • ,STHM
  • ,TAMPERE
  • ,UKGPCS
  • ,ULM
  • ,WUGS
GWAS Catalog: GCST001942
Europe PMC: 23535732
22,548 individuals European BPC3, CAPS, CGEMS
GWAS Catalog: GCST001148
Europe PMC: 21743467
13,560 individuals European CGEMS, ProtecT, UKGPCS
GWAS Catalog: GCST002944
Europe PMC: 26034056
37,272 individuals European 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
3,226 individuals East Asian CMHS, GERA, ProHealth, RPGEH
GWAS Catalog: GCST002944
Europe PMC: 26034056
3,629 individuals Hispanic or Latin American CMHS, GERA, ProHealth, RPGEH
Europe PMC: 19767752
[
  • 1,906 cases
  • , 1,934 controls
]
,
100.0 % Male samples
European ProtecT, UKGPCS
GWAS Catalog: GCST000489
Europe PMC: 19767754
37,350 individuals European ICR, IGD, deCODE
GWAS Catalog: GCST000153
Europe PMC: 18264098
23,226 individuals European ICR, IGD, deCODE

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
PPM002522 PSS001140|
European Ancestry|
1,237 individuals
PGP000227 |
Xu J et al. Prostate (2021)
Reported Trait: Number of positive prostate cancer tumour cores at diagnostic biposy OR: 1.23 [1.06, 1.41] Age at diagnosis, study site
PPM002523 PSS001140|
European Ancestry|
1,237 individuals
PGP000227 |
Xu J et al. Prostate (2021)
Reported Trait: Number of positive prostate cancer tumour cores at surveillance biposy OR: 1.26 [1.11, 1.44] Age at diagnosis, study site
PPM002524 PSS001140|
European Ancestry|
1,237 individuals
PGP000227 |
Xu J et al. Prostate (2021)
Reported Trait: Bilateral positive prostate cancer tumor cores at diagnostic biopsy OR: 1.27 [1.01, 1.61] Age at diagnosis, study site
PPM002525 PSS001140|
European Ancestry|
1,237 individuals
PGP000227 |
Xu J et al. Prostate (2021)
Reported Trait: Bilateral positive prostate cancer tumor cores at surveillance biopsy OR: 1.19 [1.04, 1.36] Age at diagnosis, study site

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
PSS001140 All individuals were prostate cancer cases undergoing active surveillance. Patients with favourable-risk prostate cancer and low-volume favourable intermediate-risk prostate cancer were enrolled. Favorable‐risk PCa was defined as Gleason grade group (GG) = 1 and prostate‐specific antigen (PSA) < 10 ng/ml. Low‐volume favorable intermediate‐risk in our study was defined as ≤2 positive cores, and only one of the following characteristics: GG ≤ 2 and/or PSA 10–20 ng/ml. At diagnostic biopsy 765 individuals had 1 tumour core, 272 had 2 tumour cores and 152 had ≥3 tumour cores. Of the individuals with 1, 2 or ≥3 positive cores at diagnostic biopsy, 1127 were unilateral and 95 were bilateral. At any surveillance biopsy 408 individuals had 1 tumour core, 297 had 2 tumour cores and 506 had ≥3 tumour cores. Of the individuals with 1, 2 or ≥3 positive cores at any surveillance biopsy, 635 were unilateral and 582 were bilateral. 1,237 individuals,
100.0 % Male samples
Mean = 65.16 years European JHH, NSUHS