Polygenic Score (PGS) ID: PGS000733

Predicted Trait
Reported Trait Prostate cancer
Mapped Trait(s) prostate carcinoma (EFO_0001663)
Released in PGS Catalog: Feb. 23, 2021
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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 PHS46+African
Development Method
Name 46 variants from Seibert et al (PGS000067). Effect weights from Huynh-Le et al (DOI: 10.1101/19012237)
Parameters Multivariable logistic regression adjusting for PHS46 and 4PCs used to determine additional SNPs. p<1e-6
Variants
Original Genome Build GRCh37
Number of Variants 49
Effect Weight Type beta
PGS Source
PGS Catalog Publication (PGP) ID PGP000139
Citation (link to publication) Karunamuni RA et al. Int J Cancer (2020)
Ancestry Distribution
Source of Variant
Associations (GWAS)
European: 100%
31,747 individuals (100%)
Score Development/Training
African: 100%
6,271 individuals (100%)
PGS Evaluation
African: 100%
1 Sample Sets

Development Samples

Source of Variant Associations (GWAS)
Study Identifiers Sample Numbers Sample Ancestry Cohort(s)
Europe PMC: 29321194
[
  • 18,868 cases
  • , 12,879 controls
]
,
100.0 % Male samples
European 19 cohorts
  • CAPS
  • ,CPCS
  • ,EPIC
  • ,EPIC-Norfolk
  • ,ESTHER_ELDERLY
  • ,IPO-Porto
  • ,MAYO
  • ,MOFFITT
  • ,PCMUS
  • ,PPF-UNIS
  • ,Poland
  • ,ProMPT
  • ,SEARCH
  • ,STHLM1
  • ,TAMPERE
  • ,UKGPCS
  • ,ULM_FPCS
  • ,UTAHSTUD
  • ,WUGS
Score Development/Training
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
Clinically significant cancer were any of: Gleason score ≥ 7, stage T3-T4, PSA concentration ≥ 10 ng/mL, pelvic lymph nodal metastasis or distant metastasis.
[
  • 3,031 cases
  • , 3,240 controls
]
,
100.0 % Male samples
African unspecified 18 cohorts
  • BioVu
  • ,CPDR
  • ,CeRePP
  • ,EPICAP
  • ,KARUPROSTATE
  • ,MIAMI-WFPCS
  • ,MOFFITT
  • ,NMHS
  • ,PCaP
  • ,PROtEuS
  • ,SABOR
  • ,SCCS
  • ,SCPCS
  • ,SELECT
  • ,SFPCS
  • ,SWOG-PCPT
  • ,UKGPCS
  • ,WUGS
PRACTICAL consortium

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
PPM001674 PSS000874|
African Ancestry|
6,271 individuals
PGP000139 |
Karunamuni RA et al. Int J Cancer (2020)
Reported Trait: Age at diagnosis of any prostate cancer Hazard Ratio (HR top 20% vs. bottom 20%): 4.42 [4.16, 4.67] Overlap between score development and testing samples for 3 new SNPs - 10-fold cross-validation
PPM001676 PSS000874|
African Ancestry|
6,271 individuals
PGP000139 |
Karunamuni RA et al. Int J Cancer (2020)
Reported Trait: Age at diagnosis of any prostate cancer Hazard Ratio (HR top 2% vs. middle 40%): 3.67 [3.48, 3.87] Overlap between score development and testing samples for 3 new SNPs - 10-fold cross-validation
PPM001678 PSS000874|
African Ancestry|
6,271 individuals
PGP000139 |
Karunamuni RA et al. Int J Cancer (2020)
Reported Trait: Age at diagnosis of any prostate cancer Hazard Ratio (HR bottom 20% vs. middle 40%): 0.51 [0.49, 0.52] Overlap between score development and testing samples for 3 new SNPs - 10-fold cross-validation
PPM001680 PSS000874|
African Ancestry|
6,271 individuals
PGP000139 |
Karunamuni RA et al. Int J Cancer (2020)
Reported Trait: Age at diagnosis of clinically significant prostate cancer Hazard Ratio (top 20% vs. bottom 20%): 4.71 [4.38, 5.05] Overlap between score development and testing samples for 3 new SNPs - 10-fold cross-validation
PPM001682 PSS000874|
African Ancestry|
6,271 individuals
PGP000139 |
Karunamuni RA et al. Int J Cancer (2020)
Reported Trait: Age at diagnosis of clinically significant prostate cancer Hazard Ratio (top 2% vs. middle 40%): 3.89 [3.64, 4.13] Overlap between score development and testing samples for 3 new SNPs - 10-fold cross-validation
PPM001684 PSS000874|
African Ancestry|
6,271 individuals
PGP000139 |
Karunamuni RA et al. Int J Cancer (2020)
Reported Trait: Age at diagnosis of clinically significant prostate cancer Hazard Ratio (bottom 20% vs. middle 40%): 0.5 [0.48, 0.52] Overlap between score development and testing samples for 3 new SNPs - 10-fold cross-validation

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
PSS000874 Clinically significant cancer were any of: Gleason score ≥ 7, stage T3-T4, PSA concentration ≥ 10 ng/mL, pelvic lymph nodal metastasis or distant metastasis.
[
  • 3,031 cases
  • , 3,240 controls
]
,
100.0 % Male samples
African unspecified 18 cohorts
  • BioVu
  • ,CPDR
  • ,CeRePP
  • ,EPICAP
  • ,KARUPROSTATE
  • ,MIAMI-WFPCS
  • ,MOFFITT
  • ,NMHS
  • ,PCaP
  • ,PROtEuS
  • ,SABOR
  • ,SCCS
  • ,SCPCS
  • ,SELECT
  • ,SFPCS
  • ,SWOG-PCPT
  • ,UKGPCS
  • ,WUGS
PRACTICAL consortium