Polygenic Score (PGS) ID: PGS000742

Predicted Trait
Reported Trait Prostate cancer
Mapped Trait(s) prostate carcinoma (EFO_0001663)
Released in PGS Catalog: March 22, 2021
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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 PHS166
Development Method
Name LASSO-regularized Cox PH regression of 180 SNPs from Seibert et al (PGS000067) and Schumacher et al (PGS000030).
Parameters R^2 > 0.95, 10-fold cross-validation
Variants
Original Genome Build NR
Number of Variants 166
Effect Weight Type beta
PGS Source
PGS Catalog Publication (PGP) ID PGP000150
Citation (link to publication) Karunamuni RA et al. Prostate Cancer Prostatic Dis (2021)
Ancestry Distribution
Source of Variant
Associations (GWAS)
European: 100%
172,001 individuals (100%)
Score Development/Training
European: 100%
75,596 individuals (100%)
PGS Evaluation
European: 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 18 cohorts
  • CAPS
  • ,CPCS
  • ,EPIC
  • ,EPIC-Norfolk
  • ,ESTHER
  • ,IPO-Porto
  • ,MAYO
  • ,MOFFITT
  • ,PCMUS
  • ,PPF-UNIS
  • ,Poland
  • ,ProMPT
  • ,SEARCH
  • ,STHM
  • ,TAMPERE
  • ,UKGPCS
  • ,UTAH
  • ,WUGS
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
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
[
  • 50,469 cases
  • , 25,127 controls
]
,
100.0 % Male samples
European 47 cohorts
  • AHS
  • ,ATBC
  • ,Aarhus
  • ,CCI
  • ,COH
  • ,CONOR
  • ,COSM
  • ,CPCS
  • ,CeRePP
  • ,EPIC
  • ,ERSPC
  • ,ESTHER
  • ,FHCRC
  • ,Gene-PARE
  • ,HPFS
  • ,HZ
  • ,IMPACT
  • ,IPO-Porto
  • ,KULEUVEN
  • ,LAAPC
  • ,MCC-Spain
  • ,MCCS
  • ,MDACCS
  • ,MEC
  • ,MOFFITT
  • ,PASS
  • ,PCMUS
  • ,PCPT
  • ,PHS
  • ,PLCO
  • ,PRAGGA
  • ,PROCAP
  • ,PROFILE
  • ,Poland
  • ,ProMPT
  • ,QLD
  • ,RAPPER
  • ,SEARCH
  • ,SFPCS
  • ,SNP_Prostate_Ghent
  • ,SPAG
  • ,STHM
  • ,SWOG-SELECT
  • ,TAMPERE
  • ,Toronto
  • ,UKGPCS
  • ,WUGS
Cases included individuals with any type of prostate cancer (PCa). For any clinically significant PCa, cases were defined as individuals with any of the following: Gleason score ≥ 7, stage T3-T4, PSA concentration ≥ 10 ng/mL, pelvic lymph nodal metastasis, or distant metastasis. PRACTICAL consortium also including cases and controls from (1) Malaysia, (2) the Prostate Cancer Group, Santiago, Spain, (3) the Familial Prostate Cancer Study, University of Ulm, Germany

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
PPM001822 PSS000926|
European Ancestry|
6,411 individuals
PGP000150 |
Karunamuni RA et al. Prostate Cancer Prostatic Dis (2021)
Reported Trait: Non-clinically significant prostate cancer (age at onset) Hazard Ratio (HR, bottom 20% vs. middle 40%): 0.37 [0.33, 0.42]
PPM001821 PSS000926|
European Ancestry|
6,411 individuals
PGP000150 |
Karunamuni RA et al. Prostate Cancer Prostatic Dis (2021)
Reported Trait: Non-clinically significant prostate cancer (age at onset) Hazard Ratio (HR, top 20% vs. bottom 20%): 7.47 [5.49, 9.07]
PPM001820 PSS000926|
European Ancestry|
6,411 individuals
PGP000150 |
Karunamuni RA et al. Prostate Cancer Prostatic Dis (2021)
Reported Trait: Non-clinically significant prostate cancer (age at onset) Hazard Ratio (HR, top 5% vs. middle 40%): 4.28 [3.49, 4.96]
PPM001816 PSS000926|
European Ancestry|
6,411 individuals
PGP000150 |
Karunamuni RA et al. Prostate Cancer Prostatic Dis (2021)
Reported Trait: Clinically significant prostate cancer (age at onset) Hazard Ratio (HR, bottom 20% vs. middle 40%): 0.34 [0.29, 0.39]
PPM001815 PSS000926|
European Ancestry|
6,411 individuals
PGP000150 |
Karunamuni RA et al. Prostate Cancer Prostatic Dis (2021)
Reported Trait: Clinically significant prostate cancer (age at onset) Hazard Ratio (HR, top 20% vs. bottom 20%): 9.45 [6.17, 11.79]
PPM001814 PSS000926|
European Ancestry|
6,411 individuals
PGP000150 |
Karunamuni RA et al. Prostate Cancer Prostatic Dis (2021)
Reported Trait: Clinically significant prostate cancer (age at onset) Hazard Ratio (HR, top 5% vs. middle 40%): 5.09 [3.84, 6.05]
PPM001810 PSS000926|
European Ancestry|
6,411 individuals
PGP000150 |
Karunamuni RA et al. Prostate Cancer Prostatic Dis (2021)
Reported Trait: Prostate cancer (age of onset) Hazard Ratio (HR, bottom 20% vs. middle 40%): 0.37 [0.33, 0.4]
PPM001809 PSS000926|
European Ancestry|
6,411 individuals
PGP000150 |
Karunamuni RA et al. Prostate Cancer Prostatic Dis (2021)
Reported Trait: Prostate cancer (age of onset) Hazard Ratio (HR, top 20% vs. bottom 20%): 7.85 [6.04, 9.33]
PPM001808 PSS000926|
European Ancestry|
6,411 individuals
PGP000150 |
Karunamuni RA et al. Prostate Cancer Prostatic Dis (2021)
Reported Trait: Prostate cancer (age of onset) Hazard Ratio (HR, top 5% vs. middle 40%): 4.45 [3.68, 5.06]

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
PSS000926 Cases included individuals with any type of prostate cancer (PCa). For any clinically significant PCa, cases were defined as individuals with any of the following: Gleason score ≥ 7, stage T3-T4, PSA concentration ≥ 10 ng/mL, pelvic lymph nodal metastasis, or distant metastasis.
[
  • 1,583 cases
  • , 4,828 controls
]
,
100.0 % Male samples
European ProtecT, UKGPCS