Polygenic Score (PGS) ID: PGS000741

Predicted Trait
Reported Trait Prostate cancer
Mapped Trait(s) prostate carcinoma (EFO_0001663)
Released in PGS Catalog: March 22, 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 PCa_PHS2
Development Method
Name Cox proportional hazard regression - reestimated weights of 46 SNPs from Seibert et al (PGS000067)
Parameters 22 proxies variants with r^2 ≥ 0.9.
Variants
Original Genome Build GRCh37
Number of Variants 46
Effect Weight Type PHS log(HR)
PGS Source
PGS Catalog Publication (PGP) ID PGP000149
Citation (link to publication) Huynh-Le MP et al. Nat Commun (2021)
Ancestry Distribution
Score Development/Training
European: 100%
43,854 individuals (100%)
PGS Evaluation
Multi-ancestry (excluding European): 60%
  • Additional Asian Ancestries
  • Not Reported
  • African
Not Reported: 20%
Multi-ancestry (including European): 20%
  • European
  • Not Reported
5 Sample Sets

Development Samples

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
12,107 individuals,
100.0 % Male samples
European NR Individuals from the PRACTICAL consotium. Used to determine proxy SNPs for SNPs that could not be identified on OncoArray.
Case numbers refer to "any prostate cancer (PCa)"; of those cases 10 635 have aggressive PCa, and 5406 have very aggressive PCa (Gleason score ≥7, stage T3-T4, PSA concentration ≥10 ng/mL, nodal metastasis, or distant metastasis).
[
  • 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
  • ,STHLM1
  • ,TAMPERE
  • ,UKGPCS
  • ,UTAH
  • ,WUGS
Individuals from the PRACTICAL consortium. Used to determine new score weights.

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
PPM001790 PSS000925|
Multi-ancestry (excluding European)|
80,491 individuals
PGP000149 |
Huynh-Le MP et al. Nat Commun (2021)
Reported Trait: Prostate cancer (age at diagnosis) Hazard ratio (HR, top 20% vs. bottom 20%): 5.32 [4.99, 5.7]
PPM001791 PSS000924|
Multi-ancestry (including European)|
71,856 individuals
PGP000149 |
Huynh-Le MP et al. Nat Commun (2021)
Reported Trait: Prostate cancer (age at diagnosis) Hazard ratio (HR, top 20% vs. bottom 20%): 5.54 [5.18, 5.93]
PPM001792 PSS000923|
Multi-ancestry (excluding European)|
2,382 individuals
PGP000149 |
Huynh-Le MP et al. Nat Commun (2021)
Reported Trait: Prostate cancer (age at diagnosis) Hazard ratio (HR, top 20% vs. bottom 20%): 4.49 [3.23, 6.33]
PPM001793 PSS000922|
Multi-ancestry (excluding European)|
6,253 individuals
PGP000149 |
Huynh-Le MP et al. Nat Commun (2021)
Reported Trait: Prostate cancer (age at diagnosis) Hazard ratio (HR, top 20% vs. bottom 20%): 2.54 [2.08, 3.1]
PPM001797 PSS000922|
Multi-ancestry (excluding European)|
6,253 individuals
PGP000149 |
Huynh-Le MP et al. Nat Commun (2021)
Reported Trait: Aggressive prostate cancer (age at diagnosis) Hazard ratio (HR, top 20% vs. bottom 20%): 2.43 [1.51, 4.05]
PPM001798 PSS000925|
Multi-ancestry (excluding European)|
80,491 individuals
PGP000149 |
Huynh-Le MP et al. Nat Commun (2021)
Reported Trait: Prostate cancer mortality (age at death) Hazard ratio (HR, top 20% vs. bottom 20%): 5.68 [5.07, 6.46]
PPM001800 PSS000924|
Multi-ancestry (including European)|
71,856 individuals
PGP000149 |
Huynh-Le MP et al. Nat Commun (2021)
Reported Trait: Prostate cancer in men with a family history of prostate cancer β: 2.06 Hazard ratio (HR, top 20% vs. bottom 20%): 4.8
PPM001795 PSS000924|
Multi-ancestry (including European)|
71,856 individuals
PGP000149 |
Huynh-Le MP et al. Nat Commun (2021)
Reported Trait: Aggressive prostate cancer (age at diagnosis) Hazard ratio (HR, top 20% vs. bottom 20%): 5.62 [5.25, 6.05]
PPM001803 PSS000925|
Multi-ancestry (excluding European)|
80,491 individuals
PGP000149 |
Huynh-Le MP et al. Nat Commun (2021)
Reported Trait: Aggressive prostate cancer in men with a family history of prostate cancer β: 2.16 Hazard ratio (HR, top 20% vs. bottom 20%): 5.12
PPM001804 PSS000924|
Multi-ancestry (including European)|
71,856 individuals
PGP000149 |
Huynh-Le MP et al. Nat Commun (2021)
Reported Trait: Aggressive prostate cancer in men with a family history of prostate cancer β: 2.1 Hazard ratio (HR, top 20% vs. bottom 20%): 4.93
PPM001805 PSS000923|
Multi-ancestry (excluding European)|
2,382 individuals
PGP000149 |
Huynh-Le MP et al. Nat Commun (2021)
Reported Trait: Aggressive prostate cancer in men with a family history of prostate cancer β: 1.73 Hazard ratio (HR, top 20% vs. bottom 20%): 3.6
PPM001806 PSS000922|
Multi-ancestry (excluding European)|
6,253 individuals
PGP000149 |
Huynh-Le MP et al. Nat Commun (2021)
Reported Trait: Aggressive prostate cancer in men with a family history of prostate cancer β: 1.1 Hazard ratio (HR, top 20% vs. bottom 20%): 2.16
PPM001807 PSS000925|
Multi-ancestry (excluding European)|
80,491 individuals
PGP000149 |
Huynh-Le MP et al. Nat Commun (2021)
Reported Trait: Prostate cancer mortality in men with a family history of prostate cancer β: 2.2 Hazard ratio (HR, top 20% vs. bottom 20%): 5.29
PPM001794 PSS000925|
Multi-ancestry (excluding European)|
80,491 individuals
PGP000149 |
Huynh-Le MP et al. Nat Commun (2021)
Reported Trait: Aggressive prostate cancer (age at diagnosis) Hazard ratio (HR, top 20% vs. bottom 20%): 5.88 [5.48, 6.34]
PPM001796 PSS000923|
Multi-ancestry (excluding European)|
2,382 individuals
PGP000149 |
Huynh-Le MP et al. Nat Commun (2021)
Reported Trait: Aggressive prostate cancer (age at diagnosis) Hazard ratio (HR, top 20% vs. bottom 20%): 5.16 [3.45, 7.78]
PPM001799 PSS000925|
Multi-ancestry (excluding European)|
80,491 individuals
PGP000149 |
Huynh-Le MP et al. Nat Commun (2021)
Reported Trait: Prostate cancer in men with a family history of prostate cancer β: 1.98 Hazard ratio (HR, top 20% vs. bottom 20%): 4.48
PPM001801 PSS000923|
Multi-ancestry (excluding European)|
2,382 individuals
PGP000149 |
Huynh-Le MP et al. Nat Commun (2021)
Reported Trait: Prostate cancer in men with a family history of prostate cancer β: 1.89 Hazard ratio (HR, top 20% vs. bottom 20%): 4.17
PPM001802 PSS000922|
Multi-ancestry (excluding European)|
6,253 individuals
PGP000149 |
Huynh-Le MP et al. Nat Commun (2021)
Reported Trait: Prostate cancer in men with a family history of prostate cancer β: 1.11 Hazard ratio (HR, top 20% vs. bottom 20%): 2.22
PPM002489 PSS001118|
Ancestry Not Reported|
3,279 individuals
PGP000219 |
Huynh-Le MP et al. Prostate Cancer Prostatic Dis (2021)
|Ext.
Reported Trait: Prostate cancer mortality (age at death) HR: 3.41 [2.78, 4.17]
PPM002490 PSS001118|
Ancestry Not Reported|
3,279 individuals
PGP000219 |
Huynh-Le MP et al. Prostate Cancer Prostatic Dis (2021)
|Ext.
Reported Trait: Prostate cancer (age at diagnosis) HR: 5.35 [4.97, 5.76]
PPM002491 PSS001118|
Ancestry Not Reported|
3,279 individuals
PGP000219 |
Huynh-Le MP et al. Prostate Cancer Prostatic Dis (2021)
|Ext.
Reported Trait: Aggressive prostate cancer (age at diagnosis) HR: 3.78 [3.45, 4.13]
PPM002492 PSS001118|
Ancestry Not Reported|
3,279 individuals
PGP000219 |
Huynh-Le MP et al. Prostate Cancer Prostatic Dis (2021)
|Ext.
Reported Trait: Prostate cancer mortality (age at death) HR: 2.45 [1.99, 2.97]
β: 0.9
Family history of prostate cancer, alcohol intake, diabetes history

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
PSS000922 Cases numbers refer to 'any prostate cancer'. Of those, 1424 had aggressive prostate cancer (Gleason score ≥7, PSA ≥ 10 ng/mL, T3–T4 stage, nodal metastases, or distant metastases) and 18 had fatal prostate cancer. Death was determined by the investigators of each contributing study using cancer registries and/or medical records. Age shows the age of diagnosis. 5557 individuals had a family history of prostate cancer (≥1 first degree relative affected).
[
  • 3,240 cases
  • , 3,013 controls
]
,
100.0 % Male samples
Mean = 62.0 years
IQR = [56.0, 68.0] years
African unspecified, NR 60 cohorts
  • AHS
  • ,ATBC
  • ,Aarhus
  • ,BioVu
  • ,CCI
  • ,CHIPGECS
  • ,COH
  • ,CONOR
  • ,COSM
  • ,CPCS
  • ,CPDR
  • ,CeRePP
  • ,EPIC
  • ,EPICAP
  • ,ERSPC
  • ,ESTHER
  • ,FHCRC
  • ,Gene-PARE
  • ,HPFS
  • ,IMPACT
  • ,IPO-Porto
  • ,KARUPROSTATE
  • ,KULEUVEN
  • ,LAAPC
  • ,MCC-Spain
  • ,MCCS
  • ,MDACCS
  • ,MEC
  • ,MOFFITT
  • ,NMHS
  • ,PASS
  • ,PCMUS
  • ,PCPT
  • ,PCaP
  • ,PHS
  • ,PLCO
  • ,PRAGGA
  • ,PROCAP
  • ,PROFILE
  • ,PROGReSS_PrCa
  • ,PROtEuS
  • ,ProMPT
  • ,ProtecT
  • ,QLD
  • ,RAPPER
  • ,SABOR
  • ,SCCS
  • ,SCPCS
  • ,SEARCH
  • ,SELECT
  • ,SFPCS
  • ,SNP_Prostate_Ghent
  • ,SPAG
  • ,STHLM2
  • ,TAMPERE
  • ,Toronto
  • ,UKGPCS
  • ,ULM
  • ,WFPCS
  • ,WUGS
PSS000923 Cases numbers refer to 'any prostate cancer'. Of those, 716 had aggressive prostate cancer (Gleason score ≥7, PSA ≥ 10 ng/mL, T3–T4 stage, nodal metastases, or distant metastases) and 57 had fatal prostate cancer. Death was determined by the investigators of each contributing study using cancer registries and/or medical records. Age shows the age of diagnosis. 1028 individuals had a family history of prostate cancer (≥1 first degree relative affected).
[
  • 1,197 cases
  • , 1,185 controls
]
,
100.0 % Male samples
Mean = 68.0 years
IQR = [62.0, 74.0] years
Asian unspecified, NR 60 cohorts
  • AHS
  • ,ATBC
  • ,Aarhus
  • ,BioVu
  • ,CCI
  • ,CHIPGECS
  • ,COH
  • ,CONOR
  • ,COSM
  • ,CPCS
  • ,CPDR
  • ,CeRePP
  • ,EPIC
  • ,EPICAP
  • ,ERSPC
  • ,ESTHER
  • ,FHCRC
  • ,Gene-PARE
  • ,HPFS
  • ,IMPACT
  • ,IPO-Porto
  • ,KARUPROSTATE
  • ,KULEUVEN
  • ,LAAPC
  • ,MCC-Spain
  • ,MCCS
  • ,MDACCS
  • ,MEC
  • ,MOFFITT
  • ,NMHS
  • ,PASS
  • ,PCMUS
  • ,PCPT
  • ,PCaP
  • ,PHS
  • ,PLCO
  • ,PRAGGA
  • ,PROCAP
  • ,PROFILE
  • ,PROGReSS_PrCa
  • ,PROtEuS
  • ,ProMPT
  • ,ProtecT
  • ,QLD
  • ,RAPPER
  • ,SABOR
  • ,SCCS
  • ,SCPCS
  • ,SEARCH
  • ,SELECT
  • ,SFPCS
  • ,SNP_Prostate_Ghent
  • ,SPAG
  • ,STHLM2
  • ,TAMPERE
  • ,Toronto
  • ,UKGPCS
  • ,ULM
  • ,WFPCS
  • ,WUGS
PSS000924 Cases numbers refer to 'any prostate cancer'. Of those, 24279 had aggressive prostate cancer (Gleason score ≥7, PSA ≥ 10 ng/mL, T3–T4 stage, nodal metastases, or distant metastases) and 3908 had fatal prostate cancer. Death was determined by the investigators of each contributing study using cancer registries and/or medical records. Age shows the age of diagnosis. 39,445 individuals had a family history of prostate cancer (≥1 first degree relative affected).
[
  • 45,479 cases
  • , 26,377 controls
]
,
100.0 % Male samples
Mean = 66.0 years
IQR = [60.0, 71.0] years
European, NR 60 cohorts
  • AHS
  • ,ATBC
  • ,Aarhus
  • ,BioVu
  • ,CCI
  • ,CHIPGECS
  • ,COH
  • ,CONOR
  • ,COSM
  • ,CPCS
  • ,CPDR
  • ,CeRePP
  • ,EPIC
  • ,EPICAP
  • ,ERSPC
  • ,ESTHER
  • ,FHCRC
  • ,Gene-PARE
  • ,HPFS
  • ,IMPACT
  • ,IPO-Porto
  • ,KARUPROSTATE
  • ,KULEUVEN
  • ,LAAPC
  • ,MCC-Spain
  • ,MCCS
  • ,MDACCS
  • ,MEC
  • ,MOFFITT
  • ,NMHS
  • ,PASS
  • ,PCMUS
  • ,PCPT
  • ,PCaP
  • ,PHS
  • ,PLCO
  • ,PRAGGA
  • ,PROCAP
  • ,PROFILE
  • ,PROGReSS_PrCa
  • ,PROtEuS
  • ,ProMPT
  • ,ProtecT
  • ,QLD
  • ,RAPPER
  • ,SABOR
  • ,SCCS
  • ,SCPCS
  • ,SEARCH
  • ,SELECT
  • ,SFPCS
  • ,SNP_Prostate_Ghent
  • ,SPAG
  • ,STHLM2
  • ,TAMPERE
  • ,Toronto
  • ,UKGPCS
  • ,ULM
  • ,WFPCS
  • ,WUGS
PSS000925 Cases numbers refer to 'any prostate cancer'. Of those, 24279 had aggressive prostate cancer (Gleason score ≥7, PSA ≥ 10 ng/mL, T3–T4 stage, nodal metastases, or distant metastases) and 3908 had fatal prostate cancer. Death was determined by the investigators of each contributing study using cancer registries and/or medical records. Age shows the age of diagnosis.
[
  • 45,479 cases
  • , 26,377 controls
]
,
100.0 % Male samples
Mean = 66.0 years
IQR = [60.0, 71.0] years
European, NR 60 cohorts
  • AHS
  • ,ATBC
  • ,Aarhus
  • ,BioVu
  • ,CCI
  • ,CHIPGECS
  • ,COH
  • ,CONOR
  • ,COSM
  • ,CPCS
  • ,CPDR
  • ,CeRePP
  • ,EPIC
  • ,EPICAP
  • ,ERSPC
  • ,ESTHER
  • ,FHCRC
  • ,Gene-PARE
  • ,HPFS
  • ,IMPACT
  • ,IPO-Porto
  • ,KARUPROSTATE
  • ,KULEUVEN
  • ,LAAPC
  • ,MCC-Spain
  • ,MCCS
  • ,MDACCS
  • ,MEC
  • ,MOFFITT
  • ,NMHS
  • ,PASS
  • ,PCMUS
  • ,PCPT
  • ,PCaP
  • ,PHS
  • ,PLCO
  • ,PRAGGA
  • ,PROCAP
  • ,PROFILE
  • ,PROGReSS_PrCa
  • ,PROtEuS
  • ,ProMPT
  • ,ProtecT
  • ,QLD
  • ,RAPPER
  • ,SABOR
  • ,SCCS
  • ,SCPCS
  • ,SEARCH
  • ,SELECT
  • ,SFPCS
  • ,SNP_Prostate_Ghent
  • ,SPAG
  • ,STHLM2
  • ,TAMPERE
  • ,Toronto
  • ,UKGPCS
  • ,ULM
  • ,WFPCS
  • ,WUGS
PSS000925 Cases numbers refer to 'any prostate cancer'. Of those, 716 had aggressive prostate cancer (Gleason score ≥7, PSA ≥ 10 ng/mL, T3–T4 stage, nodal metastases, or distant metastases) and 57 had fatal prostate cancer. Death was determined by the investigators of each contributing study using cancer registries and/or medical records. Age shows the age of diagnosis.
[
  • 1,197 cases
  • , 1,185 controls
]
,
100.0 % Male samples
Mean = 68.0 years
IQR = [62.0, 74.0] years
Asian unspecified, NR 60 cohorts
  • AHS
  • ,ATBC
  • ,Aarhus
  • ,BioVu
  • ,CCI
  • ,CHIPGECS
  • ,COH
  • ,CONOR
  • ,COSM
  • ,CPCS
  • ,CPDR
  • ,CeRePP
  • ,EPIC
  • ,EPICAP
  • ,ERSPC
  • ,ESTHER
  • ,FHCRC
  • ,Gene-PARE
  • ,HPFS
  • ,IMPACT
  • ,IPO-Porto
  • ,KARUPROSTATE
  • ,KULEUVEN
  • ,LAAPC
  • ,MCC-Spain
  • ,MCCS
  • ,MDACCS
  • ,MEC
  • ,MOFFITT
  • ,NMHS
  • ,PASS
  • ,PCMUS
  • ,PCPT
  • ,PCaP
  • ,PHS
  • ,PLCO
  • ,PRAGGA
  • ,PROCAP
  • ,PROFILE
  • ,PROGReSS_PrCa
  • ,PROtEuS
  • ,ProMPT
  • ,ProtecT
  • ,QLD
  • ,RAPPER
  • ,SABOR
  • ,SCCS
  • ,SCPCS
  • ,SEARCH
  • ,SELECT
  • ,SFPCS
  • ,SNP_Prostate_Ghent
  • ,SPAG
  • ,STHLM2
  • ,TAMPERE
  • ,Toronto
  • ,UKGPCS
  • ,ULM
  • ,WFPCS
  • ,WUGS
PSS000925 Cases numbers refer to 'any prostate cancer'. Of those, 1424 had aggressive prostate cancer (Gleason score ≥7, PSA ≥ 10 ng/mL, T3–T4 stage, nodal metastases, or distant metastases) and 18 had fatal prostate cancer. Death was determined by the investigators of each contributing study using cancer registries and/or medical records. Age shows the age of diagnosis.
[
  • 3,240 cases
  • , 3,013 controls
]
,
100.0 % Male samples
Mean = 62.0 years
IQR = [56.0, 68.0] years
African unspecified, NR 60 cohorts
  • AHS
  • ,ATBC
  • ,Aarhus
  • ,BioVu
  • ,CCI
  • ,CHIPGECS
  • ,COH
  • ,CONOR
  • ,COSM
  • ,CPCS
  • ,CPDR
  • ,CeRePP
  • ,EPIC
  • ,EPICAP
  • ,ERSPC
  • ,ESTHER
  • ,FHCRC
  • ,Gene-PARE
  • ,HPFS
  • ,IMPACT
  • ,IPO-Porto
  • ,KARUPROSTATE
  • ,KULEUVEN
  • ,LAAPC
  • ,MCC-Spain
  • ,MCCS
  • ,MDACCS
  • ,MEC
  • ,MOFFITT
  • ,NMHS
  • ,PASS
  • ,PCMUS
  • ,PCPT
  • ,PCaP
  • ,PHS
  • ,PLCO
  • ,PRAGGA
  • ,PROCAP
  • ,PROFILE
  • ,PROGReSS_PrCa
  • ,PROtEuS
  • ,ProMPT
  • ,ProtecT
  • ,QLD
  • ,RAPPER
  • ,SABOR
  • ,SCCS
  • ,SCPCS
  • ,SEARCH
  • ,SELECT
  • ,SFPCS
  • ,SNP_Prostate_Ghent
  • ,SPAG
  • ,STHLM2
  • ,TAMPERE
  • ,Toronto
  • ,UKGPCS
  • ,ULM
  • ,WFPCS
  • ,WUGS
PSS001118 Cases are individuals with prostate cancer. Of the 2163 cases, 1403 are aggressive prostate cancer cases defined as disease typically requiring treatment: Gleason score ≥7, clinical stage T3-T4, PSA concentration ≥10 ng/mL, or nodal/distant metastasis. 278 prostate cancer cases were fatal.
[
  • 2,163 cases
  • , 1,116 controls
]
,
100.0 % Male samples
Median = 78.0 years
IQR = [72.3, 84.1] years
Not reported COSM Sample overlap exists between this dataset and the dataset used to develop/train Karunamuni et al's PGS (PGS000741)