Polygenic Score (PGS) ID: PGS000067

Predicted Trait
Reported Trait Prostate cancer
Mapped Trait(s) prostate carcinoma (EFO_0001663)
Released in PGS Catalog: Feb. 12, 2020
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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 PCa_PHS
Development Method
Name Polygenic Hazard Score
Parameters Trend test p-value < 1e-6; selection of SNPs by logistic regresssion; SNP weights determined by C... ox proportional hazards regressionShow more
Variants
Original Genome Build GRCh37
Number of Variants 54
Effect Weight Type log(HR)
PGS Source
PGS Catalog Publication (PGP) ID PGP000047
Citation (link to publication) Seibert TM et al. BMJ (2018)
Ancestry Distribution
Score Development/Training
European: 100%
31,747 individuals (100%)
PGS Evaluation
European: 50%
African: 20%
Multi-ancestry (including European): 20%
  • European
  • East Asian
  • African
  • Additional Diverse Ancestries
  • Hispanic or Latin American
  • South Asian
  • Not Reported
Additional Asian Ancestries: 10%
10 Sample Sets

Development Samples

Score Development/Training
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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
Europe PMC: 23535732
[
  • 18,868 cases
  • , 12,879 controls
]
,
100.0 % Male samples
EuropeanNRCase numbers refer to "any prostate cancer (PCa)"; of those cases 10 635 have aggressive PCa, and 54... 06 have very aggressive PCa (Gleason score ≥7, stage T3-T4, PSA concentration ≥10 ng/mL, nodal metastasis, or distant metastasis)Show morePRACTICAL consortium
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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.

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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
PPM000182PSS000105|
European Ancestry|
5,456 individuals
PGP000047 |
Seibert TM et al. BMJ (2018)
Reported Trait: aggressive prostate cancerHR (Hazard ratio; top 2% vs. average risk): 2.9 [2.4, 3.4]
PPM000183PSS000105|
European Ancestry|
5,456 individuals
PGP000047 |
Seibert TM et al. BMJ (2018)
Reported Trait: aggressive prostate cancer (age at onset)z-test (p-value) <: 1.00e-16
PPM000184PSS000106|
European Ancestry|
6,411 individuals
PGP000047 |
Seibert TM et al. BMJ (2018)
Reported Trait: any prostate cancerHR (Hazard ratio; top 2% vs. average risk): 2.5 [2.2, 2.8]
PPM000185PSS000106|
European Ancestry|
6,411 individuals
PGP000047 |
Seibert TM et al. BMJ (2018)
Reported Trait: any prostate cancer (age at onset)z-test (p-value) <: 1.00e-16
PPM000186PSS000107|
European Ancestry|
5,048 individuals
PGP000047 |
Seibert TM et al. BMJ (2018)
Reported Trait: very aggressive prostate cancerHR (Hazard ratio; top 2% vs. average risk): 3.0 [2.2, 4.0]
PPM000187PSS000107|
European Ancestry|
5,048 individuals
PGP000047 |
Seibert TM et al. BMJ (2018)
Reported Trait: very aggressive prostate cancer (age at onset)z-test (p-value) <: 1.00e-16
PPM000390PSS000220|
Multi-ancestry (including European)|
56,994 individuals
PGP000058 |
Huynh-Le MP et al. Nat Commun (2021)
|Ext.
Reported Trait: Age of aggressive prostate cancer onsetHazard Ratio (HR; top 20% vs. rest): 5.9 [5.5, 6.3]Association between PHS and age-at-onset p-value < 10e-16. Only SNPs directly genotyped on the On... coArray genotyping array were considered. 46 of the score's 54 SNPs were used: 24 directly genotyped, and 22 with acceptable proxies (r2>0.94).Show more
PPM000391PSS000223|
European Ancestry|
50,656 individuals
PGP000058 |
Huynh-Le MP et al. Nat Commun (2021)
|Ext.
Reported Trait: Age of aggressive prostate cancer onsetHazard Ratio (HR; top 20% vs. rest): 5.6 [5.2, 6.0]Association between PHS and age-at-onset p-value < 10e-16. Only SNPs directly genotyped on the On... coArray genotyping array were considered. 46 of the score's 54 SNPs were used: 24 directly genotyped, and 22 with acceptable proxies (r2>0.94).Show more
PPM000392PSS000222|
Additional Asian Ancestries|
1,901 individuals
PGP000058 |
Huynh-Le MP et al. Nat Commun (2021)
|Ext.
Reported Trait: Age of aggressive prostate cancer onsetHazard Ratio (HR; top 20% vs. rest): 5.2 [4.8, 5.6]Association between PHS and age-at-onset p-value < 10e-16. Only SNPs directly genotyped on the On... coArray genotyping array were considered. 46 of the score's 54 SNPs were used: 24 directly genotyped, and 22 with acceptable proxies (r2>0.94).Show more
PPM000393PSS000221|
African Ancestry|
4,437 individuals
PGP000058 |
Huynh-Le MP et al. Nat Commun (2021)
|Ext.
Reported Trait: Age of aggressive prostate cancer onsetHazard Ratio (HR; top 20% vs. rest): 2.4 [2.3, 2.6]Association between PHS and age-at-onset p-value < 10e-16. Only SNPs directly genotyped on the On... coArray genotyping array were considered. 46 of the score's 54 SNPs were used: 24 directly genotyped, and 22 with acceptable proxies (r2>0.94).Show more
PPM000394PSS000224|
Multi-ancestry (including European)|
34,558 individuals
PGP000058 |
Huynh-Le MP et al. Nat Commun (2021)
|Ext.
Reported Trait: Age of prostate cancer deathHazard Ratio (HR; top 20% vs. rest): 5.7 [4.6, 7.0]Association between PHS and age-at-onset p-value < 10e-16. Only SNPs directly genotyped on the On... coArray genotyping array were considered. 46 of the score's 54 SNPs were used: 24 directly genotyped, and 22 with acceptable proxies (r2>0.94).Show more
PPM001673PSS000874|
African Ancestry|
6,271 individuals
PGP000139 |
Karunamuni RA et al. Int J Cancer (2020)
|Ext.
Reported Trait: Age at diagnosis of any prostate cancerHazard Ratio (HR top 20% vs. bottom 20%): 2.47 [2.32, 2.62]46 of the score's 54 SNPs were used: 24 directly genotyped, and 22 with acceptable proxies (r2>0.... 94).Show more
PPM001675PSS000874|
African Ancestry|
6,271 individuals
PGP000139 |
Karunamuni RA et al. Int J Cancer (2020)
|Ext.
Reported Trait: Age at diagnosis of any prostate cancerHazard Ratio (HR top 2% vs. middle 40%): 2.1 [1.99, 2.21]46 of the score's 54 SNPs were used: 24 directly genotyped, and 22 with acceptable proxies (r2>0.... 94).Show more
PPM001677PSS000874|
African Ancestry|
6,271 individuals
PGP000139 |
Karunamuni RA et al. Int J Cancer (2020)
|Ext.
Reported Trait: Age at diagnosis of any prostate cancerHazard Ratio (HR bottom 20% vs. middle 40%): 0.65 [0.63, 0.67]46 of the score's 54 SNPs were used: 24 directly genotyped, and 22 with acceptable proxies (r2>0.... 94).Show more
PPM001679PSS000874|
African Ancestry|
6,271 individuals
PGP000139 |
Karunamuni RA et al. Int J Cancer (2020)
|Ext.
Reported Trait: Age at diagnosis of clinically significant prostate cancerHazard Ratio (HR top 20% vs. bottom 20%): 2.21 [2.04, 2.38]46 of the score's 54 SNPs were used: 24 directly genotyped, and 22 with acceptable proxies (r2>0.... 94).Show more
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Evaluated Samples

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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
PSS000105Men screened with PSA testing, who did not receive a diagnosis of prostate cancer.4,828 individuals,
100.0 % Male samples
Mean = 59.0 years
IQR = [55.0, 63.0] years
EuropeanProtecT
PSS000105Men screened with PSA testing (3.0 ng/L or higher), who received a diagnosis of aggressive prostate ... cancer (defined as any of Gleason score ≥7, stage T3-T4, PSA concentration ≥10 ng/mL, nodal metastasis, or distant metastasis)Show more
[
  • 628 cases
]
,
100.0 % Male samples
Mean = 64.3 years
IQR = [60.2, 67.5] years
EuropeanProtecT
PSS000106Men screened with PSA testing, who did not receive a diagnosis of prostate cancer.4,828 individuals,
100.0 % Male samples
Mean = 59.0 years
IQR = [55.0, 63.0] years
EuropeanProtecT
PSS000106Men screened with PSA testing (3.0 ng/L or higher), who received a diagnosis of prostate cancer.
[
  • 1,583 cases
]
,
100.0 % Male samples
Mean = 63.4 years
IQR = [59.0, 67.5] years
EuropeanProtecT
PSS000107Men screened with PSA testing, who did not receive a diagnosis of prostate cancer.4,828 individuals,
100.0 % Male samples
Mean = 59.0 years
IQR = [55.0, 63.0] years
EuropeanProtecT
PSS000107Men screened with PSA testing (3.0 ng/L or higher), who received a diagnosis of very aggressive pro... state cancer (defined as any of Gleason score ≥8, stage T3-4, positive nodes, or distant metastases)Show more
[
  • 220 cases
]
,
100.0 % Male samples
EuropeanProtecT
PSS000220Age of onset of aggressive prostate cancer, defined by Gleason score ≥7, PSA ≥10 ng/mL, T3-T4 stage,...  nodal metastases, or distant metastasesShow more
[
  • 26,419 cases
  • , 30,575 controls
]
,
100.0 % Male samples
European, East Asian, African American or Afro-Caribbean, Oceanian, Hispanic or Latin American, South Asian, African unspecified, NRCombined analysis of multiple ancestries, including: European, East Asian, African American, Hawaiian, Hispanic American, South Asian, Black African, Black Caribbean, and Other (not specified)OncoArray_ProstateList of Cohorts available from dbGaP: https://www.ncbi.nlm.nih.gov/projects/gap/cgi-bin/study.cgi?st... udy_id=phs001391.v1.p1Show more
PSS000221Age of onset of aggressive prostate cancer, defined by Gleason score ≥7, PSA ≥10 ng/mL, T3-T4 stage,...  nodal metastases, or distant metastasesShow more
[
  • 1,424 cases
  • , 3,013 controls
]
,
100.0 % Male samples
African unspecifiedSubset of OncoArray_APC_onset samples. Determined from genetic PCs via FastPopOncoArray_ProstateList of Cohorts available from dbGaP: https://www.ncbi.nlm.nih.gov/projects/gap/cgi-bin/study.cgi?st... udy_id=phs001391.v1.p1Show more
PSS000222Age of onset of aggressive prostate cancer, defined by Gleason score ≥7, PSA ≥10 ng/mL, T3-T4 stage,...  nodal metastases, or distant metastasesShow more
[
  • 716 cases
  • , 1,185 controls
]
,
100.0 % Male samples
Asian unspecifiedSubset of OncoArray_APC_onset samples. Determined from genetic PCs via FastPopOncoArray_ProstateList of Cohorts available from dbGaP: https://www.ncbi.nlm.nih.gov/projects/gap/cgi-bin/study.cgi?st... udy_id=phs001391.v1.p1Show more
PSS000223Age of onset of aggressive prostate cancer, defined by Gleason score ≥7, PSA ≥10 ng/mL, T3-T4 stage,...  nodal metastases, or distant metastasesShow more
[
  • 24,279 cases
  • , 26,377 controls
]
,
100.0 % Male samples
EuropeanSubset of OncoArray_APC_onset samples. Determined from genetic PCs via FastPopOncoArray_ProstateList of Cohorts available from dbGaP: https://www.ncbi.nlm.nih.gov/projects/gap/cgi-bin/study.cgi?st... udy_id=phs001391.v1.p1Show more
PSS000224Age at death due to prostate cancer.
[
  • 3,983 cases
  • , 30,575 controls
]
,
100.0 % Male samples
Mean = 70.0 years
IQR = [63.0, 76.0] years
European, East Asian, African American or Afro-Caribbean, Oceanian, Hispanic or Latin American, South Asian, African unspecified, NRCombined analysis of multiple ancestries, including: European, East Asian, African American, Hawaiian, Hispanic American, South Asian, Black African, Black Caribbean, and Other (not specified)OncoArray_ProstateList of Cohorts available from dbGaP: https://www.ncbi.nlm.nih.gov/projects/gap/cgi-bin/study.cgi?st... udy_id=phs001391.v1.p1Show more
PSS000874Clinically significant cancer were any of: Gleason score ≥ 7, stage T3-T4, PSA concentration ≥ 10 ng... /mL, pelvic lymph nodal metastasis or distant metastasis.Show more
[
  • 3,031 cases
  • , 3,240 controls
]
,
100.0 % Male samples
African unspecified18 cohorts
  • BioVU
  • ,CPDR
  • ,CeRePP
  • ,EPICAP
  • ,KARUPROSTATE
  • ,MIAMI-WFPCS
  • ,MOFFITT
  • ,NMHS
  • ,PCPT
  • ,PCaP
  • ,PROtEuS
  • ,SABOR
  • ,SCCS
  • ,SCPCS
  • ,SELECT
  • ,SFPCS
  • ,UKGPCS
  • ,WUGS
PRACTICAL consortium
PSS000926Cases included individuals with any type of prostate cancer (PCa). For any clinically significant PC... a, 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.Show more
[
  • 1,583 cases
  • , 4,828 controls
]
,
100.0 % Male samples
EuropeanProtecT, UKGPCS
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