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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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 Cox proportional hazards regression
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
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
 European NR 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) — — — 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
PPM000182 PSS000105|
European Ancestry|
5,456 individuals
 PGP000047 |
Seibert TM et al. BMJ (2018)
 Reported Trait: aggressive prostate cancer — — HR (Hazard ratio; top 2% vs. average risk): 2.9 [2.4, 3.4] — —
PPM000184 PSS000106|
European Ancestry|
6,411 individuals
 PGP000047 |
Seibert TM et al. BMJ (2018)
 Reported Trait: any prostate cancer — — HR (Hazard ratio; top 2% vs. average risk): 2.5 [2.2, 2.8] — —
PPM001675 PSS000874|
African Ancestry|
6,271 individuals
 PGP000139 |
Karunamuni RA et al. Int J Cancer (2020)
|Ext.		 Reported Trait: Age at diagnosis of any prostate cancer — — Hazard 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).
PPM001677 PSS000874|
African Ancestry|
6,271 individuals
 PGP000139 |
Karunamuni RA et al. Int J Cancer (2020)
|Ext.		 Reported Trait: Age at diagnosis of any prostate cancer — — Hazard 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).
PPM000393 PSS000221|
African Ancestry|
4,437 individuals
 PGP000058 |
Huynh-Le MP et al. Nat Commun (2021)
|Ext.		 Reported Trait: Age of aggressive prostate cancer onset — — Hazard 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 OncoArray genotyping array were considered. 46 of the score's 54 SNPs were used: 24 directly genotyped, and 22 with acceptable proxies (r2>0.94).
PPM000392 PSS000222|
Additional Asian Ancestries|
1,901 individuals
 PGP000058 |
Huynh-Le MP et al. Nat Commun (2021)
|Ext.		 Reported Trait: Age of aggressive prostate cancer onset — — Hazard 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 OncoArray genotyping array were considered. 46 of the score's 54 SNPs were used: 24 directly genotyped, and 22 with acceptable proxies (r2>0.94).
PPM000391 PSS000223|
European Ancestry|
50,656 individuals
 PGP000058 |
Huynh-Le MP et al. Nat Commun (2021)
|Ext.		 Reported Trait: Age of aggressive prostate cancer onset — — Hazard 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 OncoArray genotyping array were considered. 46 of the score's 54 SNPs were used: 24 directly genotyped, and 22 with acceptable proxies (r2>0.94).
PPM000390 PSS000220|
Multi-ancestry (including European)|
56,994 individuals
 PGP000058 |
Huynh-Le MP et al. Nat Commun (2021)
|Ext.		 Reported Trait: Age of aggressive prostate cancer onset — — Hazard 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 OncoArray genotyping array were considered. 46 of the score's 54 SNPs were used: 24 directly genotyped, and 22 with acceptable proxies (r2>0.94).
PPM001679 PSS000874|
African Ancestry|
6,271 individuals
 PGP000139 |
Karunamuni RA et al. Int J Cancer (2020)
|Ext.		 Reported Trait: Age at diagnosis of clinically significant prostate cancer — — Hazard 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).
PPM000394 PSS000224|
Multi-ancestry (including European)|
34,558 individuals
 PGP000058 |
Huynh-Le MP et al. Nat Commun (2021)
|Ext.		 Reported Trait: Age of prostate cancer death — — Hazard 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 OncoArray genotyping array were considered. 46 of the score's 54 SNPs were used: 24 directly genotyped, and 22 with acceptable proxies (r2>0.94).
PPM001683 PSS000874|
African Ancestry|
6,271 individuals
 PGP000139 |
Karunamuni RA et al. Int J Cancer (2020)
|Ext.		 Reported Trait: Age at diagnosis of clinically significant prostate cancer — — Hazard Ratio (bottom 20% vs. middle 40%): 0.7 [0.68, 0.73] — 46 of the score's 54 SNPs were used: 24 directly genotyped, and 22 with acceptable proxies (r2>0.94).
PPM001681 PSS000874|
African Ancestry|
6,271 individuals
 PGP000139 |
Karunamuni RA et al. Int J Cancer (2020)
|Ext.		 Reported Trait: Age at diagnosis of clinically significant prostate cancer — — Hazard Ratio (top 2% vs. middle 40%): 1.91 [1.79, 2.04] — 46 of the score's 54 SNPs were used: 24 directly genotyped, and 22 with acceptable proxies (r2>0.94).
PPM000186 PSS000107|
European Ancestry|
5,048 individuals
 PGP000047 |
Seibert TM et al. BMJ (2018)
 Reported Trait: very aggressive prostate cancer — — HR (Hazard ratio; top 2% vs. average risk): 3.0 [2.2, 4.0] — —
PPM001673 PSS000874|
African Ancestry|
6,271 individuals
 PGP000139 |
Karunamuni RA et al. Int J Cancer (2020)
|Ext.		 Reported Trait: Age at diagnosis of any prostate cancer — — Hazard 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).
PPM001812 PSS000926|
European Ancestry|
6,411 individuals
 PGP000150 |
Karunamuni RA et al. Prostate Cancer Prostatic Dis (2021)
|Ext.		 Reported Trait: Prostate cancer (age of onset) — — Hazard Ratio (HR, top 20% vs. bottom 20%): 5.15 [3.29, 6.18] — Only 46 out of the 54 variants were used from Seibert et al's polygenic risk score (PGS000067)
PPM001813 PSS000926|
European Ancestry|
6,411 individuals
 PGP000150 |
Karunamuni RA et al. Prostate Cancer Prostatic Dis (2021)
|Ext.		 Reported Trait: Prostate cancer (age of onset) — — Hazard Ratio (HR, bottom 20% vs. middle 40%): 0.44 [0.4, 0.49] — Only 46 out of the 54 variants were used from Seibert et al's polygenic risk score (PGS000067)
PPM001817 PSS000926|
European Ancestry|
6,411 individuals
 PGP000150 |
Karunamuni RA et al. Prostate Cancer Prostatic Dis (2021)
|Ext.		 Reported Trait: Clinically significant prostate cancer (age at onset) — — Hazard Ratio (HR, top 5% vs. middle 40%): 3.72 [2.89, 4.43] — Only 46 out of the 54 variants were utilised from Seibert et al's polygenic risk score (PGS000067)
PPM001818 PSS000926|
European Ancestry|
6,411 individuals
 PGP000150 |
Karunamuni RA et al. Prostate Cancer Prostatic Dis (2021)
|Ext.		 Reported Trait: Clinically significant prostate cancer (age at onset) — — Hazard Ratio (HR, top 20% vs. bottom 20%): 6.12 [4.18, 7.67] — Only 46 out of the 54 variants were utilised from Seibert et al's polygenic risk score (PGS000067)
PPM001819 PSS000926|
European Ancestry|
6,411 individuals
 PGP000150 |
Karunamuni RA et al. Prostate Cancer Prostatic Dis (2021)
|Ext.		 Reported Trait: Clinically significant prostate cancer (age at onset) — — Hazard Ratio (HR, bottom 20% vs. middle 40%): 0.41 [0.35, 0.47] — Only 46 out of the 54 variants were utilised from Seibert et al's polygenic risk score (PGS000067)
PPM001823 PSS000926|
European Ancestry|
6,411 individuals
 PGP000150 |
Karunamuni RA et al. Prostate Cancer Prostatic Dis (2021)
|Ext.		 Reported Trait: Non-clinically significant prostate cancer (age at onset) — — Hazard Ratio (HR, top 5% vs. middle 40%): 3.2 [2.59, 3.78] — Only 46 out of the 54 variants were utilised from Seibert et al's polygenic risk score (PGS000067)
PPM001824 PSS000926|
European Ancestry|
6,411 individuals
 PGP000150 |
Karunamuni RA et al. Prostate Cancer Prostatic Dis (2021)
|Ext.		 Reported Trait: Non-clinically significant prostate cancer (age at onset) — — Hazard Ratio (HR, top 20% vs. bottom 20%): 4.96 [3.61, 6.14] — Only 46 out of the 54 variants were utilised from Seibert et al's polygenic risk score (PGS000067)
PPM001825 PSS000926|
European Ancestry|
6,411 individuals
 PGP000150 |
Karunamuni RA et al. Prostate Cancer Prostatic Dis (2021)
|Ext.		 Reported Trait: Non-clinically significant prostate cancer (age at onset) — — Hazard Ratio (HR, bottom 20% vs. middle 40%): 0.45 [0.39, 0.5] — Only 46 out of the 54 variants were utilised from Seibert et al's polygenic risk score (PGS000067)
PPM001811 PSS000926|
European Ancestry|
6,411 individuals
 PGP000150 |
Karunamuni RA et al. Prostate Cancer Prostatic Dis (2021)
|Ext.		 Reported Trait: Prostate cancer (age of onset) — — Hazard Ratio (HR, top 5% vs. middle 40%): 3.29 [2.73, 3.77] — Only 46 out of the 54 variants were used from Seibert et al's polygenic risk score (PGS000067)
PPM000187 PSS000107|
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 — —
PPM000183 PSS000105|
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 — —
PPM000185 PSS000106|
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 — —

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
PSS000105 Men 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		 European — ProtecT —
PSS000105 Men 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) —
[
  • 628 cases
]
,
100.0 % Male samples
 Mean = 64.3 years
IQR = [60.2, 67.5] years		 European — ProtecT —
PSS000106 Men 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		 European — ProtecT —
PSS000106 Men 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		 European — ProtecT —
PSS000107 Men 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		 European — ProtecT —
PSS000107 Men screened with PSA testing (3.0 ng/L or higher), who received a diagnosis of very aggressive prostate cancer (defined as any of Gleason score ≥8, stage T3-4, positive nodes, or distant metastases) —
[
  • 220 cases
]
,
100.0 % Male samples
 — European — ProtecT —
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
  • ,PCPT
  • ,PCaP
  • ,PROtEuS
  • ,SABOR
  • ,SCCS
  • ,SCPCS
  • ,SELECT
  • ,SFPCS
  • ,UKGPCS
  • ,WUGS
 PRACTICAL consortium
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 —
PSS000220 Age of onset of aggressive prostate cancer, defined by Gleason score ≥7, PSA ≥10 ng/mL, T3-T4 stage, nodal metastases, or distant metastases —
[
  • 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, NR Combined analysis of multiple ancestries, including: European, East Asian, African American, Hawaiian, Hispanic American, South Asian, Black African, Black Caribbean, and Other (not specified) OncoArray_Prostate List of Cohorts available from dbGaP: https://www.ncbi.nlm.nih.gov/projects/gap/cgi-bin/study.cgi?study_id=phs001391.v1.p1
PSS000221 Age of onset of aggressive prostate cancer, defined by Gleason score ≥7, PSA ≥10 ng/mL, T3-T4 stage, nodal metastases, or distant metastases —
[
  • 1,424 cases
  • , 3,013 controls
]
,
100.0 % Male samples
 — African unspecified Subset of OncoArray_APC_onset samples. Determined from genetic PCs via FastPop OncoArray_Prostate List of Cohorts available from dbGaP: https://www.ncbi.nlm.nih.gov/projects/gap/cgi-bin/study.cgi?study_id=phs001391.v1.p1
PSS000222 Age of onset of aggressive prostate cancer, defined by Gleason score ≥7, PSA ≥10 ng/mL, T3-T4 stage, nodal metastases, or distant metastases —
[
  • 716 cases
  • , 1,185 controls
]
,
100.0 % Male samples
 — Asian unspecified Subset of OncoArray_APC_onset samples. Determined from genetic PCs via FastPop OncoArray_Prostate List of Cohorts available from dbGaP: https://www.ncbi.nlm.nih.gov/projects/gap/cgi-bin/study.cgi?study_id=phs001391.v1.p1
PSS000223 Age of onset of aggressive prostate cancer, defined by Gleason score ≥7, PSA ≥10 ng/mL, T3-T4 stage, nodal metastases, or distant metastases —
[
  • 24,279 cases
  • , 26,377 controls
]
,
100.0 % Male samples
 — European Subset of OncoArray_APC_onset samples. Determined from genetic PCs via FastPop OncoArray_Prostate List of Cohorts available from dbGaP: https://www.ncbi.nlm.nih.gov/projects/gap/cgi-bin/study.cgi?study_id=phs001391.v1.p1
PSS000224 Age 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, NR Combined analysis of multiple ancestries, including: European, East Asian, African American, Hawaiian, Hispanic American, South Asian, Black African, Black Caribbean, and Other (not specified) OncoArray_Prostate List of Cohorts available from dbGaP: https://www.ncbi.nlm.nih.gov/projects/gap/cgi-bin/study.cgi?study_id=phs001391.v1.p1