Polygenic Score (PGS) ID: PGS000067

Predicted Trait
Reported Trait Prostate cancer
Mapped Trait(s) prostate carcinoma (EFO_0001663)
Released in PGS: Feb. 12, 2020

Score Details

Score Construction
PGS Name PCa_PHS
Variants
Original Genome Build NR
Number of Variants 54
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
PGS Source
PGS Catalog Publication (PGP) ID PGP000047
Citation (link to publication) Seibert TM et al. BMJ (2018)

Contributing Samples

Score Development/Training
Detailed Phenotype Description Participant Follow-up Time Sample Numbers Age of Study Participants Sample Ancestry Additional Ancestry Description Cohort(s) Additional Sample/Cohort Information
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 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 ID)
PGS Sample Set ID
(PSS ID)
Performance Source Trait PGS Effect Sizes
(per SD change)
PGS Classification Metrics Other Metrics Covariates Included in the Model PGS Performance: Other Relevant Information
PPM000183 PSS000105 PGP000047
Seibert TM et al. (2018)
Reported Trait: aggressive prostate cancer (age at onset) z-test (p-value) < 1e-16
PPM000182 PSS000105 PGP000047
Seibert TM et al. (2018)
Reported Trait: aggressive prostate cancer HR (Hazard ratio; top 2% vs. average risk): 2.9[2.4, 3.4]
PPM000184 PSS000106 PGP000047
Seibert TM et al. (2018)
Reported Trait: any prostate cancer HR (Hazard ratio; top 2% vs. average risk): 2.5[2.2, 2.8]
PPM000185 PSS000106 PGP000047
Seibert TM et al. (2018)
Reported Trait: any prostate cancer (age at onset) z-test (p-value) < 1e-16
PPM000187 PSS000107 PGP000047
Seibert TM et al. (2018)
Reported Trait: very aggressive prostate cancer (age at onset) z-test (p-value) < 1e-11
PPM000393 PSS000221 PGP000058
Huynh-Le M et al. (2019)
Ext. Pre
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 PGP000058
Huynh-Le M et al. (2019)
Ext. Pre
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 PGP000058
Huynh-Le M et al. (2019)
Ext. Pre
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 PGP000058
Huynh-Le M et al. (2019)
Ext. Pre
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).
PPM000394 PSS000224 PGP000058
Huynh-Le M et al. (2019)
Ext. Pre
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).
PPM000186 PSS000107 PGP000047
Seibert TM et al. (2018)
Reported Trait: very aggressive prostate cancer HR (Hazard ratio; top 2% vs. average risk): 3.0[2.2, 4.0]

Evaluated Samples

PGS Sample Set ID
(PSS ID)
Detailed Phenotype Description 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
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
]
,
1.0 % Male samples
Other 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
]
,
1.0 % 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
]
,
1.0 % 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
]
,
1.0 % 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
]
,
1.0 % Male samples
Mean = 70.0 years
Iqr = [63.0, 76.0] years
Other 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