Predicted Trait | |
Reported Trait | Prostate cancer |
Mapped Trait(s) | prostate carcinoma (EFO_0001663) |
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 |
Study Identifiers
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Sample Numbers
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Sample Ancestry
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Cohort(s)
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Phenotype Definitions & Methods
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Age of Study Participants
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Participant Follow-up Time
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Additional Ancestry Description
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Additional Sample/Cohort Information
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Europe PMC: 23535732 | [ ,
100.0 % Male samples | European | NR | Case 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 more | — | — | — | PRACTICAL consortium |
PGS Performance Metric ID (PPM) |
PGS Sample Set ID (PSS) |
Performance Source
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Trait
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PGS Effect Sizes (per SD change) |
Classification Metrics
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Other Metrics
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Covariates Included in the Model
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PGS Performance: Other Relevant Information |
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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] | — | — |
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 | — | — |
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] | — | — |
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 | — | — |
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] | — | — |
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 | — | — |
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 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 |
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 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 |
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 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 |
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 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 |
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 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 |
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).Show more |
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).Show more |
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).Show more |
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).Show more |
PGS Sample Set ID (PSS) |
Phenotype Definitions and Methods
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Participant Follow-up Time
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Sample Numbers
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Age of Study Participants
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Sample Ancestry
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Additional Ancestry Description
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Cohort(s)
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Additional Sample/Cohort Information
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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)Show more | — | [ ,
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. | — | [ ,
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 pro... state cancer (defined as any of Gleason score ≥8, stage T3-4, positive nodes, or distant metastases)Show more | — | [ ,
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 metastasesShow more | — | [ ,
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?st... udy_id=phs001391.v1.p1Show more |
PSS000221 | Age of onset of aggressive prostate cancer, defined by Gleason score ≥7, PSA ≥10 ng/mL, T3-T4 stage,... nodal metastases, or distant metastasesShow more | — | [ ,
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?st... udy_id=phs001391.v1.p1Show more |
PSS000222 | Age of onset of aggressive prostate cancer, defined by Gleason score ≥7, PSA ≥10 ng/mL, T3-T4 stage,... nodal metastases, or distant metastasesShow more | — | [ ,
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?st... udy_id=phs001391.v1.p1Show more |
PSS000223 | Age of onset of aggressive prostate cancer, defined by Gleason score ≥7, PSA ≥10 ng/mL, T3-T4 stage,... nodal metastases, or distant metastasesShow more | — | [ ,
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?st... udy_id=phs001391.v1.p1Show more |
PSS000224 | Age at death due to prostate cancer. | — | [ ,
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?st... udy_id=phs001391.v1.p1Show more |
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.Show more | — | [ ,
100.0 % Male samples | — | African unspecified | — | 18 cohorts
| PRACTICAL consortium |
PSS000926 | Cases 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 | — | [ ,
100.0 % Male samples | — | European | — | ProtecT, UKGPCS | — |