Polygenic Score (PGS) ID: PGS000662

Predicted Trait
Reported Trait Prostate cancer
Mapped Trait(s) prostate carcinoma (EFO_0001663)
Released in PGS Catalog: Jan. 7, 2021
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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 GRS.PCa.269
Development Method
Name Independent genome-wide significant variants identified by fine-mapping using JAM (Joint Analysis of Marginal summary statistics)
Parameters Population-specific betas were combined using an inverse Z-score-weighted fixed-effects meta-analysis to obtain multi-ancestry conditional betas.
Variants
Original Genome Build GRCh37
Number of Variants 269
Effect Weight Type beta
PGS Source
PGS Catalog Publication (PGP) ID PGP000122
Citation (link to publication) Conti DV et al. Nat Genet (2021)
Ancestry Distribution
Source of Variant
Associations (GWAS)
European: 75.8%
East Asian: 11.7%
African: 9.1%
Hispanic or Latin American: 3.4%
234,253 individuals (100%)
PGS Evaluation
European: 47.1%
Multi-ancestry (including European): 29.4%
  • African
  • Additional Asian Ancestries
  • European
  • Hispanic or Latin American
  • Not Reported
  • Additional Diverse Ancestries
  • East Asian
African: 17.6%
East Asian: 5.9%
17 Sample Sets

Development Samples

Source of Variant Associations (GWAS)
Study Identifiers Sample Numbers Sample Ancestry Cohort(s)
GWAS Catalog: GCST011049
Europe PMC: 33398198
 177,526 individuals,
100.0 % Male samples
 European 12 cohorts
  • AAPC
  • ,BBJ
  • ,BPC3
  • ,CAPS
  • ,ELLIPSE
  • ,GPS
  • ,MEC
  • ,PEGASUS_PCa
  • ,PRACTICAL
  • ,ProHealth
  • ,UKGPCS
  • ,iCOGS
GWAS Catalog: GCST011049
Europe PMC: 33398198
 21,354 individuals,
100.0 % Male samples
 African American or Afro-Caribbean, African unspecified 12 cohorts
  • AAPC
  • ,BBJ
  • ,BPC3
  • ,CAPS
  • ,ELLIPSE
  • ,GPS
  • ,MEC
  • ,PEGASUS_PCa
  • ,PRACTICAL
  • ,ProHealth
  • ,UKGPCS
  • ,iCOGS
GWAS Catalog: GCST011049
Europe PMC: 33398198
 27,420 individuals,
100.0 % Male samples
 East Asian 12 cohorts
  • AAPC
  • ,BBJ
  • ,BPC3
  • ,CAPS
  • ,ELLIPSE
  • ,GPS
  • ,MEC
  • ,PEGASUS_PCa
  • ,PRACTICAL
  • ,ProHealth
  • ,UKGPCS
  • ,iCOGS
GWAS Catalog: GCST011049
Europe PMC: 33398198
 7,953 individuals,
100.0 % Male samples
 Hispanic or Latin American 12 cohorts
  • AAPC
  • ,BBJ
  • ,BPC3
  • ,CAPS
  • ,ELLIPSE
  • ,GPS
  • ,MEC
  • ,PEGASUS_PCa
  • ,PRACTICAL
  • ,ProHealth
  • ,UKGPCS
  • ,iCOGS

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
PPM001365 PSS000596|
European Ancestry|
199,969 individuals
 PGP000122 |
Conti DV et al. Nat Genet (2021)
 Reported Trait: Prostate Cancer — AUROC: 0.833 Odds ratio (OR, top 10% versus 40-60% GRS): 4.17
Overall Net Reclassification Index (NRI [%]): 59.4		 Age, 10 PCs —
PPM001366 PSS000595|
African Ancestry|
2,633 individuals
 PGP000122 |
Conti DV et al. Nat Genet (2021)
 Reported Trait: Prostate Cancer — AUROC: 0.679 Odds ratio (OR, top 10% versus 40-60% GRS): 3.53 Age, 10 PCs, study —
PPM001951 PSS000976|
European Ancestry|
12,472 individuals
 PGP000168 |
Plym A et al. J Natl Cancer Inst (2021)
|Ext.		 Reported Trait: Prevalent prostate cancer OR: 2.04 — Odds ratio (OR, top 10% vs. middle 20%): 3.89 [3.24, 4.68] Age at blood collection, genotyping platform, PCs(1-10) Only 261 of the original 269 SNPs were available for analysis due to no imputation of the X chromosome.
PPM001952 PSS000976|
European Ancestry|
12,472 individuals
 PGP000168 |
Plym A et al. J Natl Cancer Inst (2021)
|Ext.		 Reported Trait: Prevalent prostate cancer — — Odds ratio (OR, bottom 10% vs. middle 20%): 0.34 [0.25, 0.46] Age at blood collection, genotyping platform, PCs(1-10) Only 261 of the original 269 SNPs were available for analysis due to no imputation of the X chromosome.
PPM001953 PSS000976|
European Ancestry|
12,472 individuals
 PGP000168 |
Plym A et al. J Natl Cancer Inst (2021)
|Ext.		 Reported Trait: Elevated prostate specific antigen OR: 1.54 — — Age at blood collection, genotyping platform, PCs(1-10) Only 261 of the original 269 SNPs were available for analysis due to no imputation of the X chromosome.
PPM001954 PSS000975|
African Ancestry|
524 individuals
 PGP000168 |
Plym A et al. J Natl Cancer Inst (2021)
|Ext.		 Reported Trait: Prevalent prostate cancer — — Odds ratio (OR, top 10% vs. middle 20%): 3.81 [1.48, 10.19] Age at blood collection, genotyping platform, PCs(1-2) Only 261 of the original 269 SNPs were available for analysis due to no imputation of the X chromosome.
PPM001955 PSS000975|
African Ancestry|
524 individuals
 PGP000168 |
Plym A et al. J Natl Cancer Inst (2021)
|Ext.		 Reported Trait: Prevalent prostate cancer — — Odds ratio (OR, bottom 10% vs. middle 20%): 0.15 [0.01, 0.92] Age at blood collection, genotyping platform, PCs(1-2) Only 261 of the original 269 SNPs were available for analysis due to no imputation of the X chromosome.
PPM001970 PSS000983|
European Ancestry|
81,094 individuals
 PGP000173 |
Darst BF et al. Eur Urol (2021)
|Ext.		 Reported Trait: Prostate cancer in carriers of rare pathogenic, likely pathogenic and/or deleterious germline variants OR: 2.62 [2.51, 2.74] — — Age, PCs (1-10) Only 267 SNPs from PGS000662 were utilised. 2 SNPs were not included as they were not present in the UK Biobank (UKB) data and had an imputation info score of > 0.50 (median info score = 0.99).
PPM012964 PSS009633|
Multi-ancestry (including European)|
110,706 individuals
 PGP000308 |
Schaid DJ et al. Am J Hum Genet (2022)
|Ext.		 Reported Trait: Prostate cancer — — Relative Risk (RR): 2.14 [2.09, 2.19] Ancestry, study —
PPM012965 PSS009632|
European Ancestry|
91,623 individuals
 PGP000308 |
Schaid DJ et al. Am J Hum Genet (2022)
|Ext.		 Reported Trait: Prostate cancer — — Relative Risk (RR: 30 - 55 years old): 2.56 [2.47, 2.65]
Relative Risk (RR: 55 - 60 years old): 2.39
Relative Risk (RR: 60 - 65 years old): 2.24
Relative Risk (RR: 65 - 70 years old): 2.04
Relative risk per adjusted standard error (OPERA) per year of age: 0.00014
Relative Risk (RR: 70 - 88 years old): 1.86 [1.76, 1.98]		 — —
PPM014985 PSS009945|
European Ancestry|
6,715 individuals
 PGP000367 |
Green HD et al. Br J Cancer (2022)
|Ext.		 Reported Trait: Prostate cancer incidence in men with symptoms OR: 2.12 [1.86, 2.41] — — — —
PPM014986 PSS009945|
European Ancestry|
6,715 individuals
 PGP000367 |
Green HD et al. Br J Cancer (2022)
|Ext.		 Reported Trait: Prostate cancer incidence in men with symptoms — AUROC: 0.772 [0.744, 0.8] — Age —
PPM014987 PSS009945|
European Ancestry|
6,715 individuals
 PGP000367 |
Green HD et al. Br J Cancer (2022)
|Ext.		 Reported Trait: Prostate cancer incidence in men with symptoms — AUROC: 0.782 [0.755, 0.81] — Age, family history, symptom profile —
PPM015482 PSS009959|
African Ancestry|
2,631 individuals
 PGP000373 |
Kim MS et al. Genome Biol (2022)
|Ext.		 Reported Trait: Prostate cancer OR: 1.86 [1.41, 2.47] AUROC: 0.579 [0.558, 0.601] — — —
PPM015485 PSS009959|
African Ancestry|
2,631 individuals
 PGP000373 |
Kim MS et al. Genome Biol (2022)
|Ext.		 Reported Trait: Aggressive prostate cancer (tumor stage T4) OR: 1.17 [0.95, 1.43] AUROC: 0.505 [0.435, 0.574] — — —
PPM015487 PSS009959|
African Ancestry|
2,631 individuals
 PGP000373 |
Kim MS et al. Genome Biol (2022)
|Ext.		 Reported Trait: Aggressive prostate cancer (Gleason score >=8) OR: 1.26 [1.15, 1.4] AUROC: 0.523 [0.488, 0.559] — — —
PPM015500 PSS009964|
Multi-ancestry (including European)|
10,120 individuals
 PGP000377 |
Plym A et al. Clin Cancer Res (2022)
|Ext.		 Reported Trait: Risk of prostate cancer with family history of prostate or breast cancer — — Hazard Ratio (HR, top vs. bottom quartile): 6.95 [5.57, 8.66] Age (underlying time-scale), calendar period of DNA collection (1993-1999, 2005-2006), and genetic ancestry (principal components 1-3) —
PPM015501 PSS009964|
Multi-ancestry (including European)|
10,120 individuals
 PGP000377 |
Plym A et al. Clin Cancer Res (2022)
|Ext.		 Reported Trait: Prostate cancer death with family history of prostate or breast cancer — — Hazard Ratio (HR, top vs. bottom quartile): 4.84 [2.59, 9.03] Age (underlying time-scale), calendar period of DNA collection (1993-1999, 2005-2006), and genetic ancestry (principal components 1-3) —
PPM015510 PSS009970|
Multi-ancestry (including European)|
4,448 individuals
 PGP000380 |
Chou A et al. Cancer Epidemiol Biomarkers Prev (2022)
|Ext.		 Reported Trait: Prostate cancer risk in 10 years OR: 2.12 [1.55, 2.93] — — — —
PPM015511 PSS009970|
Multi-ancestry (including European)|
4,448 individuals
 PGP000380 |
Chou A et al. Cancer Epidemiol Biomarkers Prev (2022)
|Ext.		 Reported Trait: Total prostate cancer risk in 10 years — AUROC: 0.932 [0.918, 0.947] — — —
PPM015512 PSS009970|
Multi-ancestry (including European)|
4,448 individuals
 PGP000380 |
Chou A et al. Cancer Epidemiol Biomarkers Prev (2022)
|Ext.		 Reported Trait: Gleason <=7 prostate cancer risk in 10 years — AUROC: 0.943 [0.928, 0.959] — — —
PPM015513 PSS009970|
Multi-ancestry (including European)|
4,448 individuals
 PGP000380 |
Chou A et al. Cancer Epidemiol Biomarkers Prev (2022)
|Ext.		 Reported Trait: Gleason >=8 prostate cancer risk in 10 years — AUROC: 0.942 [0.919, 0.964] — — —
PPM015514 PSS009970|
Multi-ancestry (including European)|
4,448 individuals
 PGP000380 |
Chou A et al. Cancer Epidemiol Biomarkers Prev (2022)
|Ext.		 Reported Trait: Localized prostate cancer risk in 10 years — AUROC: 0.936 [0.918, 0.953] — — —
PPM015515 PSS009970|
Multi-ancestry (including European)|
4,448 individuals
 PGP000380 |
Chou A et al. Cancer Epidemiol Biomarkers Prev (2022)
|Ext.		 Reported Trait: Non-localized prostate cancer risk in 10 years — AUROC: 0.948 [0.922, 0.974] — — —
PPM015516 PSS009970|
Multi-ancestry (including European)|
4,448 individuals
 PGP000380 |
Chou A et al. Cancer Epidemiol Biomarkers Prev (2022)
|Ext.		 Reported Trait: Lethal prostate cancer risk in 10 years — AUROC: 0.961 [0.941, 0.982] — — —
PPM017262 PSS010181|
Multi-ancestry (including European)|
655 individuals
 PGP000452 |
Schaffer KR et al. JAMA Intern Med (2023)
|Ext.		 Reported Trait: Any prostate cancer on biopsy OR: 2.0 [1.6, 2.4] — — Age —
PPM017263 PSS010181|
Multi-ancestry (including European)|
655 individuals
 PGP000452 |
Schaffer KR et al. JAMA Intern Med (2023)
|Ext.		 Reported Trait: Any prostate cancer on biopsy — C-index: 0.71 [0.66, 0.74] — Prostate Biopsy Collaborative Group risk calculator (age, PSA level prior to biopsy, digital rectal exam findings, ancestry (African vs. other), prior biopsy status, family history of prostate cancer) —
PPM018702 PSS011074|
East Asian Ancestry|
308 individuals
 PGP000494 |
Ho PJ et al. Elife (2023)
|Ext.		 Reported Trait: Prostate cancer — AUROC: 0.72 [0.7, 0.75] Hazard ratio (HR, high vs low tertile): 8.99 [5.27, 15.35] age at recruitment —
PPM019114 PSS011185|
European Ancestry|
189,338 individuals
 PGP000508 |
Dite GS et al. Prostate (2023)
|Ext.		 Reported Trait: Prostate cancer — — Hazard Ratio (HR per change in transformed PRS): 5.846 [4.264, 8.013] age, family history Effect sized based on ln(PRS)
PPM021705 PSS011753|
European Ancestry|
3,368 individuals
 PGP000659 |
Hurwitz LM et al. Environ Res (2023)
|Ext.		 Reported Trait: Prostate cancer — — Odds ratio (OR, PGS above median vs PGS below median): 1.17 [1.02, 1.35] Age at enrollment, state of residence —
PPM021706 PSS011754|
European Ancestry|
2,794 individuals
 PGP000659 |
Hurwitz LM et al. Environ Res (2023)
|Ext.		 Reported Trait: Aggressive prostate cancer — — Odds ratio (OR, PGS above median vs PGS below median): 1.17 [0.97, 1.41] Age at enrollment, state of residence —
PPM022293 PSS011904|
Multi-ancestry (including European)|
3,110 individuals
 PGP000696 |
Shi M et al. EBioMedicine (2023)
|Ext.		 Reported Trait: Prostate specific antigen level > 4 ng/mL HR: 1.45 [1.31, 1.61] — — Age at first PSA measurement, 10 PCs —

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
PSS009959 — —
[
  • 1,298 cases
  • , 1,333 controls
]
 — African unspecified — MADCaP —
PSS010181 — — 575 individuals,
100.0 % Male samples
 — European — BioVU —
PSS010181 — — 80 individuals,
100.0 % Male samples
 — African unspecified — BioVU —
PSS009964 — — 10,120 individuals,
100.0 % Male samples
 Median = 65.3 years European, Not reported 99% European HPFS —
PSS009632 — —
[
  • 54,564 cases
  • , 37,059 controls
]
,
100.0 % Male samples
 — European — BPC3, CGEMS, Ghana, PEGASUS GENEVA, ICPCG, ONCO
PSS009633 — —
[
  • 5,505 cases
  • , 5,370 controls
]
,
100.0 % Male samples
 — African American or Afro-Caribbean — BPC3, CGEMS, Ghana, PEGASUS GENEVA, ICPCG, ONCO
PSS009633 — —
[
  • 1,574 cases
  • , 1,483 controls
]
,
100.0 % Male samples
 — Asian unspecified — BPC3, CGEMS, Ghana, PEGASUS GENEVA, ICPCG, ONCO
PSS009633 — —
[
  • 54,564 cases
  • , 37,059 controls
]
,
100.0 % Male samples
 — European — BPC3, CGEMS, Ghana, PEGASUS GENEVA, ICPCG, ONCO
PSS009633 — —
[
  • 461 cases
  • , 452 controls
]
,
100.0 % Male samples
 — Sub-Saharan African
(Ghanaian)		 — BPC3, CGEMS, Ghana, PEGASUS GENEVA, ICPCG, ONCO
PSS009633 — —
[
  • 2,170 cases
  • , 2,068 controls
]
,
100.0 % Male samples
 — Hispanic or Latin American — BPC3, CGEMS, Ghana, PEGASUS GENEVA, ICPCG, ONCO
PSS009970 — —
[
  • 432 cases
  • , 422 controls
]
,
100.0 % Male samples
 — European — MEC —
PSS009970 — —
[
  • 476 cases
  • , 456 controls
]
,
100.0 % Male samples
 — African American or Afro-Caribbean
(African American)		 — MEC —
PSS009970 — —
[
  • 138 cases
  • , 139 controls
]
,
100.0 % Male samples
 — Native American
(Native Hawaiian)		 — MEC —
PSS009970 — —
[
  • 757 cases
  • , 748 controls
]
,
100.0 % Male samples
 — East Asian
(Japanese)		 — MEC —
PSS009970 — —
[
  • 442 cases
  • , 438 controls
]
,
100.0 % Male samples
 — Hispanic or Latin American
(Latino)		 — MEC —
PSS011904 — Median = 6.2 years
IQR = [3.7, 10.9] years		 3,110 individuals,
100.0 % Male samples
 Median = 56.6 years
IQR = [51.4, 61.5] years		 European, African unspecified — BioVU No prostate cancer and prostate specific antigen level < 4 mg/mL at baseline
PSS011185 — —
[
  • 8,996 cases
  • , 180,342 controls
]
,
100.0 % Male samples
 Mean = 62.1 years
Sd = 5.5 years		 European — UKB —
PSS011753 — —
[
  • 1,162 cases
  • , 2,206 controls
]
,
100.0 % Male samples
 — European — AHS —
PSS011754 — —
[
  • 588 cases
  • , 2,206 controls
]
,
100.0 % Male samples
 — European — AHS —
PSS000595 — —
[
  • 1,586 cases
  • , 1,047 controls
]
,
100.0 % Male samples
 — African unspecified — CAUG —
PSS000596 — —
[
  • 6,852 cases
  • , 193,117 controls
]
,
100.0 % Male samples
 — European — UKB —
PSS000975 Cases were defined as having a biopsy-confirmed prostate cancer documented by a pathology report or at least two prostate cancer-related billing codes any time before or within 6 months of the date of blood collection. —
[
  • 67 cases
  • , 457 controls
]
,
100.0 % Male samples
 — African unspecified — MGBB Formerly known as Partners healthcare Biobank (PHB)
PSS000976 Cases were defined as having a biopsy-confirmed prostate cancer documented by a pathology report or at least two prostate cancer-related billing codes any time before or within 6 months of the date of blood collection. —
[
  • 1,554 cases
  • , 10,918 controls
]
,
100.0 % Male samples
 — European — MGBB Formerly known as Partners healthcare Biobank (PHB)
PSS011074 — — 308 individuals,
100.0 % Male samples
 Median = 59.0 years
IQR = [54.0, 64.0] years		 East Asian
(Chinese)		 — SCHS —
PSS000983 Cases were individuals with malignant prostate cancer. All individuals (cases and controls) were carriers of rare pathogenic, likely pathogenic and/or deleterious germline variants in ATM, BRCA2, CHEK2, and HOXB13 genes. —
[
  • 3,568 cases
  • , 77,526 controls
]
,
100.0 % Male samples
 — European — UKB —
PSS009945 Patients in the symptomatic cohort that were diagnosed with prostate cancer within 2 years of the index date were treated as cases. Patients with no record of a prostate cancer diagnosis within 2 years of the index date were considered controls —
[
  • 247 cases
  • , 6,468 controls
]
,
100.0 % Male samples
 — European — UKB —