Polygenic Score (PGS) ID: PGS000084

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 CC_Prostate
Development Method
Name Genome-wide significant variants
Parameters P < 5e-8, MAF > 1%, biallelic SNPs, LD-thin r2 > 0.3
Variants
Original Genome Build GRCh37
Number of Variants 161
Effect Weight Type log(OR)
PGS Source
PGS Catalog Publication (PGP) ID PGP000050
Citation (link to publication) Graff RE et al. Nat Commun (2021)
Ancestry Distribution
Source of Variant
Associations (GWAS)
European: 93.3%
African: 2.8%
East Asian: 2.5%
Hispanic or Latin American: 1.3%
Not Reported: 0.1%
449,626 individuals (100%)
PGS Evaluation
European: 100%
3 Sample Sets

Development Samples

Source of Variant Associations (GWAS)
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Study Identifiers
Sample Numbers
Sample Ancestry
Cohort(s)
Europe PMC: 2688139
[
  • 495 cases
  • , 640 controls
]
,
100.0 % Male samples
East Asian
(Han Chinese)		CHIPGECS
GWAS Catalog: GCST000152
Europe PMC: 18264097
3,748 individualsEuropeanProtecT, UKGPCS
GWAS Catalog: GCST001147
Europe PMC: 21743057
7,240 individualsEuropeanNR
GWAS Catalog: GCST001338
Europe PMC: 22130093
545 individualsNRNR
GWAS Catalog: GCST001942
Europe PMC: 23535732
22,548 individualsEuropeanNR
GWAS Catalog: GCST002413
Europe PMC: 24740154
5,051 individualsEuropeanIllumina_iControlDB, dbGAP
GWAS Catalog: GCST002421
Europe PMC: 24753544
2,950 individualsEuropeanProtecT
GWAS Catalog: GCST002606
Europe PMC: 25217961
2,080 individualsHispanic or Latin AmericanNR
GWAS Catalog: GCST002606
Europe PMC: 25217961
6,954 individualsEast AsianNR
GWAS Catalog: GCST002606
Europe PMC: 25217961
10,463 individualsSub-Saharan African, African American or Afro-CaribbeanNR
GWAS Catalog: GCST002606
Europe PMC: 25217961
67,543 individualsEuropeanNR
GWAS Catalog: GCST002890
Europe PMC: 25939597
7,541 individualsEuropeanPLCO
GWAS Catalog: GCST002944
Europe PMC: 26034056
3,226 individualsEast AsianCMHS, GERA, ProHealth, RPGEH
GWAS Catalog: GCST002944
Europe PMC: 26034056
2,251 individualsAfrican American or Afro-CaribbeanCMHS, GERA, ProHealth, RPGEH
GWAS Catalog: GCST002944
Europe PMC: 26034056
3,629 individualsHispanic or Latin AmericanCMHS, GERA, ProHealth, RPGEH
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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
PPM000204PSS000123|
European Ancestry|
201,516 individuals
PGP000050 |
Graff RE et al. Nat Commun (2021)
Reported Trait: Prostate cancerOR: 1.44 [1.41, 1.47]——Genotyping reagent kit (GERA cohort only), genotyping array (UK Biobank only), age, 10 PCs.Results from meta-analysis of GERA and UKB. Sample overlap: the GERA dataset contributed to the effe... ct estimates for 4 of the 161 variants in the prostate cancer PRS.Show more
PPM002050PSS001023|
European Ancestry|
184,225 individuals
PGP000186 |
Kachuri L et al. Nat Commun (2020)
|Ext.		Reported Trait: Incident prostate cancerHR: 1.39 [1.35, 1.43]AUROC: 0.74
C-index: 0.738 (0.004)		—Age at assessment, family history of prostate cancer, genotyping array, PCs(1-15), family history of...  prostate cancerShow moreC-index calculated as a weighted average between 1 and 5 years and AUC at 5 years.
PPM017163PSS010151|
European Ancestry|
4,476 individuals
PGP000443 |
Byrne S et al. Int J Epidemiol (2023)
|Ext.		Reported Trait: Prostate cancerHR: 1.36 [1.32, 1.4]——age at baseline, sex (where relevant), assessment centre, 40 principal components of ancestries (PCs... ), Townsend Index, education, birth location, income, lifestyle index, additional cancer-specific covariatesShow 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
PSS000123Cancer diagnoses were obtained from reigstry data in GERA, and ICD-9/10 codes mapped to ICD-O-3 code... s in UK Biobank. Cancers for this phenotype were classified using the following SEER site recode(s): 28010Show more—
[
  • 10,810 cases
  • , 190,706 controls
]
,
100.0 % Male samples
—European—GERA, UKB—
PSS001023Individuals with at least one recorded incident diagnosis of a borderline, in situ, or malignant pri... mary cancer were defined as cases.Show more—
[
  • 4,740 cases
  • , 179,485 controls
]
,
100.0 % Male samples
—European—UKB—
PSS010151——
[
  • 383 cases
  • , 4,093 controls
]
,
100.0 % Male samples
—European—UKB—
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