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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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)
Study Identifiers Sample Numbers Sample Ancestry Cohort(s)
GWAS Catalog: GCST002890
Europe PMC: 25939597
 7,541 individuals European PLCO
GWAS Catalog: GCST002944
Europe PMC: 26034056
 3,226 individuals East Asian CMHS, GERA, ProHealth, RPGEH
GWAS Catalog: GCST002944
Europe PMC: 26034056
 2,251 individuals African American or Afro-Caribbean CMHS, GERA, ProHealth, RPGEH
GWAS Catalog: GCST002944
Europe PMC: 26034056
 3,629 individuals Hispanic or Latin American CMHS, GERA, ProHealth, RPGEH
GWAS Catalog: GCST002944
Europe PMC: 26034056
 37,272 individuals European CMHS, GERA, ProHealth, RPGEH
GWAS Catalog: GCST002421
Europe PMC: 24753544
 2,950 individuals European ProtecT
GWAS Catalog: GCST002413
Europe PMC: 24740154
 5,051 individuals European Illumina_iControlDB, dbGAP
Europe PMC: 2688139
[
  • 495 cases
  • , 640 controls
]
,
100.0 % Male samples
 East Asian
(Han Chinese)		 CHIPGECS
GWAS Catalog: GCST001338
Europe PMC: 22130093
 545 individuals NR NR
GWAS Catalog: GCST003587
Europe PMC: 27197191
 123,671 individuals European NR
GWAS Catalog: GCST006085
Europe PMC: 29892016
 140,254 individuals European NR
GWAS Catalog: GCST001942
Europe PMC: 23535732
 22,548 individuals European NR
GWAS Catalog: GCST002606
Europe PMC: 25217961
 2,080 individuals Hispanic or Latin American NR
GWAS Catalog: GCST002606
Europe PMC: 25217961
 6,954 individuals East Asian NR
GWAS Catalog: GCST002606
Europe PMC: 25217961
 10,463 individuals Sub-Saharan African, African American or Afro-Caribbean NR
GWAS Catalog: GCST001147
Europe PMC: 21743057
 7,240 individuals European NR
GWAS Catalog: GCST000152
Europe PMC: 18264097
 3,748 individuals European ProtecT, UKGPCS
—
[
  • 212 cases
  • , 1,313 controls
]
,
100.0 % Male samples
 European 37 cohorts
  • BCFR
  • ,BFBOCC
  • ,BRICOH
  • ,CBCS
  • ,CIMBA
  • ,CNIO
  • ,CONSIT
  • ,Chicago
  • ,DEMOKRITOS
  • ,DKFZ
  • ,EMBRACE
  • ,FCCC
  • ,G-FaST
  • ,GC-HBOC
  • ,GEMO
  • ,HCSC
  • ,HEBCS
  • ,HEBON
  • ,HUNBOCS
  • ,HVH
  • ,ICO
  • ,ILUH
  • ,IOVHBOCS
  • ,IPOBCS
  • ,MAYO
  • ,MSKCC
  • ,MUV
  • ,NCI
  • ,OCGN
  • ,OSU
  • ,OUH
  • ,PBCS
  • ,SWE-BRCA
  • ,UPENN
  • ,UPITT
  • ,VFCTG
  • ,kConFab
GWAS Catalog: GCST002606
Europe PMC: 25217961
 67,543 individuals European NR

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
PPM000204 PSS000123|
European Ancestry|
201,516 individuals
 PGP000050 |
Graff RE et al. Nat Commun (2021)
 Reported Trait: Prostate cancer OR: 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 effect estimates for 4 of the 161 variants in the prostate cancer PRS.
PPM002050 PSS001023|
European Ancestry|
184,225 individuals
 PGP000186 |
Kachuri L et al. Nat Commun (2020)
|Ext.		 Reported Trait: Incident prostate cancer HR: 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 cancer C-index calculated as a weighted average between 1 and 5 years and AUC at 5 years.
PPM017163 PSS010151|
European Ancestry|
4,476 individuals
 PGP000443 |
Byrne S et al. Int J Epidemiol (2023)
|Ext.		 Reported Trait: Prostate cancer HR: 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 covariates —

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
PSS010151 — —
[
  • 383 cases
  • , 4,093 controls
]
,
100.0 % Male samples
 — European — UKB —
PSS000123 Cancer diagnoses were obtained from reigstry data in GERA, and ICD-9/10 codes mapped to ICD-O-3 codes in UK Biobank. Cancers for this phenotype were classified using the following SEER site recode(s): 28010 —
[
  • 10,810 cases
  • , 190,706 controls
]
,
100.0 % Male samples
 — European — GERA, UKB —
PSS001023 Individuals with at least one recorded incident diagnosis of a borderline, in situ, or malignant primary cancer were defined as cases. —
[
  • 4,740 cases
  • , 179,485 controls
]
,
100.0 % Male samples
 — European — UKB —