Polygenic Score (PGS) ID: PGS000030

Predicted Trait
Reported Trait Prostate cancer
Mapped Trait(s) prostate carcinoma (EFO_0001663)
Released in PGS Catalog: Oct. 14, 2019
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Score Details

Score Construction
PGS Name PrCa
Variants
Original Genome Build NR
Number of Variants 147
Development Method
Name Genome-wide significant SNPs
Parameters NR
PGS Source
PGS Catalog Publication (PGP) ID PGP000019
Citation (link to publication) Schumacher FR et al. Nat Genet (2018)
Ancestry Distribution
Source of Variant
Associations (GWAS)
European: 100%
140,254 individuals (100%)
PGS Evaluation
European: 100%
2 Sample Sets

Development Samples

Source of Variant Associations (GWAS)
Study Identifiers Sample Numbers Sample Ancestry
GWAS Catalog: GCST006085
Europe PMC: 29892016
140,254 individuals European

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
PPM000061 PSS000041|
European Ancestry|
74,849 individuals
PGP000019 |
Schumacher FR et al. Nat Genet (2018)
Reported Trait: Prostate cancer OR: 1.86 [1.83, 1.89] Top 7 Genetic PCs, country Samples were also part of the variant association
PPM001971 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: 2.58 [2.45, 2.71] Age, PCs (1-10) Only 145 SNPs from PGS000030 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 = 0.997).

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
PSS000041 For each cohort core data on disease status, age at diagnosis (age at observation or questionnaire for controls), family history of PrCa, and clinical factors for cases (for example, PSA at diagnosis and Gleason score) was extracted
[
  • 46,939 cases
  • , 27,910 controls
]
,
100.0 % Male samples
European 43 cohorts
  • APCB
  • ,CONOR
  • ,COSM
  • ,CPCS
  • ,CPS
  • ,EPIC
  • ,ERSPC
  • ,FHCRC
  • ,Gene-PARE
  • ,HPFS
  • ,HZ
  • ,IMPACT
  • ,IPO-Porto
  • ,LAAPC
  • ,Leuven
  • ,MCC-Spain
  • ,MCCS
  • ,MDACCS
  • ,MEC
  • ,MOFFITT_PC
  • ,PCMUS
  • ,PHS
  • ,PLCO
  • ,PRAGGA
  • ,PROCAP
  • ,PROFILE
  • ,PROGReSS_PrCa
  • ,Poland
  • ,ProMPT
  • ,ProtecT
  • ,QLD
  • ,RAPPER
  • ,SAAR
  • ,SEARCH
  • ,SFPCS
  • ,SNP_Prostate_Ghent
  • ,SPAG
  • ,STHLM2
  • ,SWOG-PCPT
  • ,SWOG-SELECT
  • ,TAMPERE
  • ,TOR
  • ,UKGPCS
These samples (OncoArray) were also used in the GWAS meta-analysis
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