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
Development Method
Name Genome-wide significant variants
Parameters NR
Variants
Original Genome Build NR
Number of Variants 147
Effect Weight Type 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: 70%
Not Reported: 10%
African: 10%
Multi-ancestry (including European): 10%
  • African
  • Additional Asian Ancestries
  • Additional Diverse Ancestries
  • European
10 Sample Sets

Development Samples

Source of Variant Associations (GWAS)
Study Identifiers Sample Numbers Sample Ancestry Cohort(s)
GWAS Catalog: GCST006085
Europe PMC: 29892016
 140,254 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
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).
PPM005133 PSS003583|
European Ancestry|
450 individuals
 PGP000245 |
Barnes DR et al. J Natl Cancer Inst (2021)
|Ext.		 Reported Trait: Prostate cancer in BRCA1 carriers OR: 1.73 [1.28, 2.33] AUROC: 0.62 [0.54, 0.69] — PCs(1-3) —
PPM005134 PSS003583|
European Ancestry|
450 individuals
 PGP000245 |
Barnes DR et al. J Natl Cancer Inst (2021)
|Ext.		 Reported Trait: Prostate cancer in BRCA1 carriers OR: 1.74 [1.29, 2.35] — — PCs(1-3), family history of prostate cancer in first and second degree relatives —
PPM005135 PSS003584|
European Ancestry|
1,074 individuals
 PGP000245 |
Barnes DR et al. J Natl Cancer Inst (2021)
|Ext.		 Reported Trait: Prostate cancer in BRCA2 carriers OR: 1.6 [1.34, 1.91] AUROC: 0.62 [0.57, 0.67] — PCs(1-3) —
PPM005136 PSS003584|
European Ancestry|
1,074 individuals
 PGP000245 |
Barnes DR et al. J Natl Cancer Inst (2021)
|Ext.		 Reported Trait: Prostate cancer in BRCA2 carriers OR: 1.59 [1.32, 1.9] — — PCs(1-3), family history of prostate cancer in first and second degree relatives —
PPM012886 PSS009594|
Ancestry Not Reported|
4,580 individuals
 PGP000292 |
Saad M et al. Lancet Oncol (2022)
|Ext.		 Reported Trait: Prostate cancer OR: 1.835 [1.664, 2.023] AUROC: 0.672 [0.645, 0.698] — — —
PPM013015 PSS009648|
European Ancestry|
991 individuals
 PGP000322 |
Klein RJ et al. NPJ Precis Oncol (2022)
|Ext.		 Reported Trait: Prostate cancer metastasis or death HR: 1.25 [1.1, 1.41] — — — —
PPM013016 PSS009649|
European Ancestry|
1,000 individuals
 PGP000322 |
Klein RJ et al. NPJ Precis Oncol (2022)
|Ext.		 Reported Trait: Prostate cancer metastasis or death HR: 1.65 — — — —
PPM013017 PSS009648|
European Ancestry|
991 individuals
 PGP000322 |
Klein RJ et al. NPJ Precis Oncol (2022)
|Ext.		 Reported Trait: Incident prostate cancer HR: 1.25 [1.11, 1.41] — — — —
PPM013018 PSS009649|
European Ancestry|
1,000 individuals
 PGP000322 |
Klein RJ et al. NPJ Precis Oncol (2022)
|Ext.		 Reported Trait: Incident prostate cancer HR: 1.69 — — — —
PPM013019 PSS009650|
European Ancestry|
1,991 individuals
 PGP000322 |
Klein RJ et al. NPJ Precis Oncol (2022)
|Ext.		 Reported Trait: Prostate cancer metastasis or death — AUROC: 0.63 — — —
PPM015484 PSS009959|
African Ancestry|
2,631 individuals
 PGP000373 |
Kim MS et al. Genome Biol (2022)
|Ext.		 Reported Trait: Aggressive prostate cancer (tumor stage T4) OR: 1.14 [0.93, 1.4] AUROC: 0.51 [0.438, 0.578] — — —
PPM015481 PSS009959|
African Ancestry|
2,631 individuals
 PGP000373 |
Kim MS et al. Genome Biol (2022)
|Ext.		 Reported Trait: Prostate cancer OR: 1.23 [0.91, 1.67] AUROC: 0.538 [0.516, 0.56] — — —
PPM015486 PSS009959|
African Ancestry|
2,631 individuals
 PGP000373 |
Kim MS et al. Genome Biol (2022)
|Ext.		 Reported Trait: Aggressive prostate cancer (Gleason score >=8) OR: 1.13 [1.02, 1.25] AUROC: 0.511 [0.475, 0.547] — — —
PPM015519 PSS009971|
Multi-ancestry (including European)|
36,422 individuals
 PGP000381 |
Hao L et al. Nat Med (2022)
|Ext.		 Reported Trait: Prostate cancer OR: 2.22 [1.98, 2.48] — — 4 genetic 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
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 —
PSS009648 — —
[
  • 240 cases
  • , 751 controls
]
,
100.0 % Male samples
 — European — MDC —
PSS009649 — —
[
  • 235 cases
  • , 765 controls
]
,
100.0 % Male samples
 — European — VIP —
PSS009650 — —
[
  • 475 cases
  • , 1,516 controls
]
,
100.0 % Male samples
 — European — NR —
PSS003583 All individuals were BRCA1 carriers. BRCA1 pathogenic variants were categorized according to their known or predicted effect on protein function: “class I” included loss-of-function variants expected to yield unstable or no protein; “class II” included variants likely to produce stable mutant proteins. Pathology data were obtained from pathology reviews, medical, pathology or tumor registry records, or immunohistochemical staining of tissue microarrays. All cases were individuals with prostate cancer. —
[
  • 70 cases
  • , 380 controls
]
,
100.0 % Male samples
 — European — 31 cohorts
  • BCFR
  • ,BCFR-CA
  • ,BCFR-UT
  • ,BFBOCC
  • ,BRICOH
  • ,CBCS
  • ,CNIO
  • ,CONSIT_TEAM
  • ,DEMOKRITOS
  • ,DKFZ
  • ,EMBRACE
  • ,FCCC
  • ,GC-HBOC
  • ,GEMO
  • ,HEBCS
  • ,HUNBOCS
  • ,HVH
  • ,ICO
  • ,IOVHBOCS
  • ,MAYO
  • ,MSKCC
  • ,MUV
  • ,NCI
  • ,OCGN
  • ,OSUCCG
  • ,OUH
  • ,SWE-BRCA
  • ,UPENN
  • ,UPITT
  • ,VFCTG
  • ,kConFab
 Additional cases and controls were obtained from UCHICAGO
PSS003584 All individuals were BRCA2 carriers. BRCA2 pathogenic variants were categorized according to their known or predicted effect on protein function: “class I” included loss-of-function variants expected to yield unstable or no protein; “class II” included variants likely to produce stable mutant proteins. Pathology data were obtained from pathology reviews, medical, pathology or tumor registry records, or immunohistochemical staining of tissue microarrays. All cases were individuals with prostate cancer. —
[
  • 141 cases
  • , 933 controls
]
,
100.0 % Male samples
 — European — 36 cohorts
  • BCFR
  • ,BCFR-AU
  • ,BCFR-CA
  • ,BCFR-UT
  • ,BRICOH
  • ,CBCS
  • ,CNIO
  • ,CONSIT_TEAM
  • ,DKFZ
  • ,EMBRACE
  • ,FCCC
  • ,G-FaST
  • ,GC-HBOC
  • ,GEMO
  • ,HCSC
  • ,HEBCS
  • ,HEBON
  • ,HUNBOCS
  • ,HVH
  • ,ICO
  • ,ILUH
  • ,IOVHBOCS
  • ,IPOBCS
  • ,MAYO
  • ,MSKCC
  • ,MUV
  • ,NCI
  • ,OCGN
  • ,OSUCCG
  • ,OUH
  • ,PBCS
  • ,SWE-BRCA
  • ,UPENN
  • ,UPITT
  • ,VFCTG
  • ,kConFab
 Additional cases and controls were obtained from UCHICAGO
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 — 42 cohorts
  • APCB
  • ,CONOR
  • ,COSM
  • ,CPCS
  • ,CPS
  • ,EPIC
  • ,ERSPC
  • ,FHCRC
  • ,Gene-PARE
  • ,HPFS
  • ,HZ
  • ,IMPACT
  • ,IPO-Porto
  • ,LAAPC
  • ,MCC-Spain
  • ,MCCS
  • ,MDACCS
  • ,MEC
  • ,MOFFITT_PC
  • ,PCMUS
  • ,PCPT
  • ,PHS
  • ,PLCO
  • ,PRAGGA
  • ,PROCAP
  • ,PROFILE
  • ,PROGReSS_PrCa
  • ,Poland
  • ,ProMPT
  • ,ProtecT
  • ,QLD
  • ,RAPPER
  • ,SAAR
  • ,SEARCH
  • ,SFPCS
  • ,SNP_Prostate_Ghent
  • ,SPAG
  • ,STHM
  • ,SWOG-SELECT
  • ,TAMPERE
  • ,TOR
  • ,UKGPCS
 These samples (OncoArray) were also used in the GWAS meta-analysis
PSS009959 — —
[
  • 1,298 cases
  • , 1,333 controls
]
 — African unspecified — MADCaP —
PSS009971 — — 1,807 individuals — African unspecified
(Black)		 — MGBB —
PSS009971 — — 786 individuals — Asian unspecified — MGBB —
PSS009971 — — 3,113 individuals — Other — MGBB —
PSS009594 — —
[
  • 453 cases
  • , 4,127 controls
]
,
100.0 % Male samples
 — Not reported — TCGA —
PSS009971 — — 30,716 individuals — European — MGBB —