Polygenic Score (PGS) ID: PGS003331

Predicted Trait
Reported Trait Prostate cancer
Mapped Trait(s) prostate carcinoma (EFO_0001663)
Released in PGS Catalog: Nov. 23, 2022
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Score Details

Score Construction
PGS Name PHS290
Development Method
Name LASSO
Parameters r2>0.95
Variants
Original Genome Build GRCh37
Number of Variants 290
Effect Weight Type beta
PGS Source
PGS Catalog Publication (PGP) ID PGP000397
Citation (link to publication) Huynh-Le MP et al. Prostate Cancer Prostatic Dis (2022)
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%)
Score Development/Training
European: 100%
72,181 individuals (100%)
PGS Evaluation
Not Reported: 20%
African: 20%
Additional Asian Ancestries: 20%
European: 20%
Multi-ancestry (including European): 20%
  • Additional Asian Ancestries
  • African
  • European
  • Additional Diverse Ancestries
  • Not Reported
5 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 European NR
GWAS Catalog: GCST011049
Europe PMC: 33398198
 21,354 individuals African American or Afro-Caribbean,African unspecified NR
GWAS Catalog: GCST011049
Europe PMC: 33398198
 27,420 individuals East Asian NR
GWAS Catalog: GCST011049
Europe PMC: 33398198
 7,953 individuals Hispanic or Latin American NR
Score Development/Training
Study Identifiers Sample Numbers Sample Ancestry Cohort(s) Phenotype Definitions & Methods Age of Study Participants Participant Follow-up Time Additional Ancestry Description Additional Sample/Cohort Information
—
[
  • 48,171 cases
  • , 24,010 controls
]
,
100.0 % Male samples
 European PRACTICAL — — — — —

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
PPM016134 PSS010046|
Ancestry Not Reported|
6,411 individuals
 PGP000397 |
Huynh-Le MP et al. Prostate Cancer Prostatic Dis (2022)
 Reported Trait: Any prostate cancer β: 2.11 — Hazard ratio (HR, top vs bottom 20%): 11.16 [10.48, 11.88] — —
PPM016135 PSS010046|
Ancestry Not Reported|
6,411 individuals
 PGP000397 |
Huynh-Le MP et al. Prostate Cancer Prostatic Dis (2022)
 Reported Trait: Clinically significant prostate cancer β: 2.32 — Hazard ratio (HR, top vs bottom 20%): 13.73 [12.43, 15.16] — —
PPM016136 PSS010043|
African Ancestry|
6,253 individuals
 PGP000397 |
Huynh-Le MP et al. Prostate Cancer Prostatic Dis (2022)
 Reported Trait: Any prostate cancer β: 1.64 — Hazard ratio (HR, top vs bottom 20%): 5.95 [5.59, 6.34] — —
PPM016137 PSS010043|
African Ancestry|
6,253 individuals
 PGP000397 |
Huynh-Le MP et al. Prostate Cancer Prostatic Dis (2022)
 Reported Trait: Clinically significant prostate cancer β: 1.67 — Hazard ratio (HR, top vs bottom 20%): 7.07 [6.58, 7.6] — —
PPM016138 PSS010044|
Additional Asian Ancestries|
2,378 individuals
 PGP000397 |
Huynh-Le MP et al. Prostate Cancer Prostatic Dis (2022)
 Reported Trait: Any prostate cancer β: 1.99 — Hazard ratio (HR, top vs bottom 20%): 8.75 [8.21, 9.32] — —
PPM016139 PSS010044|
Additional Asian Ancestries|
2,378 individuals
 PGP000397 |
Huynh-Le MP et al. Prostate Cancer Prostatic Dis (2022)
 Reported Trait: Clinically significant prostate cancer β: 1.89 — Hazard ratio (HR, top vs bottom 20%): 10.31 [9.58, 11.11] — —
PPM016140 PSS010045|
European Ancestry|
3,279 individuals
 PGP000397 |
Huynh-Le MP et al. Prostate Cancer Prostatic Dis (2022)
 Reported Trait: Any prostate cancer β: 2.13 — Hazard ratio (HR, top vs bottom 20%): 10.87 [10.21, 11.57] — —
PPM016141 PSS010045|
European Ancestry|
3,279 individuals
 PGP000397 |
Huynh-Le MP et al. Prostate Cancer Prostatic Dis (2022)
 Reported Trait: Clinically significant prostate cancer β: 2.13 — Hazard ratio (HR, top vs bottom 20%): 11.18 [10.34, 12.09] — —
PPM016142 PSS010045|
European Ancestry|
3,279 individuals
 PGP000397 |
Huynh-Le MP et al. Prostate Cancer Prostatic Dis (2022)
 Reported Trait: Fatal prostate cancer β: 1.68 — Hazard ratio (HR, top vs bottom 20%): 7.73 [6.45, 9.27] — —
PPM016145 PSS010049|
Multi-ancestry (including European)|
590,750 individuals
 PGP000400 |
Pagadala MS et al. J Natl Cancer Inst (2022)
|Ext.		 Reported Trait: Fatal prostate cancer — — Hazard ratio (HR, highest vs. lowest quintile): 4.42 [3.91, 5.02] — —
PPM016146 PSS010049|
Multi-ancestry (including European)|
590,750 individuals
 PGP000400 |
Pagadala MS et al. J Natl Cancer Inst (2022)
|Ext.		 Reported Trait: Metastatic prostate cancer — — Hazard ratio (HR, highest vs. lowest quintile): 4.89 [4.57, 5.21] — —
PPM016147 PSS010049|
Multi-ancestry (including European)|
590,750 individuals
 PGP000400 |
Pagadala MS et al. J Natl Cancer Inst (2022)
|Ext.		 Reported Trait: Prostate cancer — — Hazard ratio (HR, highest vs. lowest quintile): 5.2 [5.09, 5.31] — —
PPM016149 PSS010049|
Multi-ancestry (including European)|
590,750 individuals
 PGP000400 |
Pagadala MS et al. J Natl Cancer Inst (2022)
|Ext.		 Reported Trait: Metastatic prostate cancer — — Hazard ratio (HR, highest vs. lowest quintile): 4.15 [3.81, 4.53] self-reported Race and Ethnicity, Family History —
PPM016150 PSS010049|
Multi-ancestry (including European)|
590,750 individuals
 PGP000400 |
Pagadala MS et al. J Natl Cancer Inst (2022)
|Ext.		 Reported Trait: Prostate cancer — — Hazard ratio (HR, highest vs. lowest quintile): 4.69 [4.57, 4.81] self-reported Race and Ethnicity, Family History —
PPM016148 PSS010049|
Multi-ancestry (including European)|
590,750 individuals
 PGP000400 |
Pagadala MS et al. J Natl Cancer Inst (2022)
|Ext.		 Reported Trait: Fatal prostate cancer — — Hazard ratio (HR, highest vs. lowest quintile): 4.17 [3.59, 4.88] self-reported Race and Ethnicity, Family History —

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
PSS010043 — —
[
  • 3,240 cases
  • , 3,013 controls
]
,
100.0 % Male samples
 — African unspecified — NR —
PSS010044 — —
[
  • 1,194 cases
  • , 1,184 controls
]
,
100.0 % Male samples
 — Asian unspecified — NR —
PSS010045 — —
[
  • 2,163 cases
  • , 1,116 controls
]
,
100.0 % Male samples
 — European
(Swedish)		 — COSM —
PSS010046 — —
[
  • 1,583 cases
  • , 4,828 controls
]
,
100.0 % Male samples
 — Not reported — ProtecT —
PSS010049 — —
[
  • 376 cases
  • , 6,268 controls
]
,
100.0 % Male samples
 Median = 67.0 years Asian unspecified — MVP —
PSS010049 — —
[
  • 15,748 cases
  • , 86,455 controls
]
,
100.0 % Male samples
 Median = 63.0 years African American or Afro-Caribbean
(Black)		 — MVP —
PSS010049 — —
[
  • 2,120 cases
  • , 25,531 controls
]
,
100.0 % Male samples
 Median = 66.0 years European
(Hispanic White)		 — MVP —
PSS010049 — —
[
  • 504 cases
  • , 5,331 controls
]
,
100.0 % Male samples
 Median = 65.0 years Native American — MVP —
PSS010049 — —
[
  • 48,339 cases
  • , 372,134 controls
]
,
100.0 % Male samples
 Median = 68.0 years European
(Non-Hispanic White)		 — MVP —
PSS010049 — —
[
  • 720 cases
  • , 7,506 controls
]
,
100.0 % Male samples
 Median = 64.0 years Other — MVP —
PSS010049 — —
[
  • 236 cases
  • , 3,010 controls
]
,
100.0 % Male samples
 Median = 65.0 years Oceanian
(Pacific Islander)		 — MVP —
PSS010049 — —
[
  • 1,094 cases
  • , 15,378 controls
]
,
100.0 % Male samples
 Median = 67.0 years Not reported — MVP —