PGS Publication: PGP000400

Publication Information (EuropePMC)
Title Polygenic risk of any, metastatic, and fatal prostate cancer in the Million Veteran Program.
PubMed ID 36305680(Europe PMC)
doi 10.1093/jnci/djac199
Publication Date Oct. 28, 2022
Journal J Natl Cancer Inst
Author(s) Pagadala MS, Lynch J, Karunamuni R, Alba PR, Lee KM, Agiri FY, Anglin T, Carter H, Gaziano JM, Jasuja GK, Deka R, Rose BS, Panizzon MS, Hauger RL, Seibert TM.
Released in PGS Catalog: Dec. 6, 2022

Associated Polygenic Score(s)

Filter PGS by Participant Ancestry
Individuals included in:
G - Source of Variant Associations (GWAS)
D - Score Development/Training
E - PGS Evaluation
List of ancestries includes:
Display options:
Ancestry legend
Multi-ancestry (including European)
Multi-ancestry (excluding European)
African
East Asian
South Asian
Additional Asian Ancestries
European
Greater Middle Eastern
Hispanic or Latin American
Additional Diverse Ancestries
Not Reported

External PGS Evaluated By This Publication

Polygenic Score ID & Name PGS Publication ID (PGP) Reported Trait Mapped Trait(s) (Ontology) Number of Variants Ancestry distribution
GWAS
Dev
Eval
 Scoring File (FTP Link)
PGS003331
(PHS290)
 PGP000397 |
Huynh-Le MP et al. Prostate Cancer Prostatic Dis (2022)
 Prostate cancer prostate carcinoma 290
https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS003331/ScoringFiles/PGS003331.txt.gz

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) 		Evaluated Score 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
PPM016145 PGS003331
(PHS290)
 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 PGS003331
(PHS290)
 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 PGS003331
(PHS290)
 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 PGS003331
(PHS290)
 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 PGS003331
(PHS290)
 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 PGS003331
(PHS290)
 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
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 —