PGS Publication: PGP000696

Publication Information (EuropePMC)
Title Clinical consequences of a genetic predisposition toward higher benign prostate-specific antigen levels.
PubMed ID 37865044(Europe PMC)
doi 10.1016/j.ebiom.2023.104838
Publication Date Oct. 20, 2023
Journal EBioMedicine
Author(s) Shi M, Shelley JP, Schaffer KR, Tosoian JJ, Bagheri M, Witte JS, Kachuri L, Mosley JD.
Released in PGS Catalog: Dec. 16, 2024

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:
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Ancestry legend
Multi-ancestry (including European)
Multi-ancestry (excluding European)
African
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Additional Asian Ancestries
European
Greater Middle Eastern
Hispanic or Latin American
Additional Diverse Ancestries
Not Reported

PGS Developed 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)
PGS005107
(PGS-PSA111)
 PGP000696 |
Shi M et al. EBioMedicine (2023)
 Prostate-specific antigen (PSA) levels prostate specific antigen amount 111
-
 https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS005107/ScoringFiles/PGS005107.txt.gz

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)
PGS000662
(GRS.PCa.269)
 PGP000122 |
Conti DV et al. Nat Genet (2021)
 Prostate cancer prostate carcinoma 269
-
 https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS000662/ScoringFiles/PGS000662.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
PPM022292 PGS005107
(PGS-PSA111)
 PSS011904|
Multi-ancestry (including European)|
3,110 individuals
 PGP000696 |
Shi M et al. EBioMedicine (2023)
 Reported Trait: Prostate specific antigen level > 4 ng/mL HR: 1.22 [1.11, 1.35] — — Age at first PSA measurement, 10 PCs —
PPM022293 PGS000662
(GRS.PCa.269)
 PSS011904|
Multi-ancestry (including European)|
3,110 individuals
 PGP000696 |
Shi M et al. EBioMedicine (2023)
|Ext.		 Reported Trait: Prostate specific antigen level > 4 ng/mL HR: 1.45 [1.31, 1.61] — — Age at first PSA measurement, 10 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
PSS011904 — Median = 6.2 years
IQR = [3.7, 10.9] years		 3,110 individuals,
100.0 % Male samples
 Median = 56.6 years
IQR = [51.4, 61.5] years		 European, African unspecified — BioVU No prostate cancer and prostate specific antigen level < 4 mg/mL at baseline