PGS Publication: PGP000452

Publication Information (EuropePMC)
Title A Polygenic Risk Score for Prostate Cancer Risk Prediction.
PubMed ID 36877498(Europe PMC)
doi 10.1001/jamainternmed.2022.6795
Publication Date March 6, 2023
Journal JAMA Intern Med
Author(s) Schaffer KR, Shi M, Shelley JP, Tosoian JJ, Kachuri L, Witte JS, Mosley JD.
Released in PGS Catalog: March 24, 2023

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
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)
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
PPM017262 PGS000662
(GRS.PCa.269)
 PSS010181|
Multi-ancestry (including European)|
655 individuals
 PGP000452 |
Schaffer KR et al. JAMA Intern Med (2023)
|Ext.		 Reported Trait: Any prostate cancer on biopsy OR: 2.0 [1.6, 2.4] — — Age —
PPM017263 PGS000662
(GRS.PCa.269)
 PSS010181|
Multi-ancestry (including European)|
655 individuals
 PGP000452 |
Schaffer KR et al. JAMA Intern Med (2023)
|Ext.		 Reported Trait: Any prostate cancer on biopsy — C-index: 0.71 [0.66, 0.74] — Prostate Biopsy Collaborative Group risk calculator (age, PSA level prior to biopsy, digital rectal exam findings, ancestry (African vs. other), prior biopsy status, family history of prostate cancer) —

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
PSS010181 — — 575 individuals,
100.0 % Male samples
 — European — BioVU —
PSS010181 — — 80 individuals,
100.0 % Male samples
 — African unspecified — BioVU —