PGS Publication: PGP000173

Publication Information (EuropePMC)
Title Combined Effect of a Polygenic Risk Score and Rare Genetic Variants on Prostate Cancer Risk.
PubMed ID 33941403(Europe PMC)
doi 10.1016/j.eururo.2021.04.013
Publication Date May 1, 2021
Journal Eur Urol
Author(s) Darst BF, Sheng X, Eeles RA, Kote-Jarai Z, Conti DV, Haiman CA.
Released in PGS Catalog: May 28, 2021

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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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
PGS000030
(PrCa)
 PGP000019 |
Schumacher FR et al. Nat Genet (2018)
 Prostate cancer prostate carcinoma 147
-
 https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS000030/ScoringFiles/PGS000030.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
PPM001971 PGS000030
(PrCa)
 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).
PPM001970 PGS000662
(GRS.PCa.269)
 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: 2.62 [2.51, 2.74] — — Age, PCs (1-10) Only 267 SNPs from PGS000662 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 = 0.99).

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 —