PGS Publication: PGP000219

Publication Information (EuropePMC)
Title Common genetic and clinical risk factors: association with fatal prostate cancer in the Cohort of Swedish Men.
PubMed ID 33723363(Europe PMC)
doi 10.1038/s41391-021-00341-4
Publication Date March 15, 2021
Journal Prostate Cancer Prostatic Dis
Author(s) Huynh-Le MP, Karunamuni R, Fan CC, Thompson WK, Muir K, Lophatananon A, Tye K, Wolk A, Håkansson N, Mills IG, Andreassen OA, Dale AM, Seibert TM, PRACTICAL Consortium.
Released in PGS Catalog: Aug. 26, 2021

Associated Polygenic Score(s)

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Individuals included in:
G - Source of Variant Associations (GWAS)
D - Score Development/Training
E - PGS Evaluation
List of ancestries includes:
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Multi-ancestry (including European)
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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 Scoring File (FTP Link)
PGS000741
(PCa_PHS2)
PGP000149 |
Huynh-Le MP et al. Nat Commun (2021)
Prostate cancer prostate carcinoma 46
-
https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS000741/ScoringFiles/PGS000741.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
PPM002489 PGS000741
(PCa_PHS2)
PSS001118|
Ancestry Not Reported|
3,279 individuals
PGP000219 |
Huynh-Le MP et al. Prostate Cancer Prostatic Dis (2021)
|Ext.
Reported Trait: Prostate cancer mortality (age at death) HR: 3.41 [2.78, 4.17]
PPM002490 PGS000741
(PCa_PHS2)
PSS001118|
Ancestry Not Reported|
3,279 individuals
PGP000219 |
Huynh-Le MP et al. Prostate Cancer Prostatic Dis (2021)
|Ext.
Reported Trait: Prostate cancer (age at diagnosis) HR: 5.35 [4.97, 5.76]
PPM002491 PGS000741
(PCa_PHS2)
PSS001118|
Ancestry Not Reported|
3,279 individuals
PGP000219 |
Huynh-Le MP et al. Prostate Cancer Prostatic Dis (2021)
|Ext.
Reported Trait: Aggressive prostate cancer (age at diagnosis) HR: 3.78 [3.45, 4.13]
PPM002492 PGS000741
(PCa_PHS2)
PSS001118|
Ancestry Not Reported|
3,279 individuals
PGP000219 |
Huynh-Le MP et al. Prostate Cancer Prostatic Dis (2021)
|Ext.
Reported Trait: Prostate cancer mortality (age at death) HR: 2.45 [1.99, 2.97]
β: 0.9
Family history of prostate cancer, alcohol intake, diabetes 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
PSS001118 Cases are individuals with prostate cancer. Of the 2163 cases, 1403 are aggressive prostate cancer cases defined as disease typically requiring treatment: Gleason score ≥7, clinical stage T3-T4, PSA concentration ≥10 ng/mL, or nodal/distant metastasis. 278 prostate cancer cases were fatal.
[
  • 2,163 cases
  • , 1,116 controls
]
,
100.0 % Male samples
Median = 78.0 years
Iqr = [72.3, 84.1] years
Not reported COSM Sample overlap exists between this dataset and the dataset used to develop/train Karunamuni et al's PGS (PGS000741)