PGS Publication: PGP000442

Publication Information (EuropePMC)
Title Polygenic risk score for tumor aggressiveness and early-onset prostate cancer in Asians.
PubMed ID 36646726(Europe PMC)
doi 10.1038/s41598-022-17515-2
Publication Date Jan. 16, 2023
Journal Sci Rep
Author(s) Song SH, Kim E, Jung YJ, Kim HM, Park MS, Kim JK, Lee H, Oh JJ, Lee S, Hong SK, Byun SS.
Released in PGS Catalog: March 3, 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:
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)
PGS002268
(PRS_csPCa)
 PGP000298 |
Song SH et al. Investig Clin Urol (2022)
 Prostate cancer prostate carcinoma 29
-
 https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS002268/ScoringFiles/PGS002268.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
PPM017160 PGS002268
(PRS_csPCa)
 PSS010141|
East Asian Ancestry|
3,695 individuals
 PGP000442 |
Song SH et al. Sci Rep (2023)
|Ext.		 Reported Trait: Aggressive prostate cancer (Grade 3 or above) — — Hazard Ratio (HR, top 25% vs bottom 25%): 2.026 [1.678, 2.446] — Only 22 SNPs from PGS002268 were utilised. 7 SNPs were not included due to inadequately low allele frequencies or call rates. rs72725879 was replaced with the next highest performing variant (rs1456315) in the same LD block (Locus PRNCR1) due to replication inconsistencies.
PPM017161 PGS002268
(PRS_csPCa)
 PSS010140|
East Asian Ancestry|
3,695 individuals
 PGP000442 |
Song SH et al. Sci Rep (2023)
|Ext.		 Reported Trait: Aggressive prostate cancer (Grade 2 or above) — — Hazard Ratio (HR, top 25% vs bottom 25%): 4.649 [3.544, 6.098] — Only 22 SNPs from PGS002268 were utilised. 7 SNPs were not included due to inadequately low allele frequencies or call rates. rs72725879 was replaced with the next highest performing variant (rs1456315) in the same LD block (Locus PRNCR1) due to replication inconsistencies.
PPM017162 PGS002268
(PRS_csPCa)
 PSS010139|
East Asian Ancestry|
3,695 individuals
 PGP000442 |
Song SH et al. Sci Rep (2023)
|Ext.		 Reported Trait: Early-onset prostate cancer — AUROC: 0.627 [0.55, 0.703] — — Only 22 SNPs from PGS002268 were utilised. 7 SNPs were not included due to inadequately low allele frequencies or call rates. rs72725879 was replaced with the next highest performing variant (rs1456315) in the same LD block (Locus PRNCR1) due to replication inconsistencies.

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
PSS010139 — —
[
  • 3,203 cases
  • , 483 controls
]
,
100.0 % Male samples
 Mean = 67.3 years East Asian
(Korean)		 — NR —
PSS010140 — —
[
  • 3,069 cases
  • , 626 controls
]
,
100.0 % Male samples
 Mean = 67.3 years East Asian
(Korean)		 — NR —
PSS010141 — —
[
  • 2,212 cases
  • , 1,483 controls
]
,
100.0 % Male samples
 Mean = 67.3 years East Asian
(Korean)		 — NR —