Polygenic Score (PGS) ID: PGS002268

Predicted Trait
Reported Trait Prostate cancer
Mapped Trait(s) prostate carcinoma (EFO_0001663)
Released in PGS Catalog: April 1, 2022
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Score Details

Score Construction
PGS Name PRS_csPCa
Development Method
Name LD clumping
Parameters p<0.001
Variants
Original Genome Build NR
Number of Variants 29
Effect Weight Type beta
PGS Source
PGS Catalog Publication (PGP) ID PGP000298
Citation (link to publication) Song SH et al. Investig Clin Urol (2022)
Ancestry Distribution
Source of Variant
Associations (GWAS)
East Asian: 100%
10,187 individuals (100%)
PGS Evaluation
East Asian: 100%
4 Sample Sets

Development Samples

Source of Variant Associations (GWAS)
Study Identifiers Sample Numbers Sample Ancestry Cohort(s)
—
[
  • 2,702 cases
  • , 7,485 controls
]
,
100.0 % Male samples
 East Asian
(Korean)		 NR

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) 		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
PPM012919 PSS009617|
East Asian Ancestry|
1,133 individuals
 PGP000298 |
Song SH et al. Investig Clin Urol (2022)
 Reported Trait: Clinically significant prostate cancer — AUROC: 0.7 [0.667, 0.734] OR (very high vs moderate group): 4.92 — —
PPM017160 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 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 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
PSS009617 — —
[
  • 311 cases
  • , 822 controls
]
,
100.0 % Male samples
 — East Asian
(Korean)		 — NR —
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 —