Polygenic Score (PGS) ID: PGS000044

Predicted Trait
Reported Trait Prostate cancer
Mapped Trait(s) prostate carcinoma (EFO_0001663)
Released in PGS Catalog: Dec. 18, 2019
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Score Details

Score Construction
PGS Name PrCa66
Variants
Original Genome Build GRCh38
Number of Variants 66
Development Method
Name Known susceptibility loci (genome-wide significant SNPs)
Parameters P-value < 5E-8, top SNP
PGS Source
PGS Catalog Publication (PGP) ID PGP000031
Citation (link to publication) Pashayan N et al. Br J Cancer (2015)
Ancestry Distribution
Source of Variant
Associations (GWAS)
European: 95.2%
East Asian: 4.8%
153,371 individuals (100%)
PGS Evaluation
European: 100%
2 Sample Sets

Development Samples

Source of Variant Associations (GWAS)
Study Identifiers Sample Numbers Sample Ancestry
GWAS Catalog: GCST001942
Europe PMC: 23535732
22,548 individuals European
GWAS Catalog: GCST001148
Europe PMC: 21743467
13,560 individuals European
GWAS Catalog: GCST000153
Europe PMC: 18264098
23,226 individuals European
GWAS Catalog: GCST000488
Europe PMC: 19767753
3,748 individuals European
GWAS Catalog: GCST000750
Europe PMC: 20676098
4,969 individuals East Asian
GWAS Catalog: GCST001147
Europe PMC: 21743057
7,240 individuals European
GWAS Catalog: GCST000152
Europe PMC: 18264097
3,748 individuals European
GWAS Catalog: GCST000489
Europe PMC: 19767754
37,350 individuals European
GWAS Catalog: GCST000154
Europe PMC: 18264096
2,329 individuals European
GWAS Catalog: GCST000019
Europe PMC: 17401366
4,517 individuals European
GWAS Catalog: GCST000017
Europe PMC: 17401363
2,329 individuals European
GWAS Catalog: GCST001702
Europe PMC: 23023329
2,425 individuals East Asian
GWAS Catalog: GCST000128
Europe PMC: 18073375
2,834 individuals European
GWAS Catalog: GCST001714
Europe PMC: 23065704
22,548 individuals European

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
PPM000105 PSS000069|
European Ancestry|
4,967 individuals
PGP000032 |
Pashayan N et al. Genet Med (2015)
|Ext.
Reported Trait: aggressive prostate cancer (Gleason score ⩾7) OR (above vs. below 50th percentile of PRS): 1.56 [1.15, 2.1]
PPM000104 PSS000068|
European Ancestry|
17,012 individuals
PGP000031 |
Pashayan N et al. Br J Cancer (2015)
Reported Trait: Elevated serum prostate-specific antigen (PSA) levels OR (per 1-point increase in PRS): 1.23 [1.1, 1.37] cancer stage, Gleason score

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
PSS000068 Prostate cancer was classified as localized disease with tumor-node-metastasis stage T2 and below and advanced disease (regional-distant) was classified as localized disease with tumor-node-metastasis stage T3 and above (low aggressive tumor, Gleason score <7; intermediate to highly aggressive tumor, Gleason score ≥7). Elevated serum prostate-specific antigen (PSA) levels were defined as ≥4 ng/ml.
[
  • 3,157 cases
  • , 0 controls
]
,
100.0 % Male samples
Range = [50.0, 60.0] years European UKGPCS
PSS000069 Prostate cancer was classified as localised disease with tumour-node-metastasis (TNM) stage T1-2 N0 M0; and advanced disease (regional-distant) with stage T3 and above or any T N1 M1; as non-aggressive tumour, Gleason score <7, and aggressive tumour, Gleason score ⩾7. Median = 13.0 years
[
  • 1,089 cases
  • , 3,878 controls
]
,
100.0 % Male samples
Range = [55.0, 71.0] years European
(Finnish)
ERSPC
PSS000068 Prostate cancer was classified as localized disease with tumor-node-metastasis stage T2 and below and advanced disease (regional-distant) was classified as localized disease with tumor-node-metastasis stage T3 and above (low aggressive tumor, Gleason score <7; intermediate to highly aggressive tumor, Gleason score ≥7). Elevated serum prostate-specific antigen (PSA) levels were defined as ≥4 ng/ml.
[
  • 2,148 cases
  • , 6,648 controls
]
,
100.0 % Male samples
Range = [50.0, 69.0] years European ProtecT
PSS000068 Prostate cancer was classified as localized disease with tumor-node-metastasis stage T2 and below and advanced disease (regional-distant) was classified as localized disease with tumor-node-metastasis stage T3 and above (low aggressive tumor, Gleason score <7; intermediate to highly aggressive tumor, Gleason score ≥7). Elevated serum prostate-specific antigen (PSA) levels were defined as ≥4 ng/ml.
[
  • 4,099 cases
  • , 960 controls
]
,
100.0 % Male samples
Range = [50.0, 69.0] years European SEARCH