Polygenic Score (PGS) ID: PGS000044

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

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)

Contributing Samples

Source of Variant Associations (GWAS)
Study Identifiers Sample Numbers Sample Ancestry
GWAS Catalog: GCST001942
EuropePMC: 23535732
22,548 individuals European
GWAS Catalog: GCST001148
EuropePMC: 21743467
13,560 individuals European
GWAS Catalog: GCST000153
EuropePMC: 18264098
23,226 individuals European
GWAS Catalog: GCST000488
EuropePMC: 19767753
3,748 individuals European
GWAS Catalog: GCST000750
EuropePMC: 20676098
4,969 individuals East Asian
GWAS Catalog: GCST001147
EuropePMC: 21743057
7,240 individuals European
GWAS Catalog: GCST000152
EuropePMC: 18264097
3,748 individuals European
GWAS Catalog: GCST000489
EuropePMC: 19767754
37,350 individuals European
GWAS Catalog: GCST000154
EuropePMC: 18264096
2,329 individuals European
GWAS Catalog: GCST000017
EuropePMC: 17401363
2,329 individuals European
GWAS Catalog: GCST001702
EuropePMC: 23023329
2,425 individuals East Asian
GWAS Catalog: GCST000128
EuropePMC: 18073375
2,834 individuals European
GWAS Catalog: GCST001714
EuropePMC: 23065704
22,548 individuals European
GWAS Catalog: GCST000019
EuropePMC: 17401366
4,517 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 ID)
PGS Sample Set ID
(PSS ID)
Performance Source Trait PGS Effect Sizes
(per SD change)
PGS Classification Metrics Other Metrics Covariates Included in the Model PGS Performance: Other Relevant Information
PPM000104 PSS000068 PGP000031
Pashayan N et al. (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
PPM000105 PSS000069 PGP000032
Pashayan N et al. (2015)
Ext.
Reported Trait: aggressive prostate cancer (Gleason score ⩾7) OR (above vs. below 50th percentile of PRS): 1.56[1.15, 2.1]

Evaluated Samples

PGS Sample Set ID
(PSS ID)
Detailed Phenotype Description 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