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(Variants and weights)

Polygenic Score (PGS) ID: PGS000044

Predicted Trait

Reported Trait: Prostate cancer
Mapped Trait(s) (Experimental Factor Ontology (EFO) IDs): prostate carcinoma

Score Details

Name: PrCa66

Original Genome Build: GRCh38
Number of Variants: 66

PGS Development Method: Known susceptibility loci (genome-wide significant SNPs)
PGS Development Details/Relevant Parameters: P-value < 5E-8, top SNP

Citation: Pashayan N et al. Br J Cancer (2015) | PGS Catalog Publication ID: PGP000031

Contributing Samples

Source of Variant Associations (GWAS)
Study Identifiers Sample Numbers Sample Ancestry
GWAS Catalog: GCST001942
PubMed: 23535732
22,548 individuals European
GWAS Catalog: GCST001148
PubMed: 21743467
13,560 individuals European
GWAS Catalog: GCST000153
PubMed: 18264098
23,226 individuals European
GWAS Catalog: GCST000488
PubMed: 19767753
3,748 individuals European
GWAS Catalog: GCST000750
PubMed: 20676098
4,969 individuals East Asian
GWAS Catalog: GCST001147
PubMed: 21743057
7,240 individuals European
GWAS Catalog: GCST000152
PubMed: 18264097
3,748 individuals European
GWAS Catalog: GCST000489
PubMed: 19767754
37,350 individuals European
GWAS Catalog: GCST000154
PubMed: 18264096
2,329 individuals European
GWAS Catalog: GCST000019
PubMed: 17401366
4,517 individuals European
GWAS Catalog: GCST000017
PubMed: 17401363
2,329 individuals European
GWAS Catalog: GCST001702
PubMed: 23023329
2,425 individuals East Asian
GWAS Catalog: GCST000128
PubMed: 18073375
2,834 individuals European
GWAS Catalog: GCST001714
PubMed: 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 (PPM) ID PGS Catalog Sample Set (PSS) ID Performance Source Trait PGS Effect Sizes
(per SD change)
PGS Classification Metrics Other Metrics Covariates Included in PGS Model PGS Performance: Other Relevant Information
PPM000104 PSS000068 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 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 Catalog Sample Set (PSS) ID Detailed Phenotype Description (e.g. ICD/SNOMED codes used to identify cases) Sample Numbers 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. 8,796 individuals
[ 2,148 cases, 6,648 controls]
100.00 %% Male samples
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. 5,059 individuals
[ 4,099 cases, 960 controls]
100.00 %% Male samples
European SEARCH
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 individuals
[ 3,157 cases, 0 controls]
100.00 %% Male samples
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. 4,967 individuals
[ 1,089 cases, 3,878 controls]
100.00 %% Male samples
European
(Finnish)
ERSPC