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(Variants and weights)

Polygenic Score (PGS) ID: PGS000084

Predicted Trait

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

Score Details

Name: CC_Prostate

Original Genome Build: GRCh37
Number of Variants: 161

PGS Development Method: Genome-wide significant SNPs
PGS Development Details/Relevant Parameters: P < 5x10-8, MAF > 1%, biallelic SNPs, LD-thin r2 > 0.3

Citation: Graff RE et al. bioRxiv (2020) | PGS Catalog Publication ID: PGP000050

Contributing Samples

Source of Variant Associations (GWAS)
Study Identifiers Sample Numbers Sample Ancestry
GWAS Catalog: GCST002606
PubMed: 25217961
67,543 individuals European
GWAS Catalog: GCST002606
PubMed: 25217961
2,080 individuals Hispanic or Latin American
GWAS Catalog: GCST002606
PubMed: 25217961
6,954 individuals East Asian
GWAS Catalog: GCST002606
PubMed: 25217961
10,463 individuals Sub-Saharan African, African American or Afro-Caribbean
GWAS Catalog: GCST002890
PubMed: 25939597
7,541 individuals European
GWAS Catalog: GCST000152
PubMed: 18264097
3,748 individuals European
GWAS Catalog: GCST001942
PubMed: 23535732
22,548 individuals European
GWAS Catalog: GCST003587
PubMed: 27197191
123,671 individuals European
GWAS Catalog: GCST002944
PubMed: 26034056
3,226 individuals East Asian
GWAS Catalog: GCST002944
PubMed: 26034056
2,251 individuals African American or Afro-Caribbean
GWAS Catalog: GCST002944
PubMed: 26034056
3,629 individuals Hispanic or Latin American
GWAS Catalog: GCST002944
PubMed: 26034056
37,272 individuals European
GWAS Catalog: GCST002421
PubMed: 24753544
2,950 individuals European
GWAS Catalog: GCST001148
PubMed: 21743467
13,560 individuals European
GWAS Catalog: GCST002413
PubMed: 24740154
5,051 individuals European
PubMed: 26881390.0 1,135 individuals
[ 495 cases, 640 controls]
100.00 % Male samples
East Asian
(Han Chinese)
GWAS Catalog: GCST001338
PubMed: 22130093
545 individuals NR
GWAS Catalog: GCST001147
PubMed: 21743057
7,240 individuals European
GWAS Catalog: GCST006085
PubMed: 29892016
140,254 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
PPM000204 PSS000123 Graff RE et al. (2020) Reported Trait: Prostate cancer OR: 1.44 [1.41 - 1.47] Genotyping reagent kit (GERA cohort only), genotyping array (UK Biobank only), age, 10 PCs. Results from meta-analysis of GERA and UKB

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
PSS000123 Cancer diagnoses were obtained from reigstry data in GERA, and ICD-9/10 codes mapped to ICD-O-3 codes in UK Biobank. Cancers for this phenotype were classified using the following SEER site recode(s): 28010 201,516 individuals
[ 10,810 cases, 190,706 controls]
1.00 % Male samples
European GERA, UKB