Polygenic Score (PGS) ID: PGS000084

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Predicted Trait
Reported Trait Prostate cancer
Mapped Trait(s) prostate carcinoma (EFO_0001663)
Released in PGS: Feb. 12, 2020

Score Details

Score Construction
PGS Name CC_Prostate
Variants
Original Genome Build GRCh37
Number of Variants 161
Development Method
Name Genome-wide significant SNPs
Parameters P < 5x10-8, MAF > 1%, biallelic SNPs, LD-thin r2 > 0.3
PGS Source
PGS Catalog Publication (PGP) ID PGP000050
Citation (link to publication) Graff RE et al. bioRxiv (2020) Preprint

Contributing Samples

Source of Variant Associations (GWAS)
Study Identifiers Sample Numbers Sample Ancestry
EuropePMC: 2688139
[
  • 495 cases
  • , 640 controls
]
,
100.0 % Male samples
 East Asian
(Han Chinese)
GWAS Catalog: GCST002606
EuropePMC: 25217961		 67,543 individuals European
GWAS Catalog: GCST002606
EuropePMC: 25217961		 2,080 individuals Hispanic or Latin American
GWAS Catalog: GCST002606
EuropePMC: 25217961		 6,954 individuals East Asian
GWAS Catalog: GCST002606
EuropePMC: 25217961		 10,463 individuals Sub-Saharan African, African American or Afro-Caribbean
GWAS Catalog: GCST002890
EuropePMC: 25939597		 7,541 individuals European
GWAS Catalog: GCST000152
EuropePMC: 18264097		 3,748 individuals European
GWAS Catalog: GCST001942
EuropePMC: 23535732		 22,548 individuals European
GWAS Catalog: GCST003587
EuropePMC: 27197191		 123,671 individuals European
GWAS Catalog: GCST002944
EuropePMC: 26034056		 3,226 individuals East Asian
GWAS Catalog: GCST002944
EuropePMC: 26034056		 2,251 individuals African American or Afro-Caribbean
GWAS Catalog: GCST002944
EuropePMC: 26034056		 3,629 individuals Hispanic or Latin American
GWAS Catalog: GCST002944
EuropePMC: 26034056		 37,272 individuals European
GWAS Catalog: GCST002421
EuropePMC: 24753544		 2,950 individuals European
GWAS Catalog: GCST001148
EuropePMC: 21743467		 13,560 individuals European
GWAS Catalog: GCST002413
EuropePMC: 24740154		 5,051 individuals European
GWAS Catalog: GCST001338
EuropePMC: 22130093		 545 individuals NR
GWAS Catalog: GCST001147
EuropePMC: 21743057		 7,240 individuals European
GWAS Catalog: GCST006085
EuropePMC: 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 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
PPM000204 PSS000123 PGP000050
Graff RE et al. (2020) Pre		 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 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
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 —
[
  • 10,810 cases
  • , 190,706 controls
]
,
1.0 % Male samples
 — European — GERA, UKB —