Polygenic Score (PGS) ID: PGS000158

Predicted Trait
Reported Trait Ovarian cancer
Mapped Trait(s) ovarian carcinoma (EFO_0001075)
Released in PGS: April 29, 2020

Score Details

Score Construction
PGS Name cGRS_Ovarian
Original Genome Build NR
Number of Variants 11
Development Method
Name Pruning + Thresholding
Parameters GWAS significant and r2 < 0.2. PGS levels were computed as product(dosage*weight/expected risk effect), where the expected risk effect for each variant was calculated based on the risk allele frequence (f) and risk allele weight (OR) as f^2*OR^2 + 2f(1-f)OR + (1-f)^2.
PGS Source
PGS Catalog Publication (PGP) ID PGP000075
Citation (link to publication) Shi Z et al. Cancer Med (2019)

Contributing Samples

Source of Variant Associations (GWAS)
Study Identifiers Sample Numbers Sample Ancestry
GWAS Catalog: GCST001941
EuropePMC: 23535730
8,165 individuals European
GWAS Catalog: GCST001917
EuropePMC: 23544013
2,727 individuals European
GWAS Catalog: GCST000802
EuropePMC: 20852632
4,122 individuals European
GWAS Catalog: GCST002748
EuropePMC: 25581431
13,491 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
PGS Sample Set 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
PPM000478 PSS000278 PGP000075
Shi Z et al. (2019)
Reported Trait: Ovarian cancer Mean realative risk: 1.12[1.08, 1.16]
Wilcoxon test (case vs. control) p-value: 0.000145
PPM000489 PSS000278 PGP000075
Shi Z et al. (2019)
Reported Trait: Ovarian cancer Odds Ratio (OR; high vs. average risk groups): 1.63[1.3, 2.06]

Evaluated Samples

PGS Sample Set 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
PSS000278 Primary tumor samples from TCGA
  • 531 cases
  • , 0 controls
0.0 % Male samples
Mean = 60.0 years
Sd = 12.0 years
European TCGA
  • 0 cases
  • , 7,020 controls
0.0 % Male samples
European eMERGE