Polygenic Score (PGS) ID: PGS000158

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

Score Construction
PGS Name cGRS_Ovarian
Variants
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)
Ancestry Distribution
Source of Variant
Associations (GWAS)
European: 100%
28,505 individuals (100%)
PGS Evaluation
European: 100%
1 Sample Sets

Development Samples

Source of Variant Associations (GWAS)
Study Identifiers Sample Numbers Sample Ancestry
GWAS Catalog: GCST001941
Europe PMC: 2353573
8,165 individuals European
GWAS Catalog: GCST001917
Europe PMC: 23544013
2,727 individuals European
GWAS Catalog: GCST000802
Europe PMC: 20852632
4,122 individuals European
GWAS Catalog: GCST002748
Europe PMC: 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 (PPM)
PGS Sample Set ID
(PSS)
Performance Source Trait PGS Effect Sizes
(per SD change)
Classification Metrics Other Metrics Covariates Included in the Model PGS Performance:
Other Relevant Information
PPM000489 PSS000278|
European Ancestry|
7,551 individuals
PGP000075 |
Shi Z et al. Cancer Med (2019)
Reported Trait: Ovarian cancer Odds Ratio (OR; high vs. average risk groups): 1.63 [1.3, 2.06]
PPM000478 PSS000278|
European Ancestry|
7,551 individuals
PGP000075 |
Shi Z et al. Cancer Med (2019)
Reported Trait: Ovarian cancer Mean realative risk: 1.12 [1.08, 1.16]
Wilcoxon test (case vs. control) p-value: 0.00015

Evaluated Samples

PGS Sample Set ID
(PSS)
Phenotype Definitions and Methods 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
PSS000278
[
  • 0 cases
  • , 7,020 controls
]
,
0.0 % Male samples
European eMERGE