Polygenic Score (PGS) ID: PGS000559

Predicted Trait
Reported Trait Malignant neoplasm of ovary
Mapped Trait(s) ovarian neoplasm (EFO_0003893)
Additional Trait Information PheCode 184.11
Released in PGS Catalog: Dec. 15, 2020
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Score Details

Score Construction
PGS Name PRSWEB_PHECODE184.11_Phelan-SIOC_P_5e-08_MGI_20200608
Development Method
Name GWAS Hits
Parameters LD Clumping (MAF >= 1%, r^2 <= 0.1) & P<=5e-08
Variants
Original Genome Build GRCh37
Number of Variants 21
Effect Weight Type NR
PGS Source
PGS Catalog Publication (PGP) ID PGP000118
Citation (link to publication) Fritsche LG et al. Am J Hum Genet (2020)
Ancestry Distribution
Source of Variant
Associations (GWAS)
European: 100%
314,752 individuals (100%)
Score Development/Training
European: 100%
2,122 individuals (100%)
PGS Evaluation
European: 100%
1 Sample Sets

Development Samples

Source of Variant Associations (GWAS)
Study Identifiers Sample Numbers Sample Ancestry Cohort(s)
Europe PMC: 28346442
[
  • 2,810 cases
  • , 40,941 controls
]
 European NR
Europe PMC: 28346442
[
  • 25,509 cases
  • , 40,941 controls
]
 European NR
Europe PMC: 28346442
[
  • 22,406 cases
  • , 40,941 controls
]
 European NR
Europe PMC: 28346442
[
  • 2,966 cases
  • , 40,941 controls
]
 European NR
Europe PMC: 28346442
[
  • 1,366 cases
  • , 40,941 controls
]
 European NR
Europe PMC: 28346442
[
  • 14,049 cases
  • , 40,941 controls
]
 European NR
Score Development/Training
Study Identifiers Sample Numbers Sample Ancestry Cohort(s) Phenotype Definitions & Methods Age of Study Participants Participant Follow-up Time Additional Ancestry Description Additional Sample/Cohort Information
Europe PMC: 32991828
[
  • 193 cases
  • , 1,929 controls
]
 European MGI PheCode:184.11; ICD9CM:183.0, V10.43; ICD10CM:C56, C56.1, C56.2, C56.9 — — — —

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
PPM001244 PSS000550|
European Ancestry|
1,904 individuals
 PGP000118 |
Fritsche LG et al. Am J Hum Genet (2020)
 Reported Trait: Malignant neoplasm of ovary OR: 1.183 [1.015, 1.378]
β: 0.168 (0.078)		 AUROC: 0.554 [0.509, 0.597] Nagelkerke's Pseudo-R²: 0.00516
Brier score: 0.0827
Odds Ratio (OR, top 1% vs. Rest): 0.784 [0.142, 4.32]		 age, sex, batch PCs 1-4 Cancer PRSweb PheWAS Results: PRSWEB_PHECODE184.11_Phelan-SIOC_P_5e-08_MGI_20200608

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
PSS000550 PheCode:184.11; ICD9CM:183.0, V10.43; ICD10CM:C56, C56.1, C56.2, C56.9 —
[
  • 174 cases
  • , 1,730 controls
]
 — European — MGI —