Polygenic Score (PGS) ID: PGS000556

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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Terms and Licenses
PGS obtained from the Catalog should be cited appropriately, and used in accordance with any licensing restrictions set by the authors. See EBI Terms of Use (https://www.ebi.ac.uk/about/terms-of-use/) for additional details.

Score Details

Score Construction
PGS Name PRSWEB_PHECODE184.11_Phelan-LSASBOC_LASSOSUM_UKB_20200608
Development Method
Name lassosum
Parameters s=0.2;Lambda=0.008859
Variants
Original Genome Build GRCh37
Number of Variants 486,841
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%
5,130 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
[
  • 466 cases
  • , 4,664 controls
]
 European UKB PheCode:184.11; ICD9:183.0; ICD10:C56 — — — —

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
PPM001241 PSS000572|
European Ancestry|
5,196 individuals
 PGP000118 |
Fritsche LG et al. Am J Hum Genet (2020)
 Reported Trait: Malignant neoplasm of ovary OR: 1.122 [1.022, 1.233]
β: 0.116 (0.0478)		 AUROC: 0.516 [0.489, 0.544] Nagelkerke's Pseudo-R²: 0.00242
Brier score: 0.0826
Odds Ratio (OR, top 1% vs. Rest): 2.4 [1.24, 4.62]		 age, sex, batch PCs 1-4 Cancer PRSweb PheWAS Results: PRSWEB_PHECODE184.11_Phelan-LSASBOC_LASSOSUM_UKB_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
PSS000572 PheCode:184.11; ICD9:183.0; ICD10:C56 —
[
  • 473 cases
  • , 4,723 controls
]
 — European — UKB —