Polygenic Score (PGS) ID: PGS000542

Predicted Trait
Reported Trait Malignant neoplasm of uterus
Mapped Trait(s) uterine cancer (MONDO_0002715)
Additional Trait Information PheCode 182
Released in PGS Catalog: Dec. 15, 2020
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Score Details

Score Construction
PGS Name PRSWEB_PHECODE182_GWAS-Catalog-r2019-05-03-X182_PT_UKB_20200608
Development Method
Name Pruning and Thresholding (P+T)
Parameters LD Clumping (MAF >= 1%, r^2 <= 0.1) & P<=1e-07
Variants
Original Genome Build GRCh37
Number of Variants 20
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%
243,283 individuals (100%)
Score Development/Training
European: 100%
7,131 individuals (100%)
PGS Evaluation
European: 100%
1 Sample Sets

Development Samples

Source of Variant Associations (GWAS)
Study Identifiers Sample Numbers Sample Ancestry Cohort(s)
GWAS Catalog: GCST001040
Europe PMC: 21499250
 6,455 individuals European
(U.K.)		 NR
GWAS Catalog: GCST003524
Europe PMC: 27135401
 11,756 individuals European NR
GWAS Catalog: GCST003525
Europe PMC: 27135401
 11,626 individuals European NR
GWAS Catalog: GCST006464
Europe PMC: 30093612
 121,885 individuals European NR
GWAS Catalog: GCST006465
Europe PMC: 30093612
 54,884 individuals European NR
GWAS Catalog: GCST006466
Europe PMC: 30093612
 36,677 individuals 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
[
  • 648 cases
  • , 6,483 controls
]
 European UKB PheCode:182; ICD9:179, 182, 182.0, 182.1, 182.8, 233.2; ICD10:C54.0, C54.1, C54.2, C54.3, C54.8, C54.9, C55, D07.0 — — — —

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
PPM001227 PSS000571|
European Ancestry|
6,987 individuals
 PGP000118 |
Fritsche LG et al. Am J Hum Genet (2020)
 Reported Trait: Malignant neoplasm of uterus OR: 1.302 [1.2, 1.413]
β: 0.264 (0.0416)		 AUROC: 0.572 [0.549, 0.596] Nagelkerke's Pseudo-R²: 0.0126
Brier score: 0.082
Odds Ratio (OR, top 1% vs. Rest): 2.6 [1.5, 4.51]		 age, sex, batch PCs 1-4 Cancer PRSweb PheWAS Results: PRSWEB_PHECODE182_GWAS-Catalog-r2019-05-03-X182_PT_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
PSS000571 PheCode:182; ICD9:179, 182, 182.0, 182.1, 182.8, 233.2; ICD10:C54.0, C54.1, C54.2, C54.3, C54.8, C54.9, C55, D07.0 —
[
  • 634 cases
  • , 6,353 controls
]
 — European — UKB —