Polygenic Score (PGS) ID: PGS000075

Predicted Trait
Reported Trait Endometrial cancer
Mapped Trait(s) endometrial carcinoma (EFO_1001512)
Released in PGS Catalog: Feb. 12, 2020
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Score Details

Score Construction
PGS Name CC_Endo
Development Method
Name Genome-wide significant variants
Parameters P < 5e-8, MAF > 1%, biallelic SNPs, LD-thin r2 > 0.3
Variants
Original Genome Build GRCh37
Number of Variants 9
Effect Weight Type NR
PGS Source
PGS Catalog Publication (PGP) ID PGP000050
Citation (link to publication) Graff RE et al. Nat Commun (2021)
Ancestry Distribution
Source of Variant
Associations (GWAS)
European: 66.4%
Not Reported: 33.6%
43,054 individuals (100%)
PGS Evaluation
European: 100%
2 Sample Sets

Development Samples

Source of Variant Associations (GWAS)
Study Identifiers Sample Numbers Sample Ancestry Cohort(s)
GWAS Catalog: GCST003436
Europe PMC: 27008869
16,852 individuals European NR
GWAS Catalog: GCST003524
Europe PMC: 27135401
11,756 individuals European NR
GWAS Catalog: GCST005906
Europe PMC: 29608257
14,446 individuals NR NR

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
PPM000195 PSS000114|
European Ancestry|
221,699 individuals
PGP000050 |
Graff RE et al. Nat Commun (2021)
Reported Trait: Endometrial cancer OR: 1.19 [1.14, 1.24] Genotyping reagent kit (GERA cohort only), genotyping array (UK Biobank only), age, 10 PCs. Results from meta-analysis of GERA and UKB
PPM002041 PSS001014|
European Ancestry|
212,156 individuals
PGP000186 |
Kachuri L et al. Nat Commun (2020)
|Ext.
Reported Trait: Incident endometrial cancer HR: 1.19 [1.1, 1.29] AUROC: 0.755
C-index: 0.749 (0.011)
Age at assessment, family history of cancer, genotyping array, PCs(1-15), parity ( ≥1 live birth vs. none), age at menarche, body mass index, Menopausal status (pre-menopausal vs. post-menopausal vs. unknown or hysterectomy), ever used hormone replacement therapy, oral contraceptive use (never used (0) vs. <20 years vs. ≥20 years), C-index calculated as a weighted average between 1 and 5 years and AUC at 5 years.

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
PSS000114 Cancer diagnoses were obtained from reigstry data in GERA, and ICD-9/10 codes mapped to ICD-O-3 codes in UK Biobank. Cancers for this phenotype were classified using the following SEER site recode(s): 27020
[
  • 2,051 cases
  • , 219,648 controls
]
,
0.0 % Male samples
European GERA, UKB
PSS001014 Individuals with at least one recorded incident diagnosis of a borderline, in situ, or malignant primary cancer were defined as cases.
[
  • 643 cases
  • , 211,513 controls
]
,
0.0 % Male samples
European UKB