Polygenic Score (PGS) ID: PGS003388

Predicted Trait
Reported Trait Esophageal adenocarcinoma
Mapped Trait(s) esophageal adenocarcinoma (EFO_0000478)
Released in PGS Catalog: Jan. 19, 2023
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Score Details

Score Construction
PGS Name best_ESCA_EA
Development Method
Name lassosum
Parameters s = 0.5, lambda = 0.01128838
Variants
Original Genome Build GRCh37
Number of Variants 356,743
Effect Weight Type beta
PGS Source
PGS Catalog Publication (PGP) ID PGP000413
Citation (link to publication) Namba S et al. Cancer Res (2022)
Ancestry Distribution
Source of Variant
Associations (GWAS)
European: 100%
21,271 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: GCST003739
Europe PMC: 27527254
 21,271 individuals European 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
PPM016263 PSS010077|
European Ancestry|
270,026 individuals
 PGP000413 |
Namba S et al. Cancer Res (2022)
 Reported Trait: esophageal adenocarcinoma — AUROC: 0.814 R²: 0.00875 age, sex, top 20 genetic principal components —

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
PSS010077 C15, histology was one of the followings: Adenocarcinoma, NOS; Adenocarcinoma, intestinal type; Adenocarcinoma in tubulovillous adenoma —
[
  • 482 cases
  • , 269,544 controls
]
 — European
(British)		 — UKB Controls were samples without any cancer diagnosis or self-reported cancer