Polygenic Score (PGS) ID: PGS004320

Predicted Trait
Reported Trait Upper gastrointestinal cancer
Mapped Trait(s) Digestive System Carcinoma (EFO_1000218)
Released in PGS Catalog: Jan. 11, 2024
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Score Details

Score Construction
PGS Name PRS16_UGI
Development Method
Name Genome-wide significant SNPs
Parameters r2>0.2
Variants
Original Genome Build NR
Number of Variants 16
Effect Weight Type beta
PGS Source
PGS Catalog Publication (PGP) ID PGP000551
Citation (link to publication) Liu W et al. Nutrients (2023)
Ancestry Distribution
Source of Variant
Associations (GWAS)
European: 100%
234,865 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 BEACON
GWAS Catalog: GCST002232
Europe PMC: 24121790
 5,442 individuals European BEACON
GWAS Catalog: GCST002992
Europe PMC: 26098866
 208,152 individuals European ICR

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
PPM020419 PSS011353|
European Ancestry|
415,589 individuals
 PGP000551 |
Liu W et al. Nutrients (2023)
 Reported Trait: Upper gastrointestinal cancer with unfavourable diet — — Hazard ratio (HR, unfavourable diet and PRS in top quintile vs favourable diet with PRS in bottom quintile): 1.6 [1.2, 2.13] age at recruitment, sex, assessment center (10 regions), ethnicity, Townsend deprivation index, education, BMI, glycosylated hemoglobin (HbA1c), smoking status, alcohol intake frequency, physical activity, multimorbidity, family history of cancer, and the first 10 principal components of ancestry —

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
PSS011353 — Median = 1.12 years
[
  • 1,389 cases
  • , 414,200 controls
]
,
46.46 % Male samples
 — European — UKB —