Polygenic Score (PGS) ID: PGS002299

Predicted Trait
Reported Trait Gastric cancer
Mapped Trait(s) gastric cancer (MONDO_0001056)
Released in PGS Catalog: June 9, 2022
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Score Details

Score Construction
PGS Name PRS3_gastric
Development Method
Name Genome-wide significant variants
Parameters r2>=0.93
Variants
Original Genome Build hg19
Number of Variants 3
Effect Weight Type NR
PGS Source
PGS Catalog Publication (PGP) ID PGP000328
Citation (link to publication) Choi J et al. Int J Cancer (2020)
Ancestry Distribution
Source of Variant
Associations (GWAS)
European: 100%
208,152 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: GCST002992
Europe PMC: 26098866
 208,152 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
PPM013028 PSS009662|
European Ancestry|
272 individuals
 PGP000328 |
Choi J et al. Int J Cancer (2020)
 Reported Trait: Gastric cancer — AUROC: 0.56 [0.54, 0.58] — — —
PPM013036 PSS009662|
European Ancestry|
272 individuals
 PGP000328 |
Choi J et al. Int J Cancer (2020)
 Reported Trait: Gastric cancer — — Hazard ratio (HR top 5% vs average): 1.27 [0.75, 2.15] Age, birth cohort, genotyping array, top 10 PCs for ancestry and sex (for nonsex specific cancer only) —

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
PSS009662 gastric cancer (ICD- 9 = 151 or ICD-10 = C16) — 272 individuals — European — UKB —