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(Variants and weights)

Polygenic Score (PGS) ID: PGS000085

Predicted Trait

Reported Trait: Esophageal and stomach cancers
Mapped Trait(s) (Experimental Factor Ontology (EFO) IDs): gastric carcinoma Barrett's esophagus

Score Details

Name: CC_Stomach

Original Genome Build: GRCh37
Number of Variants: 13

PGS Development Method: Genome-wide significant SNPs
PGS Development Details/Relevant Parameters: P < 5x10-8, MAF > 1%, biallelic SNPs, LD-thin r2 > 0.3

Citation: Graff RE et al. bioRxiv (2020) | PGS Catalog Publication ID: PGP000050

Contributing Samples

Source of Variant Associations (GWAS)
Study Identifiers Sample Numbers Sample Ancestry
GWAS Catalog: GCST003738
PubMed: 27527254
23,326 individuals European
GWAS Catalog: GCST002992
PubMed: 26098866
208,152 individuals European
GWAS Catalog: GCST001675
PubMed: 22961001
7,024 individuals European

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 (PPM) ID PGS Catalog Sample Set (PSS) ID Performance Source Trait PGS Effect Sizes
(per SD change)
PGS Classification Metrics Other Metrics Covariates Included in PGS Model PGS Performance: Other Relevant Information
PPM000205 PSS000124 Graff RE et al. (2020) Reported Trait: Esophageal and stomach cancers OR: 1.07 [1.0 - 1.13] Genotyping reagent kit (GERA cohort only), genotyping array (UK Biobank only), age, sex, 10 PCs. Results from meta-analysis of GERA and UKB

Evaluated Samples

PGS Catalog Sample Set (PSS) ID Detailed Phenotype Description (e.g. ICD/SNOMED codes used to identify cases) Sample Numbers Sample Ancestry Additional Ancestry Description Cohort(s) Additional Sample/Cohort Information
PSS000124 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): 21010 and 21020 411,448 individuals
[ 1,094 cases, 410,354 controls]
0.46 % Male samples
European GERA, UKB