Polygenic Score (PGS) ID: PGS000085

Predicted Trait
Reported Trait Esophageal and stomach cancers
Mapped Trait(s)
Released in PGS: Feb. 12, 2020

Score Details

Score Construction
PGS Name CC_Stomach
Original Genome Build GRCh37
Number of Variants 13
Development Method
Name Genome-wide significant SNPs
Parameters P < 5x10-8, MAF > 1%, biallelic SNPs, LD-thin r2 > 0.3
PGS Source
PGS Catalog Publication (PGP) ID PGP000050
Citation (link to publication) Graff RE et al. bioRxiv (2020) Preprint

Contributing Samples

Source of Variant Associations (GWAS)
Study Identifiers Sample Numbers Sample Ancestry
GWAS Catalog: GCST003738
EuropePMC: 27527254
23,326 individuals European
GWAS Catalog: GCST002992
EuropePMC: 26098866
208,152 individuals European
GWAS Catalog: GCST001675
EuropePMC: 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 ID
PGS Sample Set ID
Performance Source Trait PGS Effect Sizes
(per SD change)
PGS Classification Metrics Other Metrics Covariates Included in the Model PGS Performance: Other Relevant Information
PPM000205 PSS000124 PGP000050
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 Sample Set ID
Detailed Phenotype Description Participant Follow-up Time Sample Numbers Age of Study Participants 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
  • 1,094 cases
  • , 410,354 controls
0.46 % Male samples
Mean = 58.0 years European GERA, UKB