Polygenic Score (PGS) ID: PGS002747

Predicted Trait
Reported Trait Gastrointestinal cancer
Mapped Trait(s) Digestive System Carcinoma (EFO_1000218)
Released in PGS Catalog: Sept. 8, 2022
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Score Details

Score Construction
Development Method
Name Genome-wide significant SNPs
Parameters r2>0.8, p<5E-08
Original Genome Build GRCh37
Number of Variants 106
Effect Weight Type beta
PGS Source
PGS Catalog Publication (PGP) ID PGP000359
Citation (link to publication) Liu Y et al. Cancer Med (2022)
Ancestry Distribution
Source of Variant
Associations (GWAS)
Not Reported: 58.7%
European: 41.3%
561,306 individuals (100%)
PGS Evaluation
European: 100%
1 Sample Sets

Development Samples

Source of Variant Associations (GWAS)
Study Identifiers Sample Numbers Sample Ancestry Cohort(s)
Europe PMC: 30243622
329,463 individuals Not reported NR
GWAS Catalog: GCST002992
Europe PMC: 26098866
208,152 individuals European NR
GWAS Catalog: GCST012877
Europe PMC: 30510241
23,691 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
Performance Source Trait PGS Effect Sizes
(per SD change)
Classification Metrics Other Metrics Covariates Included in the Model PGS Performance:
Other Relevant Information
PPM014926 PSS009932|
European Ancestry|
430,036 individuals
PGP000359 |
Liu Y et al. Cancer Med (2022)
Reported Trait: Incident gastrointestinal cancer Hazard Ratio (HR, high vs low): 2.28 [2.09, 2.49] Age group, gender, qualification, Townsend Deprivation Index, family history of cancer, smoking status, alcohol consumption and the top 10 genetic principal components
PPM014927 PSS009932|
European Ancestry|
430,036 individuals
PGP000359 |
Liu Y et al. Cancer Med (2022)
Reported Trait: Incident gastrointestinal cancer (with metabolic syndrome) Hazard Ratio (HR, high vs low): 2.75 [2.43, 3.12]

Evaluated Samples

PGS Sample Set ID
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
PSS009932 MetS is defined as having any three or more of five MetS components, including central obesity, hypertension, dyslipidemia, hypertriglyceridemia, and hyperglyce- mia, according to the National Cholesterol Education Programme Adult Treatment Panel III criteria (NCEP- ATP III)
  • 5,494 cases
  • , 424,542 controls
European UKB