PGS Publication: PGP000551

Publication Information (EuropePMC)
Title Healthy Diet, Polygenic Risk Score, and Upper Gastrointestinal Cancer Risk: A Prospective Study from UK Biobank.
PubMed ID 36986074(Europe PMC)
doi 10.3390/nu15061344
Publication Date March 10, 2023
Journal Nutrients
Author(s) Liu W, Wang T, Zhu M, Jin G.
Released in PGS Catalog: Jan. 11, 2024

Associated Polygenic Score(s)

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Individuals included in:
G - Source of Variant Associations (GWAS)
D - Score Development/Training
E - PGS Evaluation
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Additional Diverse Ancestries
Not Reported

PGS Developed By This Publication

Polygenic Score ID & Name PGS Publication ID (PGP) Reported Trait Mapped Trait(s) (Ontology) Number of Variants Ancestry distribution
GWAS
Dev
Eval
 Scoring File (FTP Link)
PGS004320
(PRS16_UGI)
 PGP000551 |
Liu W et al. Nutrients (2023)
 Upper gastrointestinal cancer Digestive System Carcinoma 16
-
 https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS004320/ScoringFiles/PGS004320.txt.gz

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) 		Evaluated Score 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 PGS004320
(PRS16_UGI)
 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 —