PGS Publication: PGP000607

Publication Information (EuropePMC)
Title Polygenic inheritance and its interplay with smoking history in predicting lung cancer diagnosis: a French-Canadian case-control cohort.
PubMed ID 38970920(Europe PMC)
doi 10.1016/j.ebiom.2024.105234
Publication Date July 5, 2024
Journal EBioMedicine
Author(s) Boumtje V, Manikpurage HD, Li Z, Gaudreault N, Armero VS, Boudreau DK, Renaut S, Henry C, Racine C, Eslami A, Bougeard S, Vigneau E, Morissette M, Arsenault BJ, Labbé C, Laliberté AS, Martel S, Maltais F, Couture C, Desmeules P, Mathieu P, Thériault S, Joubert P, Bossé Y.
Released in PGS Catalog: July 31, 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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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)
PGS004860
(Genome-wide-PRS)
 PGP000607 |
Boumtje V et al. EBioMedicine (2024)
 Lung cancer lung carcinoma 1,143,554
-
 https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS004860/ScoringFiles/PGS004860.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
PPM021091 PGS004860
(Genome-wide-PRS)
 PSS011520|
European Ancestry|
24,012 individuals
 PGP000607 |
Boumtje V et al. EBioMedicine (2024)
 Reported Trait: Incident lung cancer OR: 1.33 AUROC: 0.893 [0.887, 0.898] R²: 0.49 Sex, age,BMI, smocking status(ever or never smoker), and the first 10 ancestry-based PCA —

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
PSS011520 Lung cancer diagnosis was confirmed by pathological examination using resected specimens. —
[
  • 4,002 cases
  • , 20,010 controls
]
,
45.72 % Male samples
 Mean = 59.65 years European
(French cancadian)		 — CARTaGENE, LORD CARTaGENE data application number 890519