Polygenic Score (PGS) ID: PGS003393

Predicted Trait
Reported Trait Lung adenocarcinoma
Mapped Trait(s) lung adenocarcinoma (EFO_0000571)
Released in PGS Catalog: Jan. 19, 2023
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Score Details

Score Construction
PGS Name best_LUAD
Development Method
Name Pruning and Thresholding (P+T)
Parameters p < 1×10^-4, r2 < 0.1
Variants
Original Genome Build GRCh37
Number of Variants 74
Effect Weight Type beta
PGS Source
PGS Catalog Publication (PGP) ID PGP000413
Citation (link to publication) Namba S et al. Cancer Res (2022)
Ancestry Distribution
Source of Variant
Associations (GWAS)
European: 100%
66,756 individuals (100%)
PGS Evaluation
European: 100%
1 Sample Sets

Development Samples

Source of Variant Associations (GWAS)
Study Identifiers Sample Numbers Sample Ancestry Cohort(s)
GWAS Catalog: GCST004744
Europe PMC: 28604730
 66,756 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
(PSS) 		Performance Source Trait PGS Effect Sizes
(per SD change) 		Classification Metrics Other Metrics Covariates Included in the Model PGS Performance:
Other Relevant Information
PPM016268 PSS010080|
European Ancestry|
270,412 individuals
 PGP000413 |
Namba S et al. Cancer Res (2022)
 Reported Trait: lung adenocarcinoma — AUROC: 0.743 R²: 0.00649 age, sex, top 20 genetic principal components —

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
PSS010080 C34, histology was one of the followings: Squamous cell carcinoma; Squamous cell carcinoma, keratinizing; Squamous cell carcinoma, large cell, non-keratinizing; Squamous cell carcinoma, micro-invasive; Squamous cell carcinoma, small cell, non-keratinizing —
[
  • 868 cases
  • , 269,544 controls
]
 — European
(British)		 — UKB Controls were samples without any cancer diagnosis or self-reported cancer