Polygenic Score (PGS) ID: PGS003392

Predicted Trait
Reported Trait Lung squamous cell carcinoma
Mapped Trait(s) squamous cell lung carcinoma (EFO_0000708)
Released in PGS Catalog: Jan. 19, 2023
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Score Details

Score Construction
PGS Name best_LUSC
Development Method
Name Pruning and Thresholding (P+T)
Parameters p < 1×10^-4, r2 < 0.1
Original Genome Build GRCh37
Number of Variants 90
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%
63,053 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: GCST004750
Europe PMC: 28604730
63,053 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
PPM016267 PSS010082|
European Ancestry|
270,054 individuals
PGP000413 |
Namba S et al. Cancer Res (2022)
Reported Trait: lung squamous cell carcinoma AUROC: 0.778 : 0.00075 age, sex, top 20 genetic principal components

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
PSS010082 C34, histology was one of the followings: Adenocarcinoma, intestinal type; Adenocarcinoma in tubulovillous adenoma; Adenocarcinoma in villous adenoma; Adenocarcinoma (NOS)
  • 510 cases
  • , 269,544 controls
UKB Controls were samples without any cancer diagnosis or self-reported cancer