Polygenic Score (PGS) ID: PGS000789

Predicted Trait
Reported Trait Lung cancer
Mapped Trait(s) lung carcinoma (EFO_0001071)
Released in PGS Catalog: May 28, 2021
Download Score FTP directory
Terms and Licenses
PGS obtained from the Catalog should be cited appropriately, and used in accordance with any licensing restrictions set by the authors. See EBI Terms of Use (https://www.ebi.ac.uk/about/terms-of-use/) for additional details.

Score Details

Score Construction
PGS Name CC_Lung_IV
Development Method
Name 109 variants from Graff et al (PGS000078) with inverse variant weights
Parameters NR
Variants
Original Genome Build GRCh37
Number of Variants 109
Effect Weight Type Inverse-variance weighting
PGS Source
PGS Catalog Publication (PGP) ID PGP000186
Citation (link to publication) Kachuri L et al. Nat Commun (2020)
Ancestry Distribution
Source of Variant
Associations (GWAS)
European: 100%
215,467 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: GCST006088
Europe PMC: 29924316
 31,930 individuals European 6 cohorts
  • EAGLE
  • ,GELCC
  • ,IARC
  • ,PLCO
  • ,SLRI
  • ,deCODE
Europe PMC: 21303977
[
  • 2,783 cases
  • , 40,358 controls
]
 European ICR, ODZH
GWAS Catalog: GCST001638
Europe PMC: 22899653
 44,385 individuals European 16 cohorts
  • ATBC
  • ,CARET
  • ,EAGLE
  • ,HGF
  • ,HUNT2
  • ,Harvard
  • ,IARC
  • ,ICR-GWAS
  • ,LLP
  • ,MDACCS
  • ,PLCO
  • ,SLRI
  • ,Tromso
  • ,UKBS
  • ,WTCCC
  • ,deCODE
GWAS Catalog: GCST000257
Europe PMC: 18978787
 10,295 individuals European B58C, GELCAPS, IARC, MDACCS
GWAS Catalog: GCST004748
Europe PMC: 2860473
 85,716 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
PPM002060 PSS001017|
European Ancestry|
392,539 individuals
 PGP000186 |
Kachuri L et al. Nat Commun (2020)
 Reported Trait: Incident lung cancer HR: 1.17 [1.12, 1.23] AUROC: 0.846
C-index: 0.849 (0.006)		 R²: 0.799 Age at assessment, sex, genotyping array, PCs(1-15), family history of lung cancer, PM2.5 in 2010, cigarettes per day, years of smoking, smoking status (never vs. former vs. current), smoking status*cigarettes per day, smoking stutus*years of smoking C-index calculated as a weighted average between 1 and 5 years and AUC at 5 years.
PPM002072 PSS001017|
European Ancestry|
392,539 individuals
 PGP000186 |
Kachuri L et al. Nat Commun (2020)
 Reported Trait: Incident lung cancer — AUROC: 0.71
C-index: 0.711 (0.007)		 R²: 0.322 Age, sex, genotyping array, PCs(1-15) C-index calculated as a weighted average between 1 and 5 years and AUC at 5 years.
PPM002073 PSS001017|
European Ancestry|
392,539 individuals
 PGP000186 |
Kachuri L et al. Nat Commun (2020)
 Reported Trait: Incident lung cancer in never smokers — AUROC: 0.723
C-index: 0.723 (0.02)		 R²: 0.354 Age, sex, genotyping array, PCs(1-15), family history of lung cancer, PM2.5 level in 2010 C-index calculated as a weighted average between 1 and 5 years and AUC at 5 years.
PPM002074 PSS001017|
European Ancestry|
392,539 individuals
 PGP000186 |
Kachuri L et al. Nat Commun (2020)
 Reported Trait: Incident lung cancer in smokers — AUROC: 0.808
C-index: 0.809 (0.007)		 R²: 0.657 Age, sex, genotyping array, PCs(1-15), family history of lung cancer, PM2.5 level in 2010, cigarettes per day, years of smoking, smoking status (former vs. current), years since quitting, (smoking status)*(cigarettes per day), (smoking status*years of smoking) C-index calculated as a weighted average between 1 and 5 years and AUC at 5 years.

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
PSS001017 Individuals with at least one recorded incident diagnosis of a borderline, in situ, or malignant primary cancer were defined as cases. 207 of the cases were in non-smokers and 1334 were in smokers. —
[
  • 1,541 cases
  • , 390,998 controls
]
 — European — UKB —