Polygenic Score (PGS) ID: PGS000078

Predicted Trait
Reported Trait Lung cancer
Mapped Trait(s) lung carcinoma (EFO_0001071)
Released in PGS Catalog: Feb. 12, 2020
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Score Details

Score Construction
PGS Name CC_Lung
Development Method
Name Genome-wide significant variants
Parameters P < 5e-8, MAF > 1%, biallelic SNPs, LD-thin r2 > 0.3
Variants
Original Genome Build GRCh37
Number of Variants 109
Effect Weight Type NR
PGS Source
PGS Catalog Publication (PGP) ID PGP000050
Citation (link to publication) Graff RE et al. Nat Commun (2021)
Ancestry Distribution
Source of Variant
Associations (GWAS)
European: 100%
183,537 individuals (100%)
PGS Evaluation
European: 100%
4 Sample Sets

Development Samples

Source of Variant Associations (GWAS)
Study Identifiers Sample Numbers Sample Ancestry Cohort(s)
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
Europe PMC: 21303977
[
  • 2,783 cases
  • , 40,358 controls
]
 European NR
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

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
PPM000198 PSS000117|
European Ancestry|
412,842 individuals
 PGP000050 |
Graff RE et al. Nat Commun (2021)
 Reported Trait: Lung cancer OR: 1.12 [1.08, 1.17] — — Genotyping reagent kit (GERA cohort only), genotyping array (UK Biobank only), age, sex, 10 PCs. Results from meta-analysis of GERA and UKB
PPM002044 PSS001017|
European Ancestry|
392,539 individuals
 PGP000186 |
Kachuri L et al. Nat Commun (2020)
|Ext.		 Reported Trait: Incident lung cancer HR: 1.16 [1.11, 1.22] AUROC: 0.846
C-index: 0.849 (0.006)		 — 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.
PPM017166 PSS010146|
European Ancestry|
1,256 individuals
 PGP000443 |
Byrne S et al. Int J Epidemiol (2023)
|Ext.		 Reported Trait: Lung cancer HR: 1.26 [1.19, 1.33] — — age at baseline, sex (where relevant), assessment centre, 40 principal components of ancestries (PCs), Townsend Index, education, birth location, income, lifestyle index, additional cancer-specific covariates —
PPM020285 PSS011324|
European Ancestry|
1,202 individuals
 PGP000539 |
Lebrett MB et al. Genet Med (2023)
|Ext.		 Reported Trait: Lung cancer — AUROC: 0.728 [0.7, 0.756] — Age, sex, current smoking status, BMI, forced expiratory volume in 1 second/forced vital capacity ratio —

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
PSS011324 — —
[
  • 652 cases
  • , 550 controls
]
,
47.0 % Male samples
 Median = 65.0 years European — MCRC —
PSS010146 — —
[
  • 104 cases
  • , 1,152 controls
]
 — European — UKB —
PSS000117 Cancer diagnoses were obtained from reigstry data in GERA, and ICD-9/10 codes mapped to ICD-O-3 codes in UK Biobank. Cancers for this phenotype were classified using the following SEER site recode(s): 22030 —
[
  • 2,488 cases
  • , 410,354 controls
]
,
46.0 % Male samples
 Mean = 58.0 years European — GERA, UKB —
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 —