Polygenic Score (PGS) ID: PGS000721

Predicted Trait
Reported Trait Lung cancer
Mapped Trait(s) lung carcinoma (EFO_0001071)
Released in PGS Catalog: Feb. 3, 2021
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Score Details

Score Construction
PGS Name PRS_Lung
Development Method
Name Genome-wide significant variants
Parameters NR
Variants
Original Genome Build hg19
Number of Variants 19
Effect Weight Type beta
PGS Source
PGS Catalog Publication (PGP) ID PGP000135
Citation (link to publication) Jia G et al. JNCI Cancer Spectr (2020)
Ancestry Distribution
Source of Variant
Associations (GWAS)
European: 100%
293,065 individuals (100%)
PGS Evaluation
European: 66.7%
East Asian: 33.3%
3 Sample Sets

Development Samples

Source of Variant Associations (GWAS)
Study Identifiers Sample Numbers Sample Ancestry Cohort(s)
Europe PMC: 27288692
[
  • 12,160 cases
  • , 16,838 controls
]
 European 6 cohorts
  • GLC
  • ,IARC
  • ,ICR-GWAS
  • ,MDACCS
  • ,NCI
  • ,SLRI
GWAS Catalog: GCST003588
Europe PMC: 27197191
 123,671 individuals European GAME-ON, GECCO
GWAS Catalog: GCST004748
Europe PMC: 2860473
 85,716 individuals European NR
GWAS Catalog: GCST000257
Europe PMC: 18978787
 10,295 individuals European B58C, GELCAPS, IARC, MDACCS
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
PPM001650 PSS000857|
European Ancestry|
400,812 individuals
 PGP000135 |
Jia G et al. JNCI Cancer Spectr (2020)
 Reported Trait: Incident lung cancer — AUROC: 0.591 [0.576, 0.606] — Genotyping array —
PPM001651 PSS000857|
European Ancestry|
400,812 individuals
 PGP000135 |
Jia G et al. JNCI Cancer Spectr (2020)
 Reported Trait: Incident lung cancer — AUROC: 0.615 [0.6, 0.629] — family history of cancer (in first-degree relatives), genotyping array —
PPM018701 PSS011072|
East Asian Ancestry|
181 individuals
 PGP000494 |
Ho PJ et al. Elife (2023)
|Ext.		 Reported Trait: Lung cancer — AUROC: 0.69 [0.65, 0.73] Hazard ratio (HR, high vs low tertile): 1.69 [1.03, 2.79] age at recruitment —
PPM020286 PSS011324|
European Ancestry|
1,202 individuals
 PGP000539 |
Lebrett MB et al. Genet Med (2023)
|Ext.		 Reported Trait: Lung cancer — AUROC: 0.738 [0.71, 0.766] — 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 —
PSS011072 — — 181 individuals,
0.0 % Male samples
 Median = 59.0 years
IQR = [55.0, 64.0] years		 East Asian
(Chinese)		 — SCHS —
PSS000857 Data and diagnoses on site-specific incident cancers were provided by the National Health Service Information Centre for participants from England and Wales (follow-up through March 31, 2016) and by the NHS Central Register Scotland for participants from Scotland (follow-up through October 31, 2015). Cancers were coded by the International Classification of Diseases, Ninth Revision (ICD-9) or the International Classification of Diseases, Tenth Revision (ICD-10). Lung cancer=(ICD-9 = 162.2–162.9 or ICD-10 = C34). Median = 5.8 years
[
  • 1,508 cases
  • , 399,304 controls
]
,
46.5 % Male samples
 — European — UKB —