Polygenic Score (PGS) ID: PGS004884

Predicted Trait
Reported Trait Lung cancer
Mapped Trait(s) lung carcinoma (EFO_0001071)
Released in PGS Catalog: June 27, 2024
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 INTERVENE_MegaPRS_Lung_cancer
Development Method
Name megaprs.auto
Parameters BayesR, p1=0.995, p2=0.005, p3=0, p4=0
Variants
Original Genome Build GRCh37
Number of Variants 655,479
Effect Weight Type beta
PGS Source
PGS Catalog Publication (PGP) ID PGP000618
Citation (link to publication) Jermy B et al. Nat Commun (2024)
Ancestry Distribution
Source of Variant
Associations (GWAS)
European: 73.4%
East Asian: 26.6%
671,529 individuals (100%)
Score Development/Training
European: 100%
404 individuals (100%)
PGS Evaluation
European: 100%
7 Sample Sets

Development Samples

Source of Variant Associations (GWAS)
Study Identifiers Sample Numbers Sample Ancestry Cohort(s)
GWAS Catalog: GCST90018875
Europe PMC: 34594039
 492,803 individuals European NR
GWAS Catalog: GCST90018875
Europe PMC: 34594039
 178,726 individuals East Asian NR
Score Development/Training
Study Identifiers Sample Numbers Sample Ancestry Cohort(s) Phenotype Definitions & Methods Age of Study Participants Participant Follow-up Time Additional Ancestry Description Additional Sample/Cohort Information
— 404 individuals European 1000G — — — non-Finnish Europeans —

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
PPM021245 PSS011607|
European Ancestry|
38,448 individuals
 PGP000618 |
Jermy B et al. Nat Commun (2024)
 Reported Trait: Incident lung cancer HR: 1.13 [1.07, 1.19] C-index: 0.54 [0.52, 0.56] — PCs 1-10 —
PPM021246 PSS011606|
European Ancestry|
69,715 individuals
 PGP000618 |
Jermy B et al. Nat Commun (2024)
 Reported Trait: Incident lung cancer HR: 1.32 [1.24, 1.4] C-index: 0.59 [0.57, 0.61] — PCs 1-10 —
PPM021247 PSS011605|
European Ancestry|
29,427 individuals
 PGP000618 |
Jermy B et al. Nat Commun (2024)
 Reported Trait: Incident lung cancer HR: 1.26 [1.2, 1.33] C-index: 0.6 [0.58, 0.62] — PCs 1-10 —
PPM021248 PSS011603|
European Ancestry|
44,187 individuals
 PGP000618 |
Jermy B et al. Nat Commun (2024)
 Reported Trait: Incident lung cancer HR: 1.43 [1.06, 1.93] — — PCs 1-10 —
PPM021249 PSS011604|
European Ancestry|
7,018 individuals
 PGP000618 |
Jermy B et al. Nat Commun (2024)
 Reported Trait: Incident lung cancer HR: 1.21 [1.03, 1.41] C-index: 0.62 [0.57, 0.67] — PCs 1-10 —
PPM021250 PSS011602|
European Ancestry|
277,400 individuals
 PGP000618 |
Jermy B et al. Nat Commun (2024)
 Reported Trait: Incident lung cancer HR: 1.24 [1.2, 1.28] C-index: 0.62 [0.61, 0.63] — PCs 1-10 —
PPM021251 PSS011601|
European Ancestry|
199,868 individuals
 PGP000618 |
Jermy B et al. Nat Commun (2024)
 Reported Trait: Incident lung cancer HR: 1.08 [1.01, 1.16] C-index: 0.57 [0.54, 0.59] — PCs 1-10 —

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
PSS011601 — —
[
  • 798 cases
  • , 199,070 controls
]
 — European — EB —
PSS011602 — —
[
  • 4,018 cases
  • , 273,382 controls
]
 — European — FinnGen —
PSS011603 — —
[
  • 44 cases
  • , 44,143 controls
]
 — European — G&H —
PSS011604 — —
[
  • 162 cases
  • , 6,856 controls
]
 — European — GS:SFHS —
PSS011605 — —
[
  • 1,388 cases
  • , 28,039 controls
]
 — European — GEL —
PSS011606 — —
[
  • 962 cases
  • , 68,753 controls
]
 — European — HUNT —
PSS011607 — —
[
  • 1,375 cases
  • , 37,073 controls
]
 — European — MGBB —