Polygenic Score (PGS) ID: PGS000391

Predicted Trait
Reported Trait Lung and bronchus cancer
Mapped Trait(s)
Additional Trait Information PheCode 165.1
Released in PGS Catalog: Dec. 15, 2020
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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 PRSWEB_PHECODE165.1_GWAS-Catalog-r2019-05-03-X165.1_PT_MGI_20200608
Development Method
Name Pruning and Thresholding (P+T)
Parameters LD Clumping (MAF >= 1%, r^2 <= 0.1) & P<=1e-10
Variants
Original Genome Build GRCh37
Number of Variants 14
Effect Weight Type NR
PGS Source
PGS Catalog Publication (PGP) ID PGP000118
Citation (link to publication) Fritsche LG et al. Am J Hum Genet (2020)
Ancestry Distribution
Source of Variant
Associations (GWAS)
European: 100%
428,696 individuals (100%)
Score Development/Training
European: 100%
4,900 individuals (100%)
PGS Evaluation
European: 100%
2 Sample Sets

Development Samples

Source of Variant Associations (GWAS)
Study Identifiers Sample Numbers Sample Ancestry Cohort(s)
GWAS Catalog: GCST000506
Europe PMC: 19836008
 11,587 individuals European NR
GWAS Catalog: GCST002466
Europe PMC: 24880342
 27,209 individuals European NR
GWAS Catalog: GCST004744
Europe PMC: 28604730
 66,756 individuals European NR
GWAS Catalog: GCST004746
Europe PMC: 28604730
 24,108 individuals European NR
GWAS Catalog: GCST004747
Europe PMC: 28604730
 9,859 individuals European NR
GWAS Catalog: GCST004748
Europe PMC: 28604730
 85,716 individuals European NR
GWAS Catalog: GCST004749
Europe PMC: 28604730
 40,187 individuals European NR
GWAS Catalog: GCST004750
Europe PMC: 28604730
 63,053 individuals European NR
GWAS Catalog: GCST006086
Europe PMC: 29924316
 35,953 individuals European NR
GWAS Catalog: GCST006087
Europe PMC: 29924316
 32,338 individuals European NR
GWAS Catalog: GCST006088
Europe PMC: 29924316
 31,930 individuals European 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
Europe PMC: 32991828
[
  • 446 cases
  • , 4,454 controls
]
 European MGI PheCode:165.1; ICD9CM:162.0, 162.2, 162.3, 162.4, 162.5, 162.8, 162.9, 209.21, 231.2, V10.11; ICD10CM:C33, C34, C34.0, C34.00, C34.01, C34.02, C34.1, C34.10, C34.11, C34.12, C34.2, C34.3, C34.30, C34.31, C34.32, C34.8, C34.80, C34.81, C34.82, C34.9, C34.90, C34.91, C34.92, C7A.090, D02.2, D02.20, D02.21, D02.22 — — — —

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
PPM001076 PSS000541|
European Ancestry|
4,698 individuals
 PGP000118 |
Fritsche LG et al. Am J Hum Genet (2020)
 Reported Trait: Cancer of bronchus; lung OR: 1.12 [1.015, 1.237]
β: 0.114 (0.0507)		 AUROC: 0.529 [0.503, 0.558] Nagelkerke's Pseudo-R²: 0.00234
Brier score: 0.0827
Odds Ratio (OR, top 1% vs. Rest): 1.75 [0.796, 3.85]		 age, sex, batch PCs 1-4 Cancer PRSweb PheWAS Results: PRSWEB_PHECODE165.1_GWAS-Catalog-r2019-05-03-X165.1_PT_MGI_20200608
PPM020287 PSS011324|
European Ancestry|
1,202 individuals
 PGP000539 |
Lebrett MB et al. Genet Med (2023)
|Ext.		 Reported Trait: Lung cancer — AUROC: 0.731 [0.703, 0.759] — 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 —
PSS000541 PheCode:165.1; ICD9CM:162.0, 162.2, 162.3, 162.4, 162.5, 162.8, 162.9, 209.21, 231.2, V10.11; ICD10CM:C33, C34, C34.0, C34.00, C34.01, C34.02, C34.1, C34.10, C34.11, C34.12, C34.2, C34.3, C34.30, C34.31, C34.32, C34.8, C34.80, C34.81, C34.82, C34.9, C34.90, C34.91, C34.92, C7A.090, D02.2, D02.20, D02.21, D02.22 —
[
  • 428 cases
  • , 4,270 controls
]
 — European — MGI —