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)
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Study Identifiers
Sample Numbers
Sample Ancestry
Cohort(s)
GWAS Catalog: GCST000506
Europe PMC: 19836008
11,587 individualsEuropeanNR
GWAS Catalog: GCST002466
Europe PMC: 24880342
27,209 individualsEuropeanNR
GWAS Catalog: GCST004744
Europe PMC: 28604730
66,756 individualsEuropeanNR
GWAS Catalog: GCST004746
Europe PMC: 28604730
24,108 individualsEuropeanNR
GWAS Catalog: GCST004747
Europe PMC: 28604730
9,859 individualsEuropeanNR
GWAS Catalog: GCST004748
Europe PMC: 28604730
85,716 individualsEuropeanNR
GWAS Catalog: GCST004749
Europe PMC: 28604730
40,187 individualsEuropeanNR
GWAS Catalog: GCST004750
Europe PMC: 28604730
63,053 individualsEuropeanNR
GWAS Catalog: GCST006086
Europe PMC: 29924316
35,953 individualsEuropeanNR
GWAS Catalog: GCST006087
Europe PMC: 29924316
32,338 individualsEuropeanNR
GWAS Catalog: GCST006088
Europe PMC: 29924316
31,930 individualsEuropeanNR
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Score Development/Training
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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
]
EuropeanMGIPheCode:165.1; ICD9CM:162.0, 162.2, 162.3, 162.4, 162.5, 162.8, 162.9, 209.21, 231.2, V10.11; ICD10C... M: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, D02.22Show more————
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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.

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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
PPM001076PSS000541|
European Ancestry|
4,698 individuals
PGP000118 |
Fritsche LG et al. Am J Hum Genet (2020)
Reported Trait: Cancer of bronchus; lungOR: 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 1-4Cancer PRSweb PheWAS Results: PRSWEB_PHECODE165.1_GWAS-Catalog-r2019-05-03-X165.1_PT_MGI_20200608
PPM020287PSS011324|
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 ra... tioShow more—
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Evaluated Samples

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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
PSS000541PheCode:165.1; ICD9CM:162.0, 162.2, 162.3, 162.4, 162.5, 162.8, 162.9, 209.21, 231.2, V10.11; ICD10C... M: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, D02.22Show more—
[
  • 428 cases
  • , 4,270 controls
]
—European—MGI—
PSS011324——
[
  • 652 cases
  • , 550 controls
]
,
47.0 % Male samples
Median = 65.0 yearsEuropean—MCRC—
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