Polygenic Score (PGS) ID: PGS000390

Predicted Trait
Reported Trait Cancer of bronchus; lung
Mapped Trait(s)
Additional Trait Information PheCode 165.1
Released in PGS Catalog: Dec. 15, 2020
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Score Details

Score Construction
PGS Name PRSWEB_PHECODE165.1_GWAS-Catalog-r2019-05-03-X165.1_P_5e-08_UKB_20200608
Variants
Original Genome Build GRCh37
Number of Variants 21
Development Method
Name GWAS Hits
Parameters LD Clumping (MAF >= 1%, r^2 <= 0.1) & P<=5e-08
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%
12,336 individuals (100%)
PGS Evaluation
European: 100%
1 Sample Sets

Development Samples

Source of Variant Associations (GWAS)
Study Identifiers Sample Numbers Sample Ancestry
GWAS Catalog: GCST000506
Europe PMC: 19836008
11,587 individuals European
GWAS Catalog: GCST002466
Europe PMC: 24880342
27,209 individuals European
GWAS Catalog: GCST004744
Europe PMC: 28604730
66,756 individuals European
GWAS Catalog: GCST004746
Europe PMC: 28604730
24,108 individuals European
GWAS Catalog: GCST004747
Europe PMC: 28604730
9,859 individuals European
GWAS Catalog: GCST004748
Europe PMC: 28604730
85,716 individuals European
GWAS Catalog: GCST004749
Europe PMC: 28604730
40,187 individuals European
GWAS Catalog: GCST004750
Europe PMC: 28604730
63,053 individuals European
GWAS Catalog: GCST006086
Europe PMC: 29924316
35,953 individuals European
GWAS Catalog: GCST006087
Europe PMC: 29924316
32,338 individuals European
GWAS Catalog: GCST006088
Europe PMC: 29924316
31,930 individuals European
Score Development/Training
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
PheCode:165.1; ICD9:162, 162.0, 162.2, 162.3, 162.4, 162.5, 162.8, 162.9, 231.2; ICD10:C33, C34.0, C34.1, C34.2, C34.3, C34.8, C34.9, D02.2
[
  • 1,121 cases
  • , 11,215 controls
]
European UKB

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
PPM001075 PSS000566|
European Ancestry|
12,201 individuals
PGP000118 |
Fritsche LG et al. Am J Hum Genet (2020)
Reported Trait: Cancer of bronchus; lung OR: 1.194 [1.124, 1.269]
β: 0.178 (0.0309)
AUROC: 0.543 [0.526, 0.562] Nagelkerke's Pseudo-R²: 0.00583
Brier score: 0.0824
Odds Ratio (OR, top 1% vs. Rest): 0.852 [0.437, 1.66]
age, sex, batch PCs 1-4 Cancer PRSweb PheWAS Results: PRSWEB_PHECODE165.1_GWAS-Catalog-r2019-05-03-X165.1_P_5e-08_UKB_20200608

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
PSS000566 PheCode:165.1; ICD9:162, 162.0, 162.2, 162.3, 162.4, 162.5, 162.8, 162.9, 231.2; ICD10:C33, C34.0, C34.1, C34.2, C34.3, C34.8, C34.9, D02.2
[
  • 1,109 cases
  • , 11,092 controls
]
European UKB