Trait: bronchus cancer

Trait Information
Identifier MONDO_0001672
Description A malignant neoplasm involving the bronchus [MONDO: DesignPattern]
Trait category
Cancer
Synonyms 4 synonyms
  • bronchus cancer
  • cancer of bronchus
  • malignant bronchus neoplasm
  • malignant neoplasm of bronchus
Mapped term(s) 6 mapped terms
  • DOID:1325
  • ICD10:C34
  • ICD10:C34.9
  • ICD9:162.8
  • ICD9:162.9
  • SCTID:363493006

Associated Polygenic Score(s)

Polygenic Score (PGS) ID PGS Name PGS Publication (PGP) ID Reported Trait Mapped Trait(s) (Ontology) Number of Variants PGS Scoring File (FTP Link)
PGS000388 PRSWEB_PHECODE165.1_C3-BRONCHUS-LUNG_PRS-CS_MGI_20200608 PGP000118 Fritsche LG et al. Am J Hum Genet (2020) Cancer of bronchus; lung bronchus cancer
lung cancer
tracheal cancer
1,109,069 http://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS000388/ScoringFiles/PGS000388.txt.gz
PGS000389 PRSWEB_PHECODE165.1_GWAS-Catalog-r2019-05-03-X165.1_P_5e-08_MGI_20200608 PGP000118 Fritsche LG et al. Am J Hum Genet (2020) Cancer of bronchus; lung bronchus cancer
lung cancer
tracheal cancer
21 http://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS000389/ScoringFiles/PGS000389.txt.gz
PGS000390 PRSWEB_PHECODE165.1_GWAS-Catalog-r2019-05-03-X165.1_P_5e-08_UKB_20200608 PGP000118 Fritsche LG et al. Am J Hum Genet (2020) Cancer of bronchus; lung bronchus cancer
lung cancer
tracheal cancer
21 http://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS000390/ScoringFiles/PGS000390.txt.gz
PGS000391 PRSWEB_PHECODE165.1_GWAS-Catalog-r2019-05-03-X165.1_PT_MGI_20200608 PGP000118 Fritsche LG et al. Am J Hum Genet (2020) Cancer of bronchus; lung bronchus cancer
lung cancer
tracheal cancer
14 http://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS000391/ScoringFiles/PGS000391.txt.gz
PGS000392 PRSWEB_PHECODE165.1_GWAS-Catalog-r2019-05-03-X165.1_PT_UKB_20200608 PGP000118 Fritsche LG et al. Am J Hum Genet (2020) Cancer of bronchus; lung bronchus cancer
lung cancer
tracheal cancer
19 http://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS000392/ScoringFiles/PGS000392.txt.gz
PGS000393 PRSWEB_PHECODE165.1_LUNG-CANCER_PRS-CS_MGI_20200608 PGP000118 Fritsche LG et al. Am J Hum Genet (2020) Cancer of bronchus; lung bronchus cancer
lung cancer
tracheal cancer
1,110,438 http://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS000393/ScoringFiles/PGS000393.txt.gz
PGS000394 PRSWEB_PHECODE165.1_LUNG-CANCER-MESOT_PRS-CS_MGI_20200608 PGP000118 Fritsche LG et al. Am J Hum Genet (2020) Cancer of bronchus; lung bronchus cancer
lung cancer
tracheal cancer
1,110,438 http://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS000394/ScoringFiles/PGS000394.txt.gz
PGS000395 PRSWEB_PHECODE165.1_UKBB-SAIGE-HRC-X165.1_PRS-CS_MGI_20200608 PGP000118 Fritsche LG et al. Am J Hum Genet (2020) Cancer of bronchus; lung bronchus cancer
lung cancer
tracheal cancer
1,119,238 http://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS000395/ScoringFiles/PGS000395.txt.gz
PGS000396 PRSWEB_PHECODE165.1_UKBB-SAIGE-HRC-X165.1_PT_MGI_20200608 PGP000118 Fritsche LG et al. Am J Hum Genet (2020) Cancer of bronchus; lung bronchus cancer
lung cancer
tracheal cancer
75 http://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS000396/ScoringFiles/PGS000396.txt.gz
PGS000397 PRSWEB_PHECODE165.1_UKBB-SAIGE-HRC-X165.1_LASSOSUM_MGI_20200608 PGP000118 Fritsche LG et al. Am J Hum Genet (2020) Cancer of bronchus; lung bronchus cancer
lung cancer
tracheal cancer
46,920 http://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS000397/ScoringFiles/PGS000397.txt.gz

PGS 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 ID)
Evaluated Score PGS Sample Set ID
(PSS ID)
Performance Source Trait PGS Effect Sizes
(per SD change)
PGS Classification Metrics Other Metrics Covariates Included in the Model PGS Performance: Other Relevant Information
PPM001073 PGS000388 (PRSWEB_PHECODE165.1_C3-BRONCHUS-LUNG_PRS-CS_MGI_20200608) PSS000541 PGP000118
Fritsche LG et al. (2020)
Reported Trait: Cancer of bronchus; lung OR: 1.132 [1.024, 1.25]
β: 0.124 (0.0508)
AUROC: 0.533 [0.505, 0.562] Nagelkerke's Pseudo-R²: 0.00265
Brier score: 0.0827
Odds Ratio (OR, top 1% vs. Rest): 1.96 [0.926, 4.14]
age, sex, batch PCs 1-4 Cancer PRSweb PheWAS Results: PRSWEB_PHECODE165.1_C3-BRONCHUS-LUNG_PRS-CS_MGI_20200608
PPM001076 PGS000391 (PRSWEB_PHECODE165.1_GWAS-Catalog-r2019-05-03-X165.1_PT_MGI_20200608) PSS000541 PGP000118
Fritsche LG et al. (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
PPM001079 PGS000394 (PRSWEB_PHECODE165.1_LUNG-CANCER-MESOT_PRS-CS_MGI_20200608) PSS000541 PGP000118
Fritsche LG et al. (2020)
Reported Trait: Cancer of bronchus; lung OR: 1.149 [1.04, 1.269]
β: 0.139 (0.0509)
AUROC: 0.539 [0.508, 0.568] Nagelkerke's Pseudo-R²: 0.00329
Brier score: 0.0826
Odds Ratio (OR, top 1% vs. Rest): 2.18 [1.06, 4.46]
age, sex, batch PCs 1-4 Cancer PRSweb PheWAS Results: PRSWEB_PHECODE165.1_LUNG-CANCER-MESOT_PRS-CS_MGI_20200608
PPM001082 PGS000397 (PRSWEB_PHECODE165.1_UKBB-SAIGE-HRC-X165.1_LASSOSUM_MGI_20200608) PSS000541 PGP000118
Fritsche LG et al. (2020)
Reported Trait: Cancer of bronchus; lung OR: 1.114 [1.009, 1.23]
β: 0.108 (0.0507)
AUROC: 0.528 [0.503, 0.556] Nagelkerke's Pseudo-R²: 0.00202
Brier score: 0.0827
Odds Ratio (OR, top 1% vs. Rest): 1.03 [0.387, 2.77]
age, sex, batch PCs 1-4 Cancer PRSweb PheWAS Results: PRSWEB_PHECODE165.1_UKBB-SAIGE-HRC-X165.1_LASSOSUM_MGI_20200608
PPM001074 PGS000389 (PRSWEB_PHECODE165.1_GWAS-Catalog-r2019-05-03-X165.1_P_5e-08_MGI_20200608) PSS000541 PGP000118
Fritsche LG et al. (2020)
Reported Trait: Cancer of bronchus; lung OR: 1.11 [1.006, 1.225]
β: 0.105 (0.0501)
AUROC: 0.52 [0.492, 0.547] Nagelkerke's Pseudo-R²: 0.00202
Brier score: 0.0827
Odds Ratio (OR, top 1% vs. Rest): 2.19 [1.07, 4.49]
age, sex, batch PCs 1-4 Cancer PRSweb PheWAS Results: PRSWEB_PHECODE165.1_GWAS-Catalog-r2019-05-03-X165.1_P_5e-08_MGI_20200608
PPM001075 PGS000390 (PRSWEB_PHECODE165.1_GWAS-Catalog-r2019-05-03-X165.1_P_5e-08_UKB_20200608) PSS000566 PGP000118
Fritsche LG et al. (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
PPM001077 PGS000392 (PRSWEB_PHECODE165.1_GWAS-Catalog-r2019-05-03-X165.1_PT_UKB_20200608) PSS000566 PGP000118
Fritsche LG et al. (2020)
Reported Trait: Cancer of bronchus; lung OR: 1.221 [1.149, 1.298]
β: 0.2 (0.0313)
AUROC: 0.552 [0.534, 0.569] Nagelkerke's Pseudo-R²: 0.00728
Brier score: 0.0824
Odds Ratio (OR, top 1% vs. Rest): 1.94 [1.22, 3.1]
age, sex, batch PCs 1-4 Cancer PRSweb PheWAS Results: PRSWEB_PHECODE165.1_GWAS-Catalog-r2019-05-03-X165.1_PT_UKB_20200608
PPM001078 PGS000393 (PRSWEB_PHECODE165.1_LUNG-CANCER_PRS-CS_MGI_20200608) PSS000541 PGP000118
Fritsche LG et al. (2020)
Reported Trait: Cancer of bronchus; lung OR: 1.149 [1.04, 1.269]
β: 0.139 (0.0509)
AUROC: 0.539 [0.508, 0.568] Nagelkerke's Pseudo-R²: 0.00329
Brier score: 0.0826
Odds Ratio (OR, top 1% vs. Rest): 2.18 [1.06, 4.46]
age, sex, batch PCs 1-4 Cancer PRSweb PheWAS Results: PRSWEB_PHECODE165.1_LUNG-CANCER_PRS-CS_MGI_20200608
PPM001080 PGS000395 (PRSWEB_PHECODE165.1_UKBB-SAIGE-HRC-X165.1_PRS-CS_MGI_20200608) PSS000541 PGP000118
Fritsche LG et al. (2020)
Reported Trait: Cancer of bronchus; lung OR: 1.133 [1.025, 1.252]
β: 0.125 (0.051)
AUROC: 0.533 [0.505, 0.562] Nagelkerke's Pseudo-R²: 0.00277
Brier score: 0.0827
Odds Ratio (OR, top 1% vs. Rest): 1.27 [0.514, 3.12]
age, sex, batch PCs 1-4 Cancer PRSweb PheWAS Results: PRSWEB_PHECODE165.1_UKBB-SAIGE-HRC-X165.1_PRS-CS_MGI_20200608
PPM001081 PGS000396 (PRSWEB_PHECODE165.1_UKBB-SAIGE-HRC-X165.1_PT_MGI_20200608) PSS000541 PGP000118
Fritsche LG et al. (2020)
Reported Trait: Cancer of bronchus; lung OR: 1.121 [1.015, 1.238]
β: 0.114 (0.0507)
AUROC: 0.525 [0.496, 0.554] Nagelkerke's Pseudo-R²: 0.00233
Brier score: 0.0827
Odds Ratio (OR, top 1% vs. Rest): 2.21 [1.08, 4.51]
age, sex, batch PCs 1-4 Cancer PRSweb PheWAS Results: PRSWEB_PHECODE165.1_UKBB-SAIGE-HRC-X165.1_PT_MGI_20200608

Evaluated Samples

PGS Sample Set ID
(PSS ID)
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
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
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