Trait: lung cancer

Trait Information
Identifier MONDO_0008903
Description A malignant neoplasm involving the lung. [MONDO: DesignPattern]
Trait category
Cancer
Synonyms 8 synonyms
  • cancer of lung
  • lung cancer
  • malignant lung neoplasm
  • malignant lung tumor
  • malignant neoplasm of lung
  • malignant neoplasm of the lung
  • malignant tumor of lung
  • malignant tumor of the lung
Mapped term(s) 12 mapped terms
  • DOID:1324
  • ICD10:C34.1
  • ICD10:C34.2
  • ICD10:C34.3
  • ICD9:162.3
  • ICD9:162.4
  • ICD9:162.5
  • ICD9:162.8
  • ICD9:162.9
  • NCIT:C7377
  • OMIM:211980
  • SCTID:363358000
Child trait(s) 2 child traits

Associated Polygenic Score(s)

Note: This table shows all PGS for "lung cancer" and any child terms of this trait in the EFO hierarchy by default.
Polygenic Score (PGS) ID PGS Name PGS Publication (PGP) ID Reported Trait Mapped Trait(s) (Ontology) Number of Variants PGS Scoring File (FTP Link)
PGS000070 PRS_LC_C PGP000049 Dai J et al. Lancet Respir Med (2019) Lung cancer lung adenocarcinoma 19 http://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS000070/ScoringFiles/PGS000070.txt.gz
PGS000078 CC_Lung PGP000050 Graff RE et al. bioRxiv (2020) Pre Lung cancer lung carcinoma 109 http://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS000078/ScoringFiles/PGS000078.txt.gz
PGS000156 cGRS_Lung PGP000075 Shi Z et al. Cancer Med (2019) Lung cancer lung carcinoma 6 http://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS000156/ScoringFiles/PGS000156.txt.gz
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
PPM000190 PGS000070 (PRS_LC_C) PSS000109 PGP000049
Dai J et al. (2019)
Reported Trait: Incident lung cancer HR (High genetic risk: top 5% vs. bottom 5% of PRS): 2.37 [1.64, 3.44]
HR (Intermediate genetic risk: 5-95% vs. bottom 5% of PRS): 1.6 [1.17, 2.2]
age, sex, source of region, smoking status
PPM000198 PGS000078 (CC_Lung) PSS000117 PGP000050
Graff RE et al. (2020)
Pre
Reported Trait: Lung cancer OR: 1.12 [1.08, 1.17] Genotyping reagent kit (GERA cohort only), genotyping array (UK Biobank only), age, sex, 10 PCs. Results from meta-analysis of GERA and UKB
PPM000487 PGS000156 (cGRS_Lung) PSS000276 PGP000075
Shi Z et al. (2019)
Reported Trait: Lung cancer Odds Ratio (OR; high vs. average risk groups): 0.88 [0.57, 1.36]
PPM000476 PGS000156 (cGRS_Lung) PSS000276 PGP000075
Shi Z et al. (2019)
Reported Trait: Lung cancer Mean realative risk: 1.01 [0.99, 1.02]
Wilcoxon test (case vs. control) p-value: 0.0116
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
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
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
PSS000109 Participants were followed-up for cancer events mainly through linkage with official death certificates, chronic disease registries, and the Chinese national health insurance system. Median = 10.44 years
[
  • 1,316 cases
  • , 94,092 controls
]
,
42.93 % Male samples
Mean = 53.67 years
Se = 10.98 years
East Asian
(Chinese)
CKB
PSS000276 Primary tumor samples from TCGA
[
  • 908 cases
  • , 0 controls
]
Mean = 67.0 years
Sd = 9.0 years
European TCGA
PSS000276
[
  • 0 cases
  • , 13,427 controls
]
European eMERGE
PSS000117 Cancer diagnoses were obtained from reigstry data in GERA, and ICD-9/10 codes mapped to ICD-O-3 codes in UK Biobank. Cancers for this phenotype were classified using the following SEER site recode(s): 22030
[
  • 2,488 cases
  • , 410,354 controls
]
,
46.0 % Male samples
Mean = 58.0 years European GERA, UKB