Trait: lung carcinoma

Experimental Factor Ontology (EFO) Information
Identifier EFO_0001071
Description A carcinoma that arises from epithelial cells of the lung [MONDO: DesignPattern]
Trait category
Cancer
Synonyms 5 synonyms
  • carcinoma OF LUNG
  • lung carcinoma
  • carcinoma of lung
  • carcinoma of the lung
  • Carcinoma of the Lung
Mapped term(s) 10 mapped terms
  • MONDO:0005138
  • NCIT:C4878
  • ICD10:C34
  • MSH:D008175
  • ICD10:C34.90
  • SNOMEDCT:448993007
  • OMIM:211980
  • DOID:3905
  • NCIt:C4878
  • UMLS:C0684249
Child trait(s) lung adenocarcinoma

Associated Polygenic Score(s)

Note: This table shows all PGS for "lung carcinoma" 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

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

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
PSS000276
[
  • 0 cases
  • , 13,427 controls
]
European eMERGE
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
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
PSS000276 Primary tumor samples from TCGA
[
  • 908 cases
  • , 0 controls
]
Mean = 67.0 years
Sd = 9.0 years
European TCGA