Experimental Factor Ontology (EFO) Information | |
Identifier | EFO_0000571 |
Description | A carcinoma that arises from the lung and is characterized by the presence of malignant glandular epithelial cells. There is a male predilection with a male to female ratio of 2:1. Usually lung adenocarcinoma is asymptomatic and is identified through screening studies or as an incidental radiologic finding. If clinical symptoms are present they include shortness of breath, cough, hemoptysis, chest pain, and fever. Tobacco smoke is a known risk factor. [NCIT: C3512] | Trait category |
Cancer
|
Synonyms |
7 synonyms
|
Mapped terms |
12 mapped terms
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Polygenic Score ID & Name | PGS Publication ID (PGP) | Reported Trait | Mapped Trait(s) (Ontology) | Number of Variants | Ancestry distribution | Scoring File (FTP Link) |
---|---|---|---|---|---|---|
PGS000070 (PRS_LC_C) |
PGP000049 | Dai J et al. Lancet Respir Med (2019) |
Lung cancer | lung adenocarcinoma | 19 | - |
https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS000070/ScoringFiles/PGS000070.txt.gz |
PGS003393 (best_LUAD) |
PGP000413 | Namba S et al. Cancer Res (2022) |
Lung adenocarcinoma | lung adenocarcinoma | 74 | - |
https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS003393/ScoringFiles/PGS003393.txt.gz |
PGS Performance Metric ID (PPM) |
Evaluated Score |
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 |
---|---|---|---|---|---|---|---|---|---|
PPM000190 | PGS000070 (PRS_LC_C) |
PSS000109| East Asian Ancestry| 95,408 individuals |
PGP000049 | Dai J et al. Lancet Respir Med (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 | — |
PPM015573 | PGS000070 (PRS_LC_C) |
PSS009987| East Asian Ancestry| 19,546 individuals |
PGP000387 | Qin N et al. Lancet Oncol (2022) |Ext. |
Reported Trait: Lung cancer | — | — | Odds ratio (OR, high vs low risk): 2.18 [2.00, 2.38] | — | — |
PPM015575 | PGS000070 (PRS_LC_C) |
PSS009987| East Asian Ancestry| 19,546 individuals |
PGP000387 | Qin N et al. Lancet Oncol (2022) |Ext. |
Reported Trait: Lung cancer x autosomal mosaic loss abnormalities interaction | OR: 2.36 [1.09, 5.08] | — | — | — | — |
PPM016268 | PGS003393 (best_LUAD) |
PSS010080| European Ancestry| 270,412 individuals |
PGP000413 | Namba S et al. Cancer Res (2022) |
Reported Trait: lung adenocarcinoma | — | AUROC: 0.743 | R²: 0.00649 | age, sex, top 20 genetic principal components | — |
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 |
---|---|---|---|---|---|---|---|---|
PSS009987 | — | — | [ ,
63.0 % Male samples |
— | East Asian (Chinese) |
— | NR | NJLCC |
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 | [ ,
42.93 % Male samples |
Mean = 53.67 years Se = 10.98 years |
East Asian (Chinese) |
— | CKB | — |
PSS010080 | C34, histology was one of the followings: Squamous cell carcinoma; Squamous cell carcinoma, keratinizing; Squamous cell carcinoma, large cell, non-keratinizing; Squamous cell carcinoma, micro-invasive; Squamous cell carcinoma, small cell, non-keratinizing | — | [
|
— | European (British) |
— | UKB | Controls were samples without any cancer diagnosis or self-reported cancer |