Trait: lung adenocarcinoma

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
  • LUAD
  • adenocarcinoma of lung
  • adenocarcinoma of the lung
  • bronchogenic lung adenocarcinoma
  • lung adenocarcinoma
  • non-small cell lung adenocarcinoma
  • nonsmall cell adenocarcinoma
Mapped terms 14 mapped terms
  • DOID:3910
  • EFO:0000571
  • EFO:0005288
  • GARD:0005742
  • MEDGEN:57744
  • MESH:C538231
  • MESH:D000077192
  • MONDO:0005061
  • NCIT:C3512
  • OMIM:211980
  • ONCOTREE:LUAD
  • Orphanet:415268
  • SCTID:254626006
  • UMLS:C0152013

Associated Polygenic Score(s)

Filter PGS by Participant Ancestry
Individuals included in:
G - Source of Variant Associations (GWAS)
D - Score Development/Training
E - PGS Evaluation
List of ancestries includes:
Display options:
Ancestry legend
Multi-ancestry (including European)
Multi-ancestry (excluding European)
African
East Asian
South Asian
Additional Asian Ancestries
European
Greater Middle Eastern
Hispanic or Latin American
Additional Diverse Ancestries
Not Reported
Polygenic Score ID & Name PGS Publication ID (PGP) Reported Trait Mapped Trait(s) (Ontology) Number of Variants Ancestry distribution
GWAS
Dev
Eval
 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

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) 		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] — — — —
PPM018700 PGS000070
(PRS_LC_C)
 PSS011073|
East Asian Ancestry|
381 individuals
 PGP000494 |
Ho PJ et al. Elife (2023)
|Ext.		 Reported Trait: Lung cancer — AUROC: 0.68 [0.65, 0.71] Hazard ratio (HR, high vs low tertile): 2.01 [1.44, 2.81] age at recruitment —
PPM020283 PGS000070
(PRS_LC_C)
 PSS011324|
European Ancestry|
1,202 individuals
 PGP000539 |
Lebrett MB et al. Genet Med (2023)
|Ext.		 Reported Trait: Lung cancer — AUROC: 0.726 [0.698, 0.754] — Age, sex, current smoking status, BMI, forced expiratory volume in 1 second/forced vital capacity ratio —
PPM021774 PGS000070
(PRS_LC_C)
 PSS011793|
East Asian Ancestry|
100,615 individuals
 PGP000678 |
Zhu M et al. Int J Epidemiol (2023)
|Ext.		 Reported Trait: Incident lung cancer HR: 1.19 [1.13, 1.25] — — Age, sex, smoking status, BMI, highest education level, family history of cancer, personal medical history (previous cancer diagnoses and chronic obstructive pulmonary disease), the forced expiratory volume in 1 second, 10 PCs —
PPM022188 PGS000070
(PRS_LC_C)
 PSS011836|
East Asian Ancestry|
1,197 individuals
 PGP000687 |
Lee PH et al. JCO Precis Oncol (2024)
|Ext.		 Reported Trait: Incident non-small cell lung cancer — — Hazard ratio (HR, high vs low PGS quartile): 2.33 [0.6, 9.04] Age, smoking, family history of lung cancer —
PPM022189 PGS000070
(PRS_LC_C)
 PSS011835|
East Asian Ancestry|
1,090 individuals
 PGP000687 |
Lee PH et al. JCO Precis Oncol (2024)
|Ext.		 Reported Trait: Incident non-small cell lung cancer — — Hazard ratio (HR, high vs low PGS quartile): 2.97 [1.25, 7.07] Age, smoking, family history of lung cancer —
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 —

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
PSS009987 — —
[
  • 10,248 cases
  • , 9,298 controls
]
,
63.0 % Male samples
 — East Asian
(Chinese)		 — NR NJLCC
PSS011835 — Median = 10.7 years
[
  • 48 cases
  • , 1,042 controls
]
,
0.0 % Male samples
 — East Asian
(Chinese)		 — TPMI —
PSS011836 — Median = 10.0 years
[
  • 30 cases
  • , 1,167 controls
]
,
100.0 % Male samples
 — East Asian
(Chinese)		 — TPMI —
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 —
[
  • 868 cases
  • , 269,544 controls
]
 — European
(British)		 — UKB Controls were samples without any cancer diagnosis or self-reported cancer
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 —
PSS011073 — — 381 individuals,
100.0 % Male samples
 Median = 60.0 years
IQR = [55.0, 64.0] years		 East Asian
(Chinese)		 — SCHS —
PSS011793 — —
[
  • 1,392 cases
  • , 99,223 controls
]
 — East Asian
(Chinese)		 — CKB —
PSS011324 — —
[
  • 652 cases
  • , 550 controls
]
,
47.0 % Male samples
 Median = 65.0 years European — MCRC —