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 the Lung
  • carcinoma OF LUNG
  • carcinoma of lung
  • carcinoma of the lung
  • lung carcinoma
Mapped term(s) 10 mapped terms
  • DOID:3905
  • ICD10:C34
  • ICD10:C34.90
  • MONDO:0005138
  • MeSH:D008175
  • NCIT:C4878
  • NCIt:C4878
  • OMIM:211980
  • SNOMEDCT:448993007
  • UMLS:C0684249
Child trait(s) lung adenocarcinoma

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
Note: This table shows all PGS for "lung carcinoma" and any child terms of this trait in the EFO hierarchy by default.
Polygenic Score ID & Name PGS Publication ID (PGP) Reported Trait Mapped Trait(s) (Ontology) Number of Variants Ancestry distribution 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
PGS000721
(PRS_Lung)
PGP000135 |
Jia G et al. JNCI Cancer Spectr (2020)
Lung cancer lung carcinoma 19
-
http://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS000721/ScoringFiles/PGS000721.txt.gz
PGS000740
(PRS128_LC)
PGP000148 |
Hung RJ et al. Cancer Res (2021)
Lung cancer lung carcinoma 128
http://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS000740/ScoringFiles/PGS000740.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
PPM000198 PGS000078
(CC_Lung)
PSS000117|
European Ancestry|
412,842 individuals
PGP000050 |
Graff RE et al. bioRxiv (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
PPM001780 PGS000740
(PRS128_LC)
PSS000921|
European Ancestry|
183,671 individuals
PGP000148 |
Hung RJ et al. Cancer Res (2021)
Reported Trait: Lung cancer in individuals who have never smoked OR: 1.28 [1.13, 1.46] Age, sex, PCs(1-5) 14/128 were omitted from the analysis (missing in HRC panel)
PPM001781 PGS000740
(PRS128_LC)
PSS000920|
European Ancestry|
118,310 individuals
PGP000148 |
Hung RJ et al. Cancer Res (2021)
Reported Trait: Lung cancer in individuals who are former smokers OR: 1.25 [1.17, 1.34] Age, sex, PCs(1-5) 14/128 were omitted from the analysis (missing in HRC panel)
PPM000487 PGS000156
(cGRS_Lung)
PSS000276|
European Ancestry|
14,335 individuals
PGP000075 |
Shi Z et al. Cancer Med (2019)
Reported Trait: Lung cancer Odds Ratio (OR; high vs. average risk groups): 0.88 [0.57, 1.36]
PPM000476 PGS000156
(cGRS_Lung)
PSS000276|
European Ancestry|
14,335 individuals
PGP000075 |
Shi Z et al. Cancer Med (2019)
Reported Trait: Lung cancer Mean realative risk: 1.01 [0.99, 1.02]
Wilcoxon test (case vs. control) p-value: 0.0116
PPM001784 PGS000740
(PRS128_LC)
PSS000916|
European Ancestry|
42,540 individuals
PGP000148 |
Hung RJ et al. Cancer Res (2021)
Reported Trait: Lung cancer in individuals with no family history of lung cancer OR: 1.29 [1.22, 1.36] Age, sex, PCs(1-5) 14/128 were omitted from the analysis (missing in HRC panel)
PPM001785 PGS000740
(PRS128_LC)
PSS000917|
European Ancestry|
330,046 individuals
PGP000148 |
Hung RJ et al. Cancer Res (2021)
Reported Trait: Lung cancer in individuals with COPD OR: 1.26 [1.09, 1.46] Age, sex, PCs(1-5) 14/128 were omitted from the analysis (missing in HRC panel)
PPM001789 PGS000740
(PRS128_LC)
PSS000913|
European Ancestry|
167,955 individuals
PGP000148 |
Hung RJ et al. Cancer Res (2021)
Reported Trait: Early onset lung cancer (< 50 years) AUROC: 0.811 [0.701, 0.922] Age, sex, education, body mass index, personal history of cancer, family history of lung cancer, lung function 14/128 were omitted from the analysis (missing in HRC panel)
PPM001650 PGS000721
(PRS_Lung)
PSS000857|
European Ancestry|
400,812 individuals
PGP000135 |
Jia G et al. JNCI Cancer Spectr (2020)
Reported Trait: Incident lung cancer AUROC: 0.591 [0.576, 0.606] Genotyping array
PPM001651 PGS000721
(PRS_Lung)
PSS000857|
European Ancestry|
400,812 individuals
PGP000135 |
Jia G et al. JNCI Cancer Spectr (2020)
Reported Trait: Incident lung cancer AUROC: 0.615 [0.6, 0.629] family history of cancer (in first-degree relatives), genotyping array
PPM001779 PGS000740
(PRS128_LC)
PSS000912|
European Ancestry|
335,931 individuals
PGP000148 |
Hung RJ et al. Cancer Res (2021)
Reported Trait: Lung cancer OR: 1.26 [1.2, 1.32] Odds Ratio (OR, top 10% vs low risk): 2.39 [1.92, 3.0] Age, sex, PCs(1-5) 14/128 were omitted from the analysis (missing in HRC panel)
PPM001782 PGS000740
(PRS128_LC)
PSS000919|
European Ancestry|
33,950 individuals
PGP000148 |
Hung RJ et al. Cancer Res (2021)
Reported Trait: Lung cancer in individuals who currently smoke OR: 1.28 [1.19, 1.38] Age, sex, PCs(1-5) 14/128 were omitted from the analysis (missing in HRC panel)
PPM001783 PGS000740
(PRS128_LC)
PSS000918|
European Ancestry|
287,620 individuals
PGP000148 |
Hung RJ et al. Cancer Res (2021)
Reported Trait: Lung cancer in individuals with a family history of lung cancer OR: 1.16 [1.05, 1.27] Age, sex, PCs(1-5) 14/128 were omitted from the analysis (missing in HRC panel)
PPM001786 PGS000740
(PRS128_LC)
PSS000915|
European Ancestry|
5,491 individuals
PGP000148 |
Hung RJ et al. Cancer Res (2021)
Reported Trait: Lung cancer in individuals with no COPD diagnosis OR: 1.26 [1.2, 1.32] Age, sex, PCs(1-5) 14/128 were omitted from the analysis (missing in HRC panel)
PPM001787 PGS000740
(PRS128_LC)
PSS000913|
European Ancestry|
167,955 individuals
PGP000148 |
Hung RJ et al. Cancer Res (2021)
Reported Trait: Lung cancer (absolute risk) β: 0.663 Age, sex, PCs(1-5) 14/128 were omitted from the analysis (missing in HRC panel)
PPM001788 PGS000740
(PRS128_LC)
PSS000914|
European Ancestry|
67,186 individuals
PGP000148 |
Hung RJ et al. Cancer Res (2021)
Reported Trait: Lung cancer in individuals who have never smoked AUROC: 0.687 [0.628, 0.746] Age, sex, education, body mass index, personal history of cancer, family history of lung cancer, lung function 14/128 were omitted from the analysis (missing in HRC panel)

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
PSS000918 Cases are individuals with a lung cancer diagnosis. Lung cancer diagnosis was obtained through record linkage with death and cancer registries with the follow‐up time up to date of death, lung cancer diagnosis, or March 31, 2016 (in England and Wales) and Oct 31, 2015 (in Scotland) per censor date defined by UKB. To minimize the possibility of including lung cancer metastasis, we excluded lung cancer that occurred within 5 years of different primary cancer.
[
  • 1,323 cases
  • , 286,297 controls
]
European UKB
PSS000919 Cases are individuals with a lung cancer diagnosis. Lung cancer diagnosis was obtained through record linkage with death and cancer registries with the follow‐up time up to date of death, lung cancer diagnosis, or March 31, 2016 (in England and Wales) and Oct 31, 2015 (in Scotland) per censor date defined by UKB. To minimize the possibility of including lung cancer metastasis, we excluded lung cancer that occurred within 5 years of different primary cancer.
[
  • 724 cases
  • , 33,226 controls
]
European UKB
PSS000920 Cases are individuals with a lung cancer diagnosis. Lung cancer diagnosis was obtained through record linkage with death and cancer registries with the follow‐up time up to date of death, lung cancer diagnosis, or March 31, 2016 (in England and Wales) and Oct 31, 2015 (in Scotland) per censor date defined by UKB. To minimize the possibility of including lung cancer metastasis, we excluded lung cancer that occurred within 5 years of different primary cancer.
[
  • 808 cases
  • , 117,502 controls
]
European UKB
PSS000921 Cases are individuals with a lung cancer diagnosis. Lung cancer diagnosis was obtained through record linkage with death and cancer registries with the follow‐up time up to date of death, lung cancer diagnosis, or March 31, 2016 (in England and Wales) and Oct 31, 2015 (in Scotland) per censor date defined by UKB. To minimize the possibility of including lung cancer metastasis, we excluded lung cancer that occurred within 5 years of different primary cancer.
[
  • 236 cases
  • , 183,435 controls
]
European UKB
PSS000915 Cases are individuals with a lung cancer diagnosis. Lung cancer diagnosis was obtained through record linkage with death and cancer registries with the follow‐up time up to date of death, lung cancer diagnosis, or March 31, 2016 (in England and Wales) and Oct 31, 2015 (in Scotland) per censor date defined by UKB. To minimize the possibility of including lung cancer metastasis, we excluded lung cancer that occurred within 5 years of different primary cancer.
[
  • 180 cases
  • , 5,311 controls
]
European UKB
PSS000857 Data and diagnoses on site-specific incident cancers were provided by the National Health Service Information Centre for participants from England and Wales (follow-up through March 31, 2016) and by the NHS Central Register Scotland for participants from Scotland (follow-up through October 31, 2015). Cancers were coded by the International Classification of Diseases, Ninth Revision (ICD-9) or the International Classification of Diseases, Tenth Revision (ICD-10). Lung cancer=(ICD-9 = 162.2–162.9 or ICD-10 = C34). Median = 5.8 years
[
  • 1,508 cases
  • , 399,304 controls
]
,
46.5 % Male samples
European UKB
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
PSS000912 Cases are individuals with a lung cancer diagnosis. Lung cancer diagnosis was obtained through record linkage with death and cancer registries with the follow‐up time up to date of death, lung cancer diagnosis, or March 31, 2016 (in England and Wales) and Oct 31, 2015 (in Scotland) per censor date defined by UKB. To minimize the possibility of including lung cancer metastasis, we excluded lung cancer that occurred within 5 years of different primary cancer.
[
  • 1,768 cases
  • , 50,772 controls
]
,
46.28 % Male samples
European UKB
PSS000913 167,955 individuals European UKB
PSS000914 67,186 individuals European UKB
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
PSS000916 Cases are individuals with a lung cancer diagnosis. Lung cancer diagnosis was obtained through record linkage with death and cancer registries with the follow‐up time up to date of death, lung cancer diagnosis, or March 31, 2016 (in England and Wales) and Oct 31, 2015 (in Scotland) per censor date defined by UKB. To minimize the possibility of including lung cancer metastasis, we excluded lung cancer that occurred within 5 years of different primary cancer.
[
  • 387 cases
  • , 42,153 controls
]
European UKB
PSS000917 Cases are individuals with a lung cancer diagnosis. Lung cancer diagnosis was obtained through record linkage with death and cancer registries with the follow‐up time up to date of death, lung cancer diagnosis, or March 31, 2016 (in England and Wales) and Oct 31, 2015 (in Scotland) per censor date defined by UKB. To minimize the possibility of including lung cancer metastasis, we excluded lung cancer that occurred within 5 years of different primary cancer.
[
  • 1,581 cases
  • , 328,465 controls
]
European UKB