| Publication Information (EuropePMC) | |
| Title | Validation of lung cancer polygenic risk scores in a high-risk case-control cohort. |
| PubMed ID | 37154150(Europe PMC) |
| doi | 10.1016/j.gim.2023.100882 |
| Publication Date | May 5, 2023 |
| Journal | Genet Med |
| Author(s) | Lebrett MB, Smith MJ, Crosbie EJ, Bowes J, Byers HJ, Evans DG, Crosbie PAJ. |
| 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) |
|---|---|---|---|---|---|---|
| PGS000740 (PRS128_LC) |
PGP000148 | Hung RJ et al. Cancer Res (2021) |
Lung cancer | lung carcinoma | 128 | https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS000740/ScoringFiles/PGS000740.txt.gz | |
| 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 |
| PGS000391 (PRSWEB_PHECODE165.1_GWAS-Catalog-r2019-05-03-X165.1_PT_MGI_20200608) |
PGP000118 | Fritsche LG et al. Am J Hum Genet (2020) |
Lung and bronchus cancer | bronchus cancer, lung cancer, tracheal cancer |
14 | https://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) |
Lung and bronchus cancer | bronchus cancer, lung cancer, tracheal cancer |
19 | https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS000392/ScoringFiles/PGS000392.txt.gz | |
| PGS000078 (CC_Lung) |
PGP000050 | Graff RE et al. Nat Commun (2021) |
Lung cancer | lung carcinoma | 109 | - |
https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS000078/ScoringFiles/PGS000078.txt.gz |
| PGS000721 (PRS_Lung) |
PGP000135 | Jia G et al. JNCI Cancer Spectr (2020) |
Lung cancer | lung carcinoma | 19 | - |
https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS000721/ScoringFiles/PGS000721.txt.gz |
| PGS000156 (cGRS_Lung) |
PGP000075 | Shi Z et al. Cancer Med (2019) |
Lung cancer | lung carcinoma | 6 | - |
https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS000156/ScoringFiles/PGS000156.txt.gz |
| PGS002270 (PRS33_LC) |
PGP000300 | Zhang P et al. Br J Cancer (2022) |
Lung cancer | lung carcinoma | 33 | - |
https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS002270/ScoringFiles/PGS002270.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 |
|---|---|---|---|---|---|---|---|---|---|
| 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 | — |
| PPM020284 | PGS000156 (cGRS_Lung) |
PSS011324| European Ancestry| 1,202 individuals |
PGP000539 | Lebrett MB et al. Genet Med (2023) |Ext. |
Reported Trait: Lung cancer | — | AUROC: 0.732 [0.704, 0.76] | — | Age, sex, current smoking status, BMI, forced expiratory volume in 1 second/forced vital capacity ratio | — |
| PPM020285 | PGS000078 (CC_Lung) |
PSS011324| European Ancestry| 1,202 individuals |
PGP000539 | Lebrett MB et al. Genet Med (2023) |Ext. |
Reported Trait: Lung cancer | — | AUROC: 0.728 [0.7, 0.756] | — | Age, sex, current smoking status, BMI, forced expiratory volume in 1 second/forced vital capacity ratio | — |
| PPM020286 | PGS000721 (PRS_Lung) |
PSS011324| European Ancestry| 1,202 individuals |
PGP000539 | Lebrett MB et al. Genet Med (2023) |Ext. |
Reported Trait: Lung cancer | — | AUROC: 0.738 [0.71, 0.766] | — | Age, sex, current smoking status, BMI, forced expiratory volume in 1 second/forced vital capacity ratio | — |
| PPM020287 | PGS000391 (PRSWEB_PHECODE165.1_GWAS-Catalog-r2019-05-03-X165.1_PT_MGI_20200608) |
PSS011324| European Ancestry| 1,202 individuals |
PGP000539 | Lebrett MB et al. Genet Med (2023) |Ext. |
Reported Trait: Lung cancer | — | AUROC: 0.731 [0.703, 0.759] | — | Age, sex, current smoking status, BMI, forced expiratory volume in 1 second/forced vital capacity ratio | — |
| PPM020288 | PGS000392 (PRSWEB_PHECODE165.1_GWAS-Catalog-r2019-05-03-X165.1_PT_UKB_20200608) |
PSS011324| European Ancestry| 1,202 individuals |
PGP000539 | Lebrett MB et al. Genet Med (2023) |Ext. |
Reported Trait: Lung cancer | — | AUROC: 0.733 [0.705, 0.761] | — | Age, sex, current smoking status, BMI, forced expiratory volume in 1 second/forced vital capacity ratio | — |
| PPM020289 | PGS000740 (PRS128_LC) |
PSS011324| European Ancestry| 1,202 individuals |
PGP000539 | Lebrett MB et al. Genet Med (2023) |Ext. |
Reported Trait: Lung cancer | — | AUROC: 0.73 [0.702, 0.758] | — | Age, sex, current smoking status, BMI, forced expiratory volume in 1 second/forced vital capacity ratio | — |
| PPM020290 | PGS002270 (PRS33_LC) |
PSS011324| European Ancestry| 1,202 individuals |
PGP000539 | Lebrett MB et al. Genet Med (2023) |Ext. |
Reported Trait: Lung cancer | — | AUROC: 0.725 [0.697, 0.754] | — | Age, sex, current smoking status, BMI, forced expiratory volume in 1 second/forced vital capacity ratio | — |
|
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 |
|---|---|---|---|---|---|---|---|---|
| PSS011324 | — | — | [ ,
47.0 % Male samples |
Median = 65.0 years | European | — | MCRC | — |