Predicted Trait | |
Reported Trait | Lung cancer |
Mapped Trait(s) | lung carcinoma (EFO_0001071) |
Score Construction | |
PGS Name | cGRS_Lung |
Development Method | |
Name | Pruning and Thresholding (P+T) |
Parameters | GWAS significant and r2 < 0.2. PGS levels were computed as product(dosage*weight/expected risk effect), where the expected risk effect for each variant was calculated based on the risk allele frequence (f) and risk allele weight (OR) as f^2*OR^2 + 2f(1-f)OR + (1-f)^2. |
Variants | |
Original Genome Build | NR |
Number of Variants | 6 |
Effect Weight Type | Odds Ratio over expected risk |
PGS Source | |
PGS Catalog Publication (PGP) ID | PGP000075 |
Citation (link to publication) | Shi Z et al. Cancer Med (2019) |
Ancestry Distribution | |
Source of Variant Associations (GWAS) | European: 100% 258,478 individuals (100%) |
PGS Evaluation | European: 100% 2 Sample Sets |
Study Identifiers | Sample Numbers | Sample Ancestry | Cohort(s) |
---|---|---|---|
GWAS Catalog: GCST002466 Europe PMC: 24880342 |
27,209 individuals | European | NR |
GWAS Catalog: GCST003587 Europe PMC: 27197191 |
123,671 individuals | European | NR |
GWAS Catalog: GCST000506 Europe PMC: 19836008 |
11,587 individuals | European | NR |
GWAS Catalog: GCST004748 Europe PMC: 2860473 |
85,716 individuals | European | NR |
GWAS Catalog: GCST000257 Europe PMC: 18978787 |
10,295 individuals | European | B58C, GELCAPS, IARC, MDACCS |
PGS Performance Metric ID (PPM) |
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 |
---|---|---|---|---|---|---|---|---|
PPM000487 | 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 | 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 |
— | — |
PPM020284 | 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 | — |
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 |
---|---|---|---|---|---|---|---|---|
PSS000276 | — | — | [
|
— | European | — | eMERGE | — |
PSS011324 | — | — | [ ,
47.0 % Male samples |
Median = 65.0 years | European | — | MCRC | — |
PSS000276 | Primary tumor samples from TCGA | — | [
|
Mean = 67.0 years Sd = 9.0 years |
European | — | TCGA | — |