Polygenic Score (PGS) ID: PGS000156

Predicted Trait
Reported Trait Lung cancer
Mapped Trait(s) lung carcinoma (EFO_0001071)
Released in PGS: April 29, 2020

Score Details

Score Construction
PGS Name cGRS_Lung
Variants
Original Genome Build NR
Number of Variants 6
Development Method
Name Pruning + Thresholding
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.
PGS Source
PGS Catalog Publication (PGP) ID PGP000075
Citation (link to publication) Shi Z et al. Cancer Med (2019)

Contributing Samples

Source of Variant Associations (GWAS)
Study Identifiers Sample Numbers Sample Ancestry
GWAS Catalog: GCST002466
EuropePMC: 24880342
27,209 individuals European
GWAS Catalog: GCST003587
EuropePMC: 27197191
123,671 individuals European
GWAS Catalog: GCST004748
EuropePMC: 2860473
85,716 individuals European
GWAS Catalog: GCST000257
EuropePMC: 18978787
10,295 individuals European
GWAS Catalog: GCST000506
EuropePMC: 19836008
11,587 individuals European

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 ID)
PGS Sample Set ID
(PSS ID)
Performance Source Trait PGS Effect Sizes
(per SD change)
PGS Classification Metrics Other Metrics Covariates Included in the Model PGS Performance: Other Relevant Information
PPM000476 PSS000276 PGP000075
Shi Z et al. (2019)
Reported Trait: Lung cancer Mean realative risk: 1.01[0.99, 1.02]
Wilcoxon test (case vs. control) p-value: 0.0116
PPM000487 PSS000276 PGP000075
Shi Z et al. (2019)
Reported Trait: Lung cancer Odds Ratio (OR; high vs. average risk groups): 0.88[0.57, 1.36]

Evaluated Samples

PGS Sample Set ID
(PSS ID)
Detailed Phenotype Description Participant Follow-up Time Sample Numbers Age of Study Participants Sample Ancestry Additional Ancestry Description Cohort(s) Additional Sample/Cohort Information
PSS000276
[
  • 0 cases
  • , 13,427 controls
]
European eMERGE
PSS000276 Primary tumor samples from TCGA
[
  • 908 cases
  • , 0 controls
]
Mean = 67.0 years
Sd = 9.0 years
European TCGA