Polygenic Score (PGS) ID: PGS000389

Predicted Trait
Reported Trait Cancer of bronchus; lung
Mapped Trait(s)
Additional Trait Information PheCode 165.1
Released in PGS Catalog: Dec. 15, 2020
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Score Details

Score Construction
PGS Name PRSWEB_PHECODE165.1_GWAS-Catalog-r2019-05-03-X165.1_P_5e-08_MGI_20200608
Variants
Original Genome Build GRCh37
Number of Variants 21
Development Method
Name GWAS Hits
Parameters LD Clumping (MAF >= 1%, r^2 <= 0.1) & P<=5e-08
PGS Source
PGS Catalog Publication (PGP) ID PGP000118
Citation (link to publication) Fritsche LG et al. Am J Hum Genet (2020)

Contributing Samples

Source of Variant Associations (GWAS)
Study Identifiers Sample Numbers Sample Ancestry
GWAS Catalog: GCST004749
EuropePMC: 28604730		 40,187 individuals European
GWAS Catalog: GCST004750
EuropePMC: 28604730		 63,053 individuals European
GWAS Catalog: GCST004744
EuropePMC: 28604730		 66,756 individuals European
GWAS Catalog: GCST004748
EuropePMC: 28604730		 85,716 individuals European
GWAS Catalog: GCST004747
EuropePMC: 28604730		 9,859 individuals European
GWAS Catalog: GCST006088
EuropePMC: 29924316		 31,930 individuals European
GWAS Catalog: GCST006087
EuropePMC: 29924316		 32,338 individuals European
GWAS Catalog: GCST006086
EuropePMC: 29924316		 35,953 individuals European
GWAS Catalog: GCST004746
EuropePMC: 28604730		 24,108 individuals European
GWAS Catalog: GCST002466
EuropePMC: 24880342		 27,209 individuals European
GWAS Catalog: GCST000506
EuropePMC: 19836008		 11,587 individuals European
Score Development/Training
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
PheCode:165.1; ICD9CM:162.0, 162.2, 162.3, 162.4, 162.5, 162.8, 162.9, 209.21, 231.2, V10.11; ICD10CM:C33, C34, C34.0, C34.00, C34.01, C34.02, C34.1, C34.10, C34.11, C34.12, C34.2, C34.3, C34.30, C34.31, C34.32, C34.8, C34.80, C34.81, C34.82, C34.9, C34.90, C34.91, C34.92, C7A.090, D02.2, D02.20, D02.21, D02.22 —
[
  • 446 cases
  • , 4,454 controls
]
 — European — MGI —

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
PPM001074 PSS000541 PGP000118
Fritsche LG et al. (2020) 		Reported Trait: Cancer of bronchus; lung OR: 1.11 [1.006, 1.225]
β: 0.105 (0.0501)		 AUROC: 0.52 [0.492, 0.547] Nagelkerke's Pseudo-R²: 0.00202
Brier score: 0.0827
Odds Ratio (OR, top 1% vs. Rest): 2.19 [1.07, 4.49]		 age, sex, batch PCs 1-4 Cancer PRSweb PheWAS Results: PRSWEB_PHECODE165.1_GWAS-Catalog-r2019-05-03-X165.1_P_5e-08_MGI_20200608

Evaluated Samples

PGS Sample Set ID
(PSS ID) 		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
PSS000541 PheCode:165.1; ICD9CM:162.0, 162.2, 162.3, 162.4, 162.5, 162.8, 162.9, 209.21, 231.2, V10.11; ICD10CM:C33, C34, C34.0, C34.00, C34.01, C34.02, C34.1, C34.10, C34.11, C34.12, C34.2, C34.3, C34.30, C34.31, C34.32, C34.8, C34.80, C34.81, C34.82, C34.9, C34.90, C34.91, C34.92, C7A.090, D02.2, D02.20, D02.21, D02.22 —
[
  • 428 cases
  • , 4,270 controls
]
 — European — MGI —