PGS Catalog - PGS000392 / Lung and bronchus cancer (Polygenic Score)

Polygenic Score (PGS) ID: PGS000392

Predicted Trait
Reported Trait	Lung and bronchus cancer
Mapped Trait(s)	bronchus cancer (MONDO_0001672) lung cancer (MONDO_0008903) tracheal cancer (MONDO_0001407)
Additional Trait Information	PheCode 165.1

Released in PGS Catalog: Dec. 15, 2020

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PGS obtained from the Catalog should be cited appropriately, and used in accordance with any licensing restrictions set by the authors. See EBI Terms of Use (https://www.ebi.ac.uk/about/terms-of-use/) for additional details.

Score Details

Score Construction
PGS Name	PRSWEB_PHECODE165.1_GWAS-Catalog-r2019-05-03-X165.1_PT_UKB_20200608
Development Method
Name	Pruning and Thresholding (P+T)
Parameters	LD Clumping (MAF >= 1%, r^2 <= 0.1) & P<=2.51e-08
Variants
Original Genome Build	GRCh37
Number of Variants	19
Effect Weight Type	NR

PGS Source
PGS Catalog Publication (PGP) ID	PGP000118
Citation (link to publication)	Fritsche LG et al. Am J Hum Genet (2020)

Ancestry Distribution
Source of Variant Associations (GWAS)	European: 100% 428,696 individuals (100%)
Score Development/Training	European: 100% 12,336 individuals (100%)
PGS Evaluation	European: 100% 2 Sample Sets

Development Samples

Source of Variant Associations (GWAS)

Study Identifiers	Sample Numbers	Sample Ancestry	Cohort(s)
GWAS Catalog: GCST002466 Europe PMC: 24880342	27,209 individuals	European	NR
GWAS Catalog: GCST004746 Europe PMC: 28604730	24,108 individuals	European	NR
GWAS Catalog: GCST004747 Europe PMC: 28604730	9,859 individuals	European	NR
GWAS Catalog: GCST004748 Europe PMC: 28604730	85,716 individuals	European	NR
GWAS Catalog: GCST004750 Europe PMC: 28604730	63,053 individuals	European	NR
GWAS Catalog: GCST006086 Europe PMC: 29924316	35,953 individuals	European	NR
GWAS Catalog: GCST006088 Europe PMC: 29924316	31,930 individuals	European	NR
GWAS Catalog: GCST000506 Europe PMC: 19836008	11,587 individuals	European	NR
GWAS Catalog: GCST004744 Europe PMC: 28604730	66,756 individuals	European	NR
GWAS Catalog: GCST004749 Europe PMC: 28604730	40,187 individuals	European	NR
GWAS Catalog: GCST006087 Europe PMC: 29924316	32,338 individuals	European	NR

Score Development/Training

Study Identifiers	Sample Numbers	Sample Ancestry	Cohort(s)	Phenotype Definitions & Methods	Age of Study Participants	Participant Follow-up Time	Additional Ancestry Description	Additional Sample/Cohort Information
Europe PMC: 32991828	12,336 individuals [ 1,121 cases , 11,215 controls ]	European	UKB	PheCode:165.1; ICD9:162, 162.0, 162.2, 162.3, 162.4, 162.5, 162.8, 162.9, 231.2; ICD10:C33, C34.0, C34.1, C34.2, C34.3, C34.8, C34.9, D02.2	—	—	—	—

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)	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
PPM001077	PSS000566\| European Ancestry\| 12,201 individuals	PGP000118 \| Fritsche LG et al. Am J Hum Genet (2020)	Reported Trait: Cancer of bronchus; lung	OR: 1.221 [1.149, 1.298] β: 0.2 (0.0313)	AUROC: 0.552 [0.534, 0.569]	Nagelkerke's Pseudo-R²: 0.00728 Brier score: 0.0824 Odds Ratio (OR, top 1% vs. Rest): 1.94 [1.22, 3.1]	age, sex, batch PCs 1-4	Cancer PRSweb PheWAS Results: PRSWEB_PHECODE165.1_GWAS-Catalog-r2019-05-03-X165.1_PT_UKB_20200608
PPM020288	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	—

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
PSS011324	—	—	1,202 individuals [ 652 cases , 550 controls ] , 47.0 % Male samples	Median = 65.0 years	European	—	MCRC	—
PSS000566	PheCode:165.1; ICD9:162, 162.0, 162.2, 162.3, 162.4, 162.5, 162.8, 162.9, 231.2; ICD10:C33, C34.0, C34.1, C34.2, C34.3, C34.8, C34.9, D02.2	—	12,201 individuals [ 1,109 cases , 11,092 controls ]	—	European	—	UKB	—