PGS Catalog - PGS000389 / Lung and bronchus cancer (Polygenic Score)

Polygenic Score (PGS) ID: PGS000389

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_P_5e-08_MGI_20200608
Development Method
Name	GWAS Hits
Parameters	LD Clumping (MAF >= 1%, r^2 <= 0.1) & P<=5e-08
Variants
Original Genome Build	GRCh37
Number of Variants	21
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% 4,900 individuals (100%)
PGS Evaluation	European: 100% 1 Sample Sets

Development Samples

Source of Variant Associations (GWAS)

Study Identifiers	Sample Numbers	Sample Ancestry	Cohort(s)
GWAS Catalog: GCST004749 Europe PMC: 28604730	40,187 individuals	European	NR
GWAS Catalog: GCST004750 Europe PMC: 28604730	63,053 individuals	European	NR
GWAS Catalog: GCST004744 Europe PMC: 28604730	66,756 individuals	European	NR
GWAS Catalog: GCST004748 Europe PMC: 28604730	85,716 individuals	European	NR
GWAS Catalog: GCST004747 Europe PMC: 28604730	9,859 individuals	European	NR
GWAS Catalog: GCST006088 Europe PMC: 29924316	31,930 individuals	European	NR
GWAS Catalog: GCST006087 Europe PMC: 29924316	32,338 individuals	European	NR
GWAS Catalog: GCST006086 Europe PMC: 29924316	35,953 individuals	European	NR
GWAS Catalog: GCST004746 Europe PMC: 28604730	24,108 individuals	European	NR
GWAS Catalog: GCST002466 Europe PMC: 24880342	27,209 individuals	European	NR
GWAS Catalog: GCST000506 Europe PMC: 19836008	11,587 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	4,900 individuals [ 446 cases , 4,454 controls ]	European	MGI	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	—	—	—	—

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
PPM001074	PSS000541\| European Ancestry\| 4,698 individuals	PGP000118 \| Fritsche LG et al. Am J Hum Genet (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)	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	—	4,698 individuals [ 428 cases , 4,270 controls ]	—	European	—	MGI	—