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(Variants and weights)

Polygenic Score (PGS) ID: PGS000078

Predicted Trait

Reported Trait: Lung cancer
Mapped Trait(s) (Experimental Factor Ontology (EFO) IDs): lung carcinoma

Score Details

Name: CC_Lung

Original Genome Build: GRCh37
Number of Variants: 109

PGS Development Method: Genome-wide significant SNPs
PGS Development Details/Relevant Parameters: P < 5x10-8, MAF > 1%, biallelic SNPs, LD-thin r2 > 0.3

Citation: Graff RE et al. bioRxiv (2020) | PGS Catalog Publication ID: PGP000050

Contributing Samples

Source of Variant Associations (GWAS)
Study Identifiers Sample Numbers Sample Ancestry
GWAS Catalog: GCST004748
PubMed: 28604730
85,716 individuals European
PubMed: 21303977.0 43,141 individuals
[ 2,783 cases, 40,358 controls]
GWAS Catalog: GCST001638
PubMed: 22899653
44,385 individuals European
GWAS Catalog: GCST000257
PubMed: 18978787
10,295 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 (PPM) ID PGS Catalog Sample Set (PSS) ID Performance Source Trait PGS Effect Sizes
(per SD change)
PGS Classification Metrics Other Metrics Covariates Included in PGS Model PGS Performance: Other Relevant Information
PPM000198 PSS000117 Graff RE et al. (2020) Reported Trait: Lung cancer OR: 1.12 [1.08 - 1.17] Genotyping reagent kit (GERA cohort only), genotyping array (UK Biobank only), age, sex, 10 PCs. Results from meta-analysis of GERA and UKB

Evaluated Samples

PGS Catalog Sample Set (PSS) ID Detailed Phenotype Description (e.g. ICD/SNOMED codes used to identify cases) Sample Numbers Sample Ancestry Additional Ancestry Description Cohort(s) Additional Sample/Cohort Information
PSS000117 Cancer diagnoses were obtained from reigstry data in GERA, and ICD-9/10 codes mapped to ICD-O-3 codes in UK Biobank. Cancers for this phenotype were classified using the following SEER site recode(s): 22030 412,842 individuals
[ 2,488 cases, 410,354 controls]
0.46 % Male samples
European GERA, UKB