Polygenic Score (PGS) ID: PGS000070

Predicted Trait
Reported Trait Lung cancer
Mapped Trait(s) lung adenocarcinoma (EFO_0000571)
Released in PGS Catalog: Feb. 12, 2020
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Score Details

Score Construction
PGS Name PRS_LC_C
Development Method
Name Genomewide-significant SNPs, filtered to be specific to Chinese ancestry individuals
Parameters Meta-anlaysis p-value ≤5·0 × 10−8; MAF < 0.01 (in Chinese populations); r2 >= 0.1; Chinese-specific association p-value < 0.00125
Variants
Original Genome Build GRCh37
Number of Variants 19
Effect Weight Type ln(OR)
PGS Source
PGS Catalog Publication (PGP) ID PGP000049
Citation (link to publication) Dai J et al. Lancet Respir Med (2019)
Ancestry Distribution
Source of Variant
Associations (GWAS)
European: 51.1%
East Asian: 48.9%
54,475 individuals (100%)
PGS Evaluation
East Asian: 100%
3 Sample Sets

Development Samples

Source of Variant Associations (GWAS)
Study Identifiers Sample Numbers Sample Ancestry Cohort(s)
GWAS Catalog: GCST008834
Europe PMC: 31326317
 26,655 individuals East Asian NR
GWAS Catalog: GCST008834
Europe PMC: 31326317
 27,820 individuals European NR

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
PPM000190 PSS000109|
East Asian Ancestry|
95,408 individuals
 PGP000049 |
Dai J et al. Lancet Respir Med (2019)
 Reported Trait: Incident lung cancer — — HR (High genetic risk: top 5% vs. bottom 5% of PRS): 2.37 [1.64, 3.44]
HR (Intermediate genetic risk: 5-95% vs. bottom 5% of PRS): 1.6 [1.17, 2.2]		 age, sex, source of region, smoking status —
PPM015573 PSS009987|
East Asian Ancestry|
19,546 individuals
 PGP000387 |
Qin N et al. Lancet Oncol (2022)
|Ext.		 Reported Trait: Lung cancer — — Odds ratio (OR, high vs low risk): 2.18 [2.00, 2.38] — —
PPM015575 PSS009987|
East Asian Ancestry|
19,546 individuals
 PGP000387 |
Qin N et al. Lancet Oncol (2022)
|Ext.		 Reported Trait: Lung cancer x autosomal mosaic loss abnormalities interaction OR: 2.36 [1.09, 5.08] — — — —
PPM018700 PSS011073|
East Asian Ancestry|
381 individuals
 PGP000494 |
Ho PJ et al. Elife (2023)
|Ext.		 Reported Trait: Lung cancer — AUROC: 0.68 [0.65, 0.71] Hazard ratio (HR, high vs low tertile): 2.01 [1.44, 2.81] age at recruitment —

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
PSS009987 — —
[
  • 10,248 cases
  • , 9,298 controls
]
,
63.0 % Male samples
 — East Asian
(Chinese)		 — NR NJLCC
PSS000109 Participants were followed-up for cancer events mainly through linkage with official death certificates, chronic disease registries, and the Chinese national health insurance system. Median = 10.44 years
[
  • 1,316 cases
  • , 94,092 controls
]
,
42.93 % Male samples
 Mean = 53.67 years
Se = 10.98 years		 East Asian
(Chinese)		 — CKB —
PSS011073 — — 381 individuals,
100.0 % Male samples
 Median = 60.0 years
IQR = [55.0, 64.0] years		 East Asian
(Chinese)		 — SCHS —