Polygenic Score (PGS) ID: PGS000740

Predicted Trait
Reported Trait Lung cancer
Mapped Trait(s) lung carcinoma (EFO_0001071)
Released in PGS Catalog: March 22, 2021
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Score Details

Score Construction
PGS Name PRS128_LC
Development Method
Name Clumped lung cancer loci (35 SNP score) combined with LASSO penalized regression (93 SNP score)
Parameters 35 SNP score: r^2 >0.2 93 SNP score: P<5e-6, INFO >0.3, r^2 > 0.2
Variants
Original Genome Build NR
Number of Variants 128
Effect Weight Type log(OR)
PGS Source
PGS Catalog Publication (PGP) ID PGP000148
Citation (link to publication) Hung RJ et al. Cancer Res (2021)
Ancestry Distribution
Source of Variant
Associations (GWAS)
European: 100%
308,645 individuals (100%)
Score Development/Training
European: 100%
32,341 individuals (100%)
PGS Evaluation
European: 92.3%
African: 7.7%
13 Sample Sets

Development Samples

Source of Variant Associations (GWAS)
Study Identifiers Sample Numbers Sample Ancestry Cohort(s)
Europe PMC: 26363033
[
  • 14,049 cases
  • , 33,456 controls
]
 European 14 cohorts
  • ATBC
  • ,CPS
  • ,EAGLE
  • ,HGF
  • ,HLCS
  • ,IARC
  • ,ICR-GWAS
  • ,LCSC
  • ,LLP
  • ,MAYOLC
  • ,MDACC
  • ,MSKLCG
  • ,PLCO
  • ,deCODE
GWAS Catalog: GCST002753
Europe PMC: 25644374
 8,683 individuals European HMGU, IARC, MDACC, Toronto
Europe PMC: 26590902
[
  • 5,164 cases
  • , 5,716 controls
]
,
56.99 % Male samples
 European 12 cohorts
  • CARET
  • ,EPIC
  • ,HLCS
  • ,LLP
  • ,MCCS
  • ,MEC
  • ,MSH
  • ,NHS
  • ,NPHS
  • ,PLCO
  • ,PMHT
  • ,RUSS
GWAS Catalog: GCST004748
Europe PMC: 28604730
 85,716 individuals European 31 cohorts
  • ATBC
  • ,BioVU
  • ,CAPUA
  • ,CARET
  • ,CPS
  • ,CanSS
  • ,CopenhagenLCS
  • ,EAGLE
  • ,EPIC
  • ,GLC
  • ,HLCS
  • ,Harvard
  • ,IARC
  • ,ICR
  • ,LCRI-DOD
  • ,LLP
  • ,MDC
  • ,MEC
  • ,MSH
  • ,NELCS
  • ,NICCC-LCA
  • ,NLC
  • ,NSHDS
  • ,NorwayLCS
  • ,PLCO
  • ,PMHT
  • ,Resolucent
  • ,SLRI
  • ,TLC
  • ,TampaLC
  • ,deCODE
GWAS Catalog: GCST004744
Europe PMC: 28604730
 66,756 individuals European 31 cohorts
  • ATBC
  • ,BioVU
  • ,CAPUA
  • ,CARET
  • ,CPS
  • ,CanSS
  • ,CopenhagenLCS
  • ,EAGLE
  • ,EPIC
  • ,GLC
  • ,HLCS
  • ,Harvard
  • ,IARC
  • ,ICR
  • ,LCRI-DOD
  • ,LLP
  • ,MDC
  • ,MEC
  • ,MSH
  • ,NELCS
  • ,NICCC-LCA
  • ,NLC
  • ,NSHDS
  • ,NorwayLCS
  • ,PLCO
  • ,PMHT
  • ,Resolucent
  • ,SLRI
  • ,TLC
  • ,TampaLC
  • ,deCODE
GWAS Catalog: GCST004750
Europe PMC: 28604730
 63,053 individuals European 31 cohorts
  • ATBC
  • ,BioVU
  • ,CAPUA
  • ,CARET
  • ,CPS
  • ,CanSS
  • ,CopenhagenLCS
  • ,EAGLE
  • ,EPIC
  • ,GLC
  • ,HLCS
  • ,Harvard
  • ,IARC
  • ,ICR
  • ,LCRI-DOD
  • ,LLP
  • ,MDC
  • ,MEC
  • ,MSH
  • ,NELCS
  • ,NICCC-LCA
  • ,NLC
  • ,NSHDS
  • ,NorwayLCS
  • ,PLCO
  • ,PMHT
  • ,Resolucent
  • ,SLRI
  • ,TLC
  • ,TampaLC
  • ,deCODE
GWAS Catalog: GCST004746
Europe PMC: 28604730
 24,108 individuals European 31 cohorts
  • ATBC
  • ,BioVU
  • ,CAPUA
  • ,CARET
  • ,CPS
  • ,CanSS
  • ,CopenhagenLCS
  • ,EAGLE
  • ,EPIC
  • ,GLC
  • ,HLCS
  • ,Harvard
  • ,IARC
  • ,ICR
  • ,LCRI-DOD
  • ,LLP
  • ,MDC
  • ,MEC
  • ,MSH
  • ,NELCS
  • ,NICCC-LCA
  • ,NLC
  • ,NSHDS
  • ,NorwayLCS
  • ,PLCO
  • ,PMHT
  • ,Resolucent
  • ,SLRI
  • ,TLC
  • ,TampaLC
  • ,deCODE
Europe PMC: 26352532
[
  • 778 cases
  • , 1,166 controls
]
 European PLuSS, UoPMC
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
—
[
  • 18,316 cases
  • , 14,025 controls
]
 European ILCCO — — — — This cohort was used to identify the variants for the 93 SNP score.

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
PPM001780 PSS000921|
European Ancestry|
183,671 individuals
 PGP000148 |
Hung RJ et al. Cancer Res (2021)
 Reported Trait: Lung cancer in individuals who have never smoked OR: 1.28 [1.13, 1.46] — — Age, sex, PCs(1-5) 14/128 were omitted from the analysis (missing in HRC panel)
PPM001781 PSS000920|
European Ancestry|
118,310 individuals
 PGP000148 |
Hung RJ et al. Cancer Res (2021)
 Reported Trait: Lung cancer in individuals who are former smokers OR: 1.25 [1.17, 1.34] — — Age, sex, PCs(1-5) 14/128 were omitted from the analysis (missing in HRC panel)
PPM001784 PSS000916|
European Ancestry|
42,540 individuals
 PGP000148 |
Hung RJ et al. Cancer Res (2021)
 Reported Trait: Lung cancer in individuals with no family history of lung cancer OR: 1.29 [1.22, 1.36] — — Age, sex, PCs(1-5) 14/128 were omitted from the analysis (missing in HRC panel)
PPM001785 PSS000917|
European Ancestry|
330,046 individuals
 PGP000148 |
Hung RJ et al. Cancer Res (2021)
 Reported Trait: Lung cancer in individuals with COPD OR: 1.26 [1.09, 1.46] — — Age, sex, PCs(1-5) 14/128 were omitted from the analysis (missing in HRC panel)
PPM001789 PSS000913|
European Ancestry|
167,955 individuals
 PGP000148 |
Hung RJ et al. Cancer Res (2021)
 Reported Trait: Early onset lung cancer (< 50 years) — AUROC: 0.811 [0.701, 0.922] — Age, sex, education, body mass index, personal history of cancer, family history of lung cancer, lung function 14/128 were omitted from the analysis (missing in HRC panel)
PPM001779 PSS000912|
European Ancestry|
335,931 individuals
 PGP000148 |
Hung RJ et al. Cancer Res (2021)
 Reported Trait: Lung cancer OR: 1.26 [1.2, 1.32] — Odds Ratio (OR, top 10% vs low risk): 2.39 [1.92, 3.0] Age, sex, PCs(1-5) 14/128 were omitted from the analysis (missing in HRC panel)
PPM001782 PSS000919|
European Ancestry|
33,950 individuals
 PGP000148 |
Hung RJ et al. Cancer Res (2021)
 Reported Trait: Lung cancer in individuals who currently smoke OR: 1.28 [1.19, 1.38] — — Age, sex, PCs(1-5) 14/128 were omitted from the analysis (missing in HRC panel)
PPM001783 PSS000918|
European Ancestry|
287,620 individuals
 PGP000148 |
Hung RJ et al. Cancer Res (2021)
 Reported Trait: Lung cancer in individuals with a family history of lung cancer OR: 1.16 [1.05, 1.27] — — Age, sex, PCs(1-5) 14/128 were omitted from the analysis (missing in HRC panel)
PPM001786 PSS000915|
European Ancestry|
5,491 individuals
 PGP000148 |
Hung RJ et al. Cancer Res (2021)
 Reported Trait: Lung cancer in individuals with no COPD diagnosis OR: 1.26 [1.2, 1.32] — — Age, sex, PCs(1-5) 14/128 were omitted from the analysis (missing in HRC panel)
PPM001787 PSS000913|
European Ancestry|
167,955 individuals
 PGP000148 |
Hung RJ et al. Cancer Res (2021)
 Reported Trait: Lung cancer (absolute risk) β: 0.663 — — Age, sex, PCs(1-5) 14/128 were omitted from the analysis (missing in HRC panel)
PPM001788 PSS000914|
European Ancestry|
67,186 individuals
 PGP000148 |
Hung RJ et al. Cancer Res (2021)
 Reported Trait: Lung cancer in individuals who have never smoked — AUROC: 0.687 [0.628, 0.746] — Age, sex, education, body mass index, personal history of cancer, family history of lung cancer, lung function 14/128 were omitted from the analysis (missing in HRC panel)
PPM020289 PSS011324|
European Ancestry|
1,202 individuals
 PGP000539 |
Lebrett MB et al. Genet Med (2023)
|Ext.		 Reported Trait: Lung cancer — AUROC: 0.73 [0.702, 0.758] — Age, sex, current smoking status, BMI, forced expiratory volume in 1 second/forced vital capacity ratio —
PPM021377 PSS011713|
European Ancestry|
1,915 individuals
 PGP000646 |
Trendowski MR et al. Cancer Epidemiol Biomarkers Prev (2023)
|Ext.		 Reported Trait: Lung cancer OR: 1.16 [1.04, 1.29] — — Age, sex, pack-years, history of COPD, family history of lung cancer, 5 PCs Only 80 of 128 SNPs were available for analysis
PPM021378 PSS011712|
African Ancestry|
1,123 individuals
 PGP000646 |
Trendowski MR et al. Cancer Epidemiol Biomarkers Prev (2023)
|Ext.		 Reported Trait: Lung cancer OR: 0.99 [0.85, 1.15] — — Age, sex, pack-years, history of COPD, family history of lung cancer, 5 PCs Only 80 of 128 SNPs were available for analysis

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
PSS000918 Cases are individuals with a lung cancer diagnosis. Lung cancer diagnosis was obtained through record linkage with death and cancer registries with the follow‐up time up to date of death, lung cancer diagnosis, or March 31, 2016 (in England and Wales) and Oct 31, 2015 (in Scotland) per censor date defined by UKB. To minimize the possibility of including lung cancer metastasis, we excluded lung cancer that occurred within 5 years of different primary cancer. —
[
  • 1,323 cases
  • , 286,297 controls
]
 — European — UKB —
PSS000919 Cases are individuals with a lung cancer diagnosis. Lung cancer diagnosis was obtained through record linkage with death and cancer registries with the follow‐up time up to date of death, lung cancer diagnosis, or March 31, 2016 (in England and Wales) and Oct 31, 2015 (in Scotland) per censor date defined by UKB. To minimize the possibility of including lung cancer metastasis, we excluded lung cancer that occurred within 5 years of different primary cancer. —
[
  • 724 cases
  • , 33,226 controls
]
 — European — UKB —
PSS000920 Cases are individuals with a lung cancer diagnosis. Lung cancer diagnosis was obtained through record linkage with death and cancer registries with the follow‐up time up to date of death, lung cancer diagnosis, or March 31, 2016 (in England and Wales) and Oct 31, 2015 (in Scotland) per censor date defined by UKB. To minimize the possibility of including lung cancer metastasis, we excluded lung cancer that occurred within 5 years of different primary cancer. —
[
  • 808 cases
  • , 117,502 controls
]
 — European — UKB —
PSS000921 Cases are individuals with a lung cancer diagnosis. Lung cancer diagnosis was obtained through record linkage with death and cancer registries with the follow‐up time up to date of death, lung cancer diagnosis, or March 31, 2016 (in England and Wales) and Oct 31, 2015 (in Scotland) per censor date defined by UKB. To minimize the possibility of including lung cancer metastasis, we excluded lung cancer that occurred within 5 years of different primary cancer. —
[
  • 236 cases
  • , 183,435 controls
]
 — European — UKB —
PSS011324 — —
[
  • 652 cases
  • , 550 controls
]
,
47.0 % Male samples
 Median = 65.0 years European — MCRC —
PSS011712 — —
[
  • 558 cases
  • , 565 controls
]
,
43.5 % Male samples
 — African unspecified — INHALE —
PSS011713 — —
[
  • 1,103 cases
  • , 812 controls
]
,
47.2 % Male samples
 — European — INHALE —
PSS000912 Cases are individuals with a lung cancer diagnosis. Lung cancer diagnosis was obtained through record linkage with death and cancer registries with the follow‐up time up to date of death, lung cancer diagnosis, or March 31, 2016 (in England and Wales) and Oct 31, 2015 (in Scotland) per censor date defined by UKB. To minimize the possibility of including lung cancer metastasis, we excluded lung cancer that occurred within 5 years of different primary cancer. —
[
  • 1,768 cases
  • , 50,772 controls
]
,
46.28 % Male samples
 — European — UKB —
PSS000913 — — 167,955 individuals — European — UKB —
PSS000914 — — 67,186 individuals — European — UKB —
PSS000915 Cases are individuals with a lung cancer diagnosis. Lung cancer diagnosis was obtained through record linkage with death and cancer registries with the follow‐up time up to date of death, lung cancer diagnosis, or March 31, 2016 (in England and Wales) and Oct 31, 2015 (in Scotland) per censor date defined by UKB. To minimize the possibility of including lung cancer metastasis, we excluded lung cancer that occurred within 5 years of different primary cancer. —
[
  • 180 cases
  • , 5,311 controls
]
 — European — UKB —
PSS000916 Cases are individuals with a lung cancer diagnosis. Lung cancer diagnosis was obtained through record linkage with death and cancer registries with the follow‐up time up to date of death, lung cancer diagnosis, or March 31, 2016 (in England and Wales) and Oct 31, 2015 (in Scotland) per censor date defined by UKB. To minimize the possibility of including lung cancer metastasis, we excluded lung cancer that occurred within 5 years of different primary cancer. —
[
  • 387 cases
  • , 42,153 controls
]
 — European — UKB —
PSS000917 Cases are individuals with a lung cancer diagnosis. Lung cancer diagnosis was obtained through record linkage with death and cancer registries with the follow‐up time up to date of death, lung cancer diagnosis, or March 31, 2016 (in England and Wales) and Oct 31, 2015 (in Scotland) per censor date defined by UKB. To minimize the possibility of including lung cancer metastasis, we excluded lung cancer that occurred within 5 years of different primary cancer. —
[
  • 1,581 cases
  • , 328,465 controls
]
 — European — UKB —