PGS Publication: PGP000148

Publication Information (EuropePMC)
Title Assessing Lung Cancer Absolute Risk Trajectory Based on a Polygenic Risk Model.
PubMed ID 33472890(Europe PMC)
doi 10.1158/0008-5472.can-20-1237
Publication Date Jan. 20, 2021
Journal Cancer Res
Author(s) Hung RJ, Warkentin MT, Brhane Y, Chatterjee N, Christiani DC, Landi MT, Caporaso NE, Liu G, Johansson M, Albanes D, Marchand LL, Tardon A, Rennert G, Bojesen SE, Chen C, Field JK, Kiemeney LA, Lazarus P, Zienolddiny S, Lam S, Andrew AS, Arnold SM, Aldrich MC, Bickeböller H, Risch A, Schabath MB, McKay JD, Brennan P, Amos CI.
Released in PGS Catalog: March 22, 2021

Associated Polygenic Score(s)

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Individuals included in:
G - Source of Variant Associations (GWAS)
D - Score Development/Training
E - PGS Evaluation
List of ancestries includes:
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Additional Diverse Ancestries
Not Reported

PGS Developed By This Publication

Polygenic Score ID & Name PGS Publication ID (PGP) Reported Trait Mapped Trait(s) (Ontology) Number of Variants Ancestry distribution
GWAS
Dev
Eval
 Scoring File (FTP Link)
PGS000740
(PRS128_LC)
 PGP000148 |
Hung RJ et al. Cancer Res (2021)
 Lung cancer lung carcinoma 128
https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS000740/ScoringFiles/PGS000740.txt.gz

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) 		Evaluated Score 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 PGS000740
(PRS128_LC)
 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 PGS000740
(PRS128_LC)
 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 PGS000740
(PRS128_LC)
 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 PGS000740
(PRS128_LC)
 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 PGS000740
(PRS128_LC)
 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 PGS000740
(PRS128_LC)
 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 PGS000740
(PRS128_LC)
 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 PGS000740
(PRS128_LC)
 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 PGS000740
(PRS128_LC)
 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 PGS000740
(PRS128_LC)
 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 PGS000740
(PRS128_LC)
 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)

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 —
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 —