PGS Publication: PGP000127

Publication Information (EuropePMC)
Title Clinical Utility of Lipoprotein(a) and LPA Genetic Risk Score in Risk Prediction of Incident Atherosclerotic Cardiovascular Disease.
PubMed ID 33021622(Europe PMC)
doi 10.1001/jamacardio.2020.5398
Publication Date Oct. 6, 2020
Journal JAMA Cardiol
Author(s) Trinder M, Uddin MM, Finneran P, Aragam KG, Natarajan P.
Released in PGS Catalog: Jan. 7, 2021

Associated Polygenic Score(s)

Filter PGS by Participant Ancestry
Individuals included in:
G - Source of Variant Associations (GWAS)
D - Score Development/Training
E - PGS Evaluation
List of ancestries includes:
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Ancestry legend
Multi-ancestry (including European)
Multi-ancestry (excluding European)
African
East Asian
South Asian
Additional Asian Ancestries
European
Greater Middle Eastern
Hispanic or Latin American
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 PGS Scoring File (FTP Link)
PGS000667
(LPA_GRS43)
PGP000127 |
Trinder M et al. JAMA Cardiol (2020)
Lipoprotein A lipoprotein A measurement 43
-
http://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS000667/ScoringFiles/PGS000667.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
PPM001378 PGS000667
(LPA_GRS43)
PSS000613|
African Ancestry|
6,521 individuals
PGP000127 |
Trinder M et al. JAMA Cardiol (2020)
Reported Trait: Measured levels of lipoprotein(a) : 0.038
Pearson correlation coefficient: 0.07
Age, sex, assessment center, genotyping batch, PCs (1-5) of ancestry
PPM001379 PGS000667
(LPA_GRS43)
PSS000614|
East Asian Ancestry|
2,774 individuals
PGP000127 |
Trinder M et al. JAMA Cardiol (2020)
Reported Trait: Measured levels of lipoprotein(a) : 0.078
Pearson correlation coefficient: 0.281
Age, sex, assessment center, genotyping batch, PCs (1-5) of ancestry
PPM001380 PGS000667
(LPA_GRS43)
PSS000615|
European Ancestry|
350,903 individuals
PGP000127 |
Trinder M et al. JAMA Cardiol (2020)
Reported Trait: Measured levels of lipoprotein(a) : 0.595
Pearson correlation coefficient: 0.717
Age, sex, assessment center, genotyping batch, PCs (1-5) of ancestry
PPM001381 PGS000667
(LPA_GRS43)
PSS000616|
South Asian Ancestry|
6,203 individuals
PGP000127 |
Trinder M et al. JAMA Cardiol (2020)
Reported Trait: Measured levels of lipoprotein(a) : 0.11
Pearson correlation coefficient: 0.371
Age, sex, assessment center, genotyping batch, PCs (1-5) of ancestry
PPM001382 PGS000667
(LPA_GRS43)
PSS000611|
European Ancestry|
283,540 individuals
PGP000127 |
Trinder M et al. JAMA Cardiol (2020)
Reported Trait: Incident composite atherosclerotic cardiovascular disease HR: 1.29 [1.26, 1.33] Age, sex, assessment center, genotyping batch, PCs (1-5) of ancestry
PPM001383 PGS000667
(LPA_GRS43)
PSS000608|
European Ancestry|
283,540 individuals
PGP000127 |
Trinder M et al. JAMA Cardiol (2020)
Reported Trait: Incident cardiovascular disease mortality HR: 1.09 [1.02, 1.16] Age, sex, assessment center, genotyping batch, PCs (1-5) of ancestry
PPM001384 PGS000667
(LPA_GRS43)
PSS000609|
European Ancestry|
283,540 individuals
PGP000127 |
Trinder M et al. JAMA Cardiol (2020)
Reported Trait: Incident myocardial infarction HR: 1.38 [1.33, 1.43] Age, sex, assessment center, genotyping batch, PCs (1-5) of ancestry
PPM001385 PGS000667
(LPA_GRS43)
PSS000607|
European Ancestry|
283,540 individuals
PGP000127 |
Trinder M et al. JAMA Cardiol (2020)
Reported Trait: Incident coronary artery disease HR: 1.45 [1.41, 1.5] Age, sex, assessment center, genotyping batch, PCs (1-5) of ancestry
PPM001386 PGS000667
(LPA_GRS43)
PSS000612|
European Ancestry|
283,540 individuals
PGP000127 |
Trinder M et al. JAMA Cardiol (2020)
Reported Trait: Incident stroke HR: 1.12 [1.04, 1.19] Age, sex, assessment center, genotyping batch, PCs (1-5) of ancestry
PPM001387 PGS000667
(LPA_GRS43)
PSS000610|
European Ancestry|
283,540 individuals
PGP000127 |
Trinder M et al. JAMA Cardiol (2020)
Reported Trait: Incident peripheral arterial disease HR: 1.34 [1.26, 1.42] Age, sex, assessment center, genotyping batch, PCs (1-5) of ancestry
PPM001388 PGS000667
(LPA_GRS43)
PSS000611|
European Ancestry|
283,540 individuals
PGP000127 |
Trinder M et al. JAMA Cardiol (2020)
Reported Trait: Incident composite atherosclerotic cardiovascular disease HR: 1.06 [1.01, 1.11] Age, sex, assessment center, genotyping batch, PCs (1-5) of ancestry, measured lipoprotein(a)
PPM001389 PGS000667
(LPA_GRS43)
PSS000609|
European Ancestry|
283,540 individuals
PGP000127 |
Trinder M et al. JAMA Cardiol (2020)
Reported Trait: Incident myocardial infarction HR: 1.09 [1.01, 1.17] Age, sex, assessment center, genotyping batch, PCs (1-5) of ancestry, measured lipoprotein(a)
PPM001390 PGS000667
(LPA_GRS43)
PSS000607|
European Ancestry|
283,540 individuals
PGP000127 |
Trinder M et al. JAMA Cardiol (2020)
Reported Trait: Incident coronary artery disease HR: 1.07 [1.0, 1.14] Age, sex, assessment center, genotyping batch, PCs (1-5) of ancestry, measured lipoprotein(a)
PPM001391 PGS000667
(LPA_GRS43)
PSS000610|
European Ancestry|
283,540 individuals
PGP000127 |
Trinder M et al. JAMA Cardiol (2020)
Reported Trait: Incident peripheral arterial disease HR: 1.15 [1.02, 1.28] Age, sex, assessment center, genotyping batch, PCs (1-5) of ancestry, measured lipoprotein(a)
PPM001392 PGS000667
(LPA_GRS43)
PSS000606|
European Ancestry|
144,350 individuals
PGP000127 |
Trinder M et al. JAMA Cardiol (2020)
Reported Trait: Incident atherosclerotic cardiovascular disease in individuals with borderline-intermediate risk of atherosclerotic cardiovascular disease AUROC: 0.642 [0.634, 0.649]
C-index: 0.641 (0.0004)
QRISK3
PPM001393 PGS000667
(LPA_GRS43)
PSS000606|
European Ancestry|
144,350 individuals
PGP000127 |
Trinder M et al. JAMA Cardiol (2020)
Reported Trait: Incident atherosclerotic cardiovascular disease in individuals with borderline-intermediate risk of atherosclerotic cardiovascular disease AUROC: 0.642 [0.635, 0.649]
C-index: 0.641 (0.0004)
QRISK3, measured lipoprotein(a)
PPM001394 PGS000667
(LPA_GRS43)
PSS000605|
European Ancestry|
113,703 individuals
PGP000127 |
Trinder M et al. JAMA Cardiol (2020)
Reported Trait: Incident atherosclerotic cardiovascular disease in individuals with borderline-intermediate risk ofatherosclerotic cardiovascular disease AUROC: 0.611 [0.603, 0.617]
C-index: 0.611 (0.004)
Pooled Cohort Equations
PPM001395 PGS000667
(LPA_GRS43)
PSS000605|
European Ancestry|
113,703 individuals
PGP000127 |
Trinder M et al. JAMA Cardiol (2020)
Reported Trait: Incident atherosclerotic cardiovascular disease in individuals with borderline-intermediate risk of atherosclerotic cardiovascular disease AUROC: 0.611 [0.603, 0.617]
C-index: 0.611 (0.004)
Pooled Cohort Equations, measured lipoprotein(a)

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
PSS000605 This subgroup included individuals with complete and imputed data and were classified as having borderline-intermediate ASCVD risk (defined by the Pooled Cohorts Equation) without prevalent ASCVD, diabetes mellitus, severe hypercholesterolemia, or use of cholesterol-lowering medication (10-year risk of 5-20%). Cases included individuals who experienced myocardial infarction, an ischemic stroke or cardiovasulcar mortality events. Median = 11.1 years
[
  • 5,938 cases
  • , 107,765 controls
]
European UKB
PSS000606 This subgroup included individuals with complete and imputed data and were classified as having borderline-intermediate ASCVD risk (defined by QRISK3) without prevalent ASCVD, diabetes mellitus, severe hypercholesterolemia, or use of cholesterol-lowering medication (10-year risk of 5-20%). Cases included individuals who experienced myocardial infarction, an ischemic stroke or cardiovasulcar mortality events. Median = 11.1 years
[
  • 5,505 cases
  • , 138,845 controls
]
European UKB
PSS000607 At the time of enrollment, particpants were without ASCVD. Participants were not using cholesterol-lowering medication. Coronary artery disease defined as: ICD-9 (410, 411, 412, 42979), ICD-10 (I21, I22, I23, I24.1, I25.2) and OCPS-4 (K40, K41, K42, K43, K44, K45, K46, K47, K48, K49, K50 and K75) Median = 11.1 years
[
  • 7,771 cases
  • , 275,769 controls
]
European UKB
PSS000608 At the time of enrollment, particpants were without ASCVD. Participants were not using cholesterol-lowering medication. Cardiovascular mortality defined as: ICD-10 (any diagnosis code for causes of death related to chapter IX diseases of the circulatory system). Median = 11.1 years
[
  • 3,539 cases
  • , 280,001 controls
]
European UKB
PSS000609 At the time of enrollment, particpants were without ASCVD. Participants were not using cholesterol-lowering medication. Myocardial infarction defined as: ICD-9 (410, 411, 412, 42979) and ICD-10 (I21, I22, I23, I24.1, I25.2). Median = 11.1 years
[
  • 5,666 cases
  • , 277,874 controls
]
European UKB
PSS000610 At the time of enrollment, particpants were without ASCVD. Participants were not using cholesterol-lowering medication. Peripheral artery disease (non-coronary or cerebrovascular events) defined as: ICD-9 (440, 444, 4438, 4439), ICD-10 (I70, I74, I73.8, I73.9) and OCPS-4 (L50, L51, L52, L54, L58, L59, L60, L63, X09). Median = 11.1 years
[
  • 2,283 cases
  • , 281,257 controls
]
European UKB
PSS000611 At the time of enrollment, particpants were without ASCVD. Participants were not using cholesterol-lowering medication. The outcomes of myocardial infarction, coronary artery disease, ischemic stroke, peripheral arterial disease, cardiovascular mortality, and a composite of the aforementioned outcomes were based on International Statistical Classification of Diseases and Related Health Problems and Office of Population Censuses and Surveys Classification of Interventions and Procedures codes. Myocardial infarction: ICD-9 (410, 411, 412, 42979) and ICD-10 (I21, I22, I23, I24.1, I25.2). Ischemic stroke: ICD-9 (434, 436) and ICD-10 (I63, I64). Cardiovascular mortality: ICD-10 (any diagnosis code for causes of death related to chapter IX diseases of the circulatory system). Coronary artery disease: ICD-9 (same as myocardial infarction codes), ICD-10 (same as myocardial infarction codes) and OCPS-4 (K40, K41, K42, K43, K44, K45, K46, K47, K48, K49, K50 and K75). Peripheral artery disease (non-coronary or cerebrovascular events): ICD-9 (440, 444, 4438, 4439), ICD-10 (I70, I74, I73.8, I73.9) and OCPS-4 (L50, L51, L52, L54, L58, L59, L60, L63, X09). Incident events were defined as the first event occurring between the date of enrollment and the end of follow-up. Median = 11.1 years
[
  • 14,697 cases
  • , 268,843 controls
]
European UKB
PSS000612 At the time of enrollment, particpants were without ASCVD. Participants were not using cholesterol-lowering medication. Ischemic stroke defined as: ICD-9 (434, 436) and ICD-10 (I63, I64) Median = 11.1 years
[
  • 2,938 cases
  • , 280,602 controls
]
European UKB
PSS000613 The outcomes of myocardial infarction, coronary artery disease, ischemic stroke, peripheral arterial disease, cardiovascular mortality, and a composite of the aforementioned outcomes were based on International Statistical Classification of Diseases and Related Health Problems and Office of Population Censuses and Surveys Classification of Interventions and Procedures codes. Myocardial infarction: ICD-9 (410, 411, 412, 42979) and ICD-10 (I21, I22, I23, I24.1, I25.2). Ischemic stroke: ICD-9 (434, 436) and ICD-10 (I63, I64). Cardiovascular mortality: ICD-10 (any diagnosis code for causes of death related to chapter IX diseases of the circulatory system). Coronary artery disease: ICD-9 (same as myocardial infarction codes), ICD-10 (same as myocardial infarction codes) and OCPS-4 (K40, K41, K42, K43, K44, K45, K46, K47, K48, K49, K50 and K75). Peripheral artery disease (non-coronary or cerebrovascular events): ICD-9 (440, 444, 4438, 4439), ICD-10 (I70, I74, I73.8, I73.9) and OCPS-4 (L50, L51, L52, L54, L58, L59, L60, L63, X09). Incident events were defined as the first event occurring between the date of enrollment and the end of follow-up. 6,521 individuals African unspecified UKB
PSS000614 The outcomes of myocardial infarction, coronary artery disease, ischemic stroke, peripheral arterial disease, cardiovascular mortality, and a composite of the aforementioned outcomes were based on International Statistical Classification of Diseases and Related Health Problems and Office of Population Censuses and Surveys Classification of Interventions and Procedures codes. Myocardial infarction: ICD-9 (410, 411, 412, 42979) and ICD-10 (I21, I22, I23, I24.1, I25.2). Ischemic stroke: ICD-9 (434, 436) and ICD-10 (I63, I64). Cardiovascular mortality: ICD-10 (any diagnosis code for causes of death related to chapter IX diseases of the circulatory system). Coronary artery disease: ICD-9 (same as myocardial infarction codes), ICD-10 (same as myocardial infarction codes) and OCPS-4 (K40, K41, K42, K43, K44, K45, K46, K47, K48, K49, K50 and K75). Peripheral artery disease (non-coronary or cerebrovascular events): ICD-9 (440, 444, 4438, 4439), ICD-10 (I70, I74, I73.8, I73.9) and OCPS-4 (L50, L51, L52, L54, L58, L59, L60, L63, X09). Incident events were defined as the first event occurring between the date of enrollment and the end of follow-up. 2,774 individuals East Asian UKB
PSS000615 The outcomes of myocardial infarction, coronary artery disease, ischemic stroke, peripheral arterial disease, cardiovascular mortality, and a composite of the aforementioned outcomes were based on International Statistical Classification of Diseases and Related Health Problems and Office of Population Censuses and Surveys Classification of Interventions and Procedures codes. Myocardial infarction: ICD-9 (410, 411, 412, 42979) and ICD-10 (I21, I22, I23, I24.1, I25.2). Ischemic stroke: ICD-9 (434, 436) and ICD-10 (I63, I64). Cardiovascular mortality: ICD-10 (any diagnosis code for causes of death related to chapter IX diseases of the circulatory system). Coronary artery disease: ICD-9 (same as myocardial infarction codes), ICD-10 (same as myocardial infarction codes) and OCPS-4 (K40, K41, K42, K43, K44, K45, K46, K47, K48, K49, K50 and K75). Peripheral artery disease (non-coronary or cerebrovascular events): ICD-9 (440, 444, 4438, 4439), ICD-10 (I70, I74, I73.8, I73.9) and OCPS-4 (L50, L51, L52, L54, L58, L59, L60, L63, X09). Incident events were defined as the first event occurring between the date of enrollment and the end of follow-up. 350,903 individuals European UKB
PSS000616 The outcomes of myocardial infarction, coronary artery disease, ischemic stroke, peripheral arterial disease, cardiovascular mortality, and a composite of the aforementioned outcomes were based on International Statistical Classification of Diseases and Related Health Problems and Office of Population Censuses and Surveys Classification of Interventions and Procedures codes. Myocardial infarction: ICD-9 (410, 411, 412, 42979) and ICD-10 (I21, I22, I23, I24.1, I25.2). Ischemic stroke: ICD-9 (434, 436) and ICD-10 (I63, I64). Cardiovascular mortality: ICD-10 (any diagnosis code for causes of death related to chapter IX diseases of the circulatory system). Coronary artery disease: ICD-9 (same as myocardial infarction codes), ICD-10 (same as myocardial infarction codes) and OCPS-4 (K40, K41, K42, K43, K44, K45, K46, K47, K48, K49, K50 and K75). Peripheral artery disease (non-coronary or cerebrovascular events): ICD-9 (440, 444, 4438, 4439), ICD-10 (I70, I74, I73.8, I73.9) and OCPS-4 (L50, L51, L52, L54, L58, L59, L60, L63, X09). Incident events were defined as the first event occurring between the date of enrollment and the end of follow-up. 6,203 individuals South Asian UKB