Polygenic Score (PGS) ID: PGS000667

Predicted Trait
Reported Trait Lipoprotein A
Mapped Trait(s) lipoprotein A measurement (EFO_0006925)
Released in PGS Catalog: Jan. 7, 2021
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Score Details

Score Construction
PGS Name LPA_GRS43
Development Method
Name Genome-wide significant variants
Parameters p<5e-8, variants in the LPA gene region
Variants
Original Genome Build hg19
Number of Variants 43
Effect Weight Type beta
PGS Source
PGS Catalog Publication (PGP) ID PGP000127
Citation (link to publication) Trinder M et al. JAMA Cardiol (2020)
Ancestry Distribution
Source of Variant
Associations (GWAS)
European: 100%
48,333 individuals (100%)
PGS Evaluation
European: 73.3%
African: 13.3%
East Asian: 6.7%
South Asian: 6.7%
15 Sample Sets

Development Samples

Source of Variant Associations (GWAS)
Study Identifiers Sample Numbers Sample Ancestry Cohort(s)
Europe PMC: 29926099
[
  • 20,793 cases
  • , 27,540 controls
]
 European CCHS, CGPS, CIHDS, EPIC, WOSCOPS

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
PPM001390 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) —
PPM001394 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 —
PPM001391 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) —
PPM001378 PSS000613|
African Ancestry|
6,521 individuals
 PGP000127 |
Trinder M et al. JAMA Cardiol (2020)
 Reported Trait: Measured levels of lipoprotein(a) — — R²: 0.038
Pearson correlation coefficient: 0.07		 Age, sex, assessment center, genotyping batch, PCs (1-5) of ancestry —
PPM001379 PSS000614|
East Asian Ancestry|
2,774 individuals
 PGP000127 |
Trinder M et al. JAMA Cardiol (2020)
 Reported Trait: Measured levels of lipoprotein(a) — — R²: 0.078
Pearson correlation coefficient: 0.281		 Age, sex, assessment center, genotyping batch, PCs (1-5) of ancestry —
PPM001380 PSS000615|
European Ancestry|
350,903 individuals
 PGP000127 |
Trinder M et al. JAMA Cardiol (2020)
 Reported Trait: Measured levels of lipoprotein(a) — — R²: 0.595
Pearson correlation coefficient: 0.717		 Age, sex, assessment center, genotyping batch, PCs (1-5) of ancestry —
PPM001381 PSS000616|
South Asian Ancestry|
6,203 individuals
 PGP000127 |
Trinder M et al. JAMA Cardiol (2020)
 Reported Trait: Measured levels of lipoprotein(a) — — R²: 0.11
Pearson correlation coefficient: 0.371		 Age, sex, assessment center, genotyping batch, PCs (1-5) of ancestry —
PPM001382 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 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 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 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 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 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 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 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) —
PPM001392 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 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) —
PPM001395 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) —
PPM020250 PSS011311|
European Ancestry|
12,815 individuals
 PGP000530 |
Lacaze P et al. J Am Coll Cardiol (2022)
|Ext.		 Reported Trait: Incidence of major adverse cardiovascular events HR: 1.14 [1.05, 1.24] — — — —
PPM020251 PSS011311|
European Ancestry|
12,815 individuals
 PGP000530 |
Lacaze P et al. J Am Coll Cardiol (2022)
|Ext.		 Reported Trait: Incidence of major adverse cardiovascular events (in placebo arm) — — Hazard ratio (HR, high vs low tertile): 1.7 [1.14, 2.55] — —
PPM020886 PSS011442|
European Ancestry|
564 individuals
 PGP000599 |
Guarischi-Sousa R et al. Circ Genom Precis Med (2023)
|Ext.		 Reported Trait: Raised coronary lesion OR: 1.11 [0.9, 1.38] — — — —
PPM020898 PSS011441|
African Ancestry|
504 individuals
 PGP000599 |
Guarischi-Sousa R et al. Circ Genom Precis Med (2023)
|Ext.		 Reported Trait: Raised coronary lesion OR: 0.99 [0.8, 1.24] — — — —

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
PSS011311 — — 12,815 individuals,
45.1 % Male samples
 Median = 75.1 years European — ASPREE —
PSS011441 — —
[
  • 165 cases
  • , 339 controls
]
,
82.0 % Male samples
 Mean = 27.5 years African unspecified — PDAY —
PSS011442 — —
[
  • 181 cases
  • , 383 controls
]
,
77.0 % Male samples
 Mean = 26.7 years European — PDAY —
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 —