| 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. |
| 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) |
|---|---|---|---|---|---|---|
| PGS000667 (LPA_GRS43) |
PGP000127 | Trinder M et al. JAMA Cardiol (2020) |
Lipoprotein A | lipoprotein A measurement | 43 | - |
https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS000667/ScoringFiles/PGS000667.txt.gz |
|
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 |
|---|---|---|---|---|---|---|---|---|---|
| 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) | — |
| 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 | — |
| 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) | — |
| 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) | — | — | R²: 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) | — | — | R²: 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) | — | — | R²: 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) | — | — | R²: 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) | — |
| 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) | — |
| 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) | — |
|
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 | [
|
— | 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 | [
|
— | 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 | [
|
— | 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 | [
|
— | 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 | [
|
— | 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 | [
|
— | 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 | [
|
— | 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 | [
|
— | 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 | — |