| Experimental Factor Ontology (EFO) Information | |
| Identifier | EFO_0006925 |
| Description | quantification of some lipoprotein A in a sample | Trait category |
Lipid or lipoprotein measurement
|
| Synonym | Lp(a) measurement |
| 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) |
|---|---|---|---|---|---|---|
| PGS000313 (GRS49_Lp(a)) |
PGP000092 | Xie T et al. Circ Genom Precis Med (2020) |
Lipoprotein A | lipoprotein A measurement | 49 | - |
https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS000313/ScoringFiles/PGS000313.txt.gz |
| 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 |
| PGS000689 (snpnet.Lipoprotein_A) |
PGP000128 | Sinnott-Armstrong N et al. Nat Genet (2021) |
Lipoprotein A [nmol/L] | lipoprotein A measurement | 8,308 | - |
https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS000689/ScoringFiles/PGS000689.txt.gz |
| PGS000752 (PGS_Lpa) |
PGP000157 | Dron JS et al. Circ Genom Precis Med (2021) |
Lipoprotein A concentration [nmol/L] | lipoprotein A measurement | 11,446 | https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS000752/ScoringFiles/PGS000752.txt.gz | |
| PGS001963 (portability-PLR_log_lipoA) |
PGP000263 | Privé F et al. Am J Hum Genet (2022) |
Lipoprotein A | lipoprotein A measurement | 7,887 | - |
https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS001963/ScoringFiles/PGS001963.txt.gz |
| PGS002181 (portability-ldpred2_log_lipoA) |
PGP000263 | Privé F et al. Am J Hum Genet (2022) |
Lipoprotein A | lipoprotein A measurement | 31,355 | - |
https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS002181/ScoringFiles/PGS002181.txt.gz |
| PGS002297 (GRS48_lpa) |
PGP000327 | Coassin S et al. Circ Genom Precis Med (2022) |
Lipoprotein A levels | lipoprotein A measurement | 48 | - |
https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS002297/ScoringFiles/PGS002297.txt.gz |
| PGS003542 (cont-decay-log_lipoA) |
PGP000457 | Ding Y et al. bioRxiv (2022) |Pre |
Lipoprotein A | lipoprotein A measurement | 979,739 | - |
https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS003542/ScoringFiles/PGS003542.txt.gz |
| PGS004201 (lpa_1) |
PGP000520 | Raben TG et al. Sci Rep (2023) |
Lipoprotein A | lipoprotein A measurement | 8,725 | - - |
https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS004201/ScoringFiles/PGS004201.txt.gz |
| PGS004202 (lpa_2) |
PGP000520 | Raben TG et al. Sci Rep (2023) |
Lipoprotein A | lipoprotein A measurement | 8,714 | - |
https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS004202/ScoringFiles/PGS004202.txt.gz |
| PGS004203 (lpa_3) |
PGP000520 | Raben TG et al. Sci Rep (2023) |
Lipoprotein A | lipoprotein A measurement | 6,935 | - |
https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS004203/ScoringFiles/PGS004203.txt.gz |
| PGS004204 (lpa_4) |
PGP000520 | Raben TG et al. Sci Rep (2023) |
Lipoprotein A | lipoprotein A measurement | 6,927 | - |
https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS004204/ScoringFiles/PGS004204.txt.gz |
| PGS004205 (lpa_5) |
PGP000520 | Raben TG et al. Sci Rep (2023) |
Lipoprotein A | lipoprotein A measurement | 8,737 | - |
https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS004205/ScoringFiles/PGS004205.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 |
|---|---|---|---|---|---|---|---|---|---|
| PPM000783 | PGS000313 (GRS49_Lp(a)) |
PSS000376| European Ancestry| 1,354 individuals |
PGP000092 | Xie T et al. Circ Genom Precis Med (2020) |
Reported Trait: Lipoprotein(a) (mg/l) | — | — | R²: 0.3959 | Sex, age, age^2 | — |
| 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) | — |
| PPM020250 | PGS000667 (LPA_GRS43) |
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 | PGS000667 (LPA_GRS43) |
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 | PGS000667 (LPA_GRS43) |
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 | PGS000667 (LPA_GRS43) |
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] | — | — | — | — |
| PPM001417 | PGS000689 (snpnet.Lipoprotein_A) |
PSS000719| African Ancestry| 5,018 individuals |
PGP000128 | Sinnott-Armstrong N et al. Nat Genet (2021) |
Reported Trait: Lipoprotein A [nmol/L] | — | — | R²: 0.00769 Spearman's ρ: 0.058 |
Age, sex, PCs(1-40) | — |
| PPM001452 | PGS000689 (snpnet.Lipoprotein_A) |
PSS000720| East Asian Ancestry| 980 individuals |
PGP000128 | Sinnott-Armstrong N et al. Nat Genet (2021) |
Reported Trait: Lipoprotein A [nmol/L] | — | — | R²: 0.06202 Spearman's ρ: 0.164 |
Age, sex, PCs(1-40) | — |
| PPM001487 | PGS000689 (snpnet.Lipoprotein_A) |
PSS000721| European Ancestry| 19,003 individuals |
PGP000128 | Sinnott-Armstrong N et al. Nat Genet (2021) |
Reported Trait: Lipoprotein A [nmol/L] | — | — | R²: 0.48522 Spearman's ρ: 0.663 |
Age, sex, PCs(1-40) | — |
| PPM001522 | PGS000689 (snpnet.Lipoprotein_A) |
PSS000722| South Asian Ancestry| 6,453 individuals |
PGP000128 | Sinnott-Armstrong N et al. Nat Genet (2021) |
Reported Trait: Lipoprotein A [nmol/L] | — | — | R²: 0.16668 Spearman's ρ: 0.375 |
Age, sex, PCs(1-40) | — |
| PPM001557 | PGS000689 (snpnet.Lipoprotein_A) |
PSS000723| European Ancestry| 50,709 individuals |
PGP000128 | Sinnott-Armstrong N et al. Nat Genet (2021) |
Reported Trait: Lipoprotein A [nmol/L] | — | — | R²: 0.51648 Spearman's ρ: 0.692 |
Age, sex, PCs(1-40) | — |
| PPM007370 | PGS000689 (snpnet.Lipoprotein_A) |
PSS007176| African Ancestry| 5,086 individuals |
PGP000244 | Tanigawa Y et al. PLoS Genet (2022) |Ext. |
Reported Trait: Lipoprotein A | — | — | R²: 0.0174 [0.0111, 0.0237] Incremental R2 (full-covars): 0.00171 PGS R2 (no covariates): 0.00657 [0.00266, 0.01049] |
age, sex, UKB array type, Genotype PCs | — |
| PPM007371 | PGS000689 (snpnet.Lipoprotein_A) |
PSS007177| East Asian Ancestry| 1,452 individuals |
PGP000244 | Tanigawa Y et al. PLoS Genet (2022) |Ext. |
Reported Trait: Lipoprotein A | — | — | R²: 0.01457 [0.0033, 0.02585] Incremental R2 (full-covars): 0.00715 PGS R2 (no covariates): 0.05715 [0.03579, 0.07851] |
age, sex, UKB array type, Genotype PCs | — |
| PPM007372 | PGS000689 (snpnet.Lipoprotein_A) |
PSS007178| European Ancestry| 19,197 individuals |
PGP000244 | Tanigawa Y et al. PLoS Genet (2022) |Ext. |
Reported Trait: Lipoprotein A | — | — | R²: 0.04874 [0.04353, 0.05396] Incremental R2 (full-covars): 0.04393 PGS R2 (no covariates): 0.49585 [0.48704, 0.50467] |
age, sex, UKB array type, Genotype PCs | — |
| PPM007373 | PGS000689 (snpnet.Lipoprotein_A) |
PSS007179| South Asian Ancestry| 6,542 individuals |
PGP000244 | Tanigawa Y et al. PLoS Genet (2022) |Ext. |
Reported Trait: Lipoprotein A | — | — | R²: 0.02102 [0.01474, 0.02731] Incremental R2 (full-covars): 0.01343 PGS R2 (no covariates): 0.13628 [0.12216, 0.1504] |
age, sex, UKB array type, Genotype PCs | — |
| PPM007374 | PGS000689 (snpnet.Lipoprotein_A) |
PSS007180| European Ancestry| 51,385 individuals |
PGP000244 | Tanigawa Y et al. PLoS Genet (2022) |Ext. |
Reported Trait: Lipoprotein A | — | — | R²: 0.17636 [0.17114, 0.18158] Incremental R2 (full-covars): 0.17582 PGS R2 (no covariates): 0.53443 [0.5293, 0.53957] |
age, sex, UKB array type, Genotype PCs | — |
| PPM001911 | PGS000752 (PGS_Lpa) |
PSS000954| European Ancestry| 43,071 individuals |
PGP000157 | Dron JS et al. Circ Genom Precis Med (2021) |
Reported Trait: Lipoprotein(a) concentration [nmol/L] | — | — | Pearson correlation coefficient (r): 0.5 | — | — |
| PPM010579 | PGS001963 (portability-PLR_log_lipoA) |
PSS009452| European Ancestry| 15,154 individuals |
PGP000263 | Privé F et al. Am J Hum Genet (2022) |
Reported Trait: Lipoprotein A | — | — | Partial Correlation (partial-r): 0.6002 [0.5899, 0.6103] | sex, age, birth date, deprivation index, 16 PCs | — |
| PPM010580 | PGS001963 (portability-PLR_log_lipoA) |
PSS009226| European Ancestry| 3,133 individuals |
PGP000263 | Privé F et al. Am J Hum Genet (2022) |
Reported Trait: Lipoprotein A | — | — | Partial Correlation (partial-r): 0.5621 [0.5376, 0.5856] | sex, age, birth date, deprivation index, 16 PCs | — |
| PPM010581 | PGS001963 (portability-PLR_log_lipoA) |
PSS008780| European Ancestry| 5,176 individuals |
PGP000263 | Privé F et al. Am J Hum Genet (2022) |
Reported Trait: Lipoprotein A | — | — | Partial Correlation (partial-r): 0.4772 [0.4558, 0.498] | sex, age, birth date, deprivation index, 16 PCs | — |
| PPM010582 | PGS001963 (portability-PLR_log_lipoA) |
PSS008554| Greater Middle Eastern Ancestry| 925 individuals |
PGP000263 | Privé F et al. Am J Hum Genet (2022) |
Reported Trait: Lipoprotein A | — | — | Partial Correlation (partial-r): 0.2941 [0.2334, 0.3525] | sex, age, birth date, deprivation index, 16 PCs | — |
| PPM010583 | PGS001963 (portability-PLR_log_lipoA) |
PSS008332| South Asian Ancestry| 5,230 individuals |
PGP000263 | Privé F et al. Am J Hum Genet (2022) |
Reported Trait: Lipoprotein A | — | — | Partial Correlation (partial-r): 0.3014 [0.2766, 0.3259] | sex, age, birth date, deprivation index, 16 PCs | — |
| PPM010584 | PGS001963 (portability-PLR_log_lipoA) |
PSS008109| East Asian Ancestry| 1,541 individuals |
PGP000263 | Privé F et al. Am J Hum Genet (2022) |
Reported Trait: Lipoprotein A | — | — | Partial Correlation (partial-r): 0.1975 [0.1487, 0.2453] | sex, age, birth date, deprivation index, 16 PCs | — |
| PPM010585 | PGS001963 (portability-PLR_log_lipoA) |
PSS007896| African Ancestry| 1,926 individuals |
PGP000263 | Privé F et al. Am J Hum Genet (2022) |
Reported Trait: Lipoprotein A | — | — | Partial Correlation (partial-r): 0.1097 [0.0651, 0.1539] | sex, age, birth date, deprivation index, 16 PCs | — |
| PPM010586 | PGS001963 (portability-PLR_log_lipoA) |
PSS009000| African Ancestry| 3,050 individuals |
PGP000263 | Privé F et al. Am J Hum Genet (2022) |
Reported Trait: Lipoprotein A | — | — | Partial Correlation (partial-r): 0.0348 | sex, age, birth date, deprivation index, 16 PCs | — |
| PPM012295 | PGS002181 (portability-ldpred2_log_lipoA) |
PSS009452| European Ancestry| 15,154 individuals |
PGP000263 | Privé F et al. Am J Hum Genet (2022) |
Reported Trait: Lipoprotein A | — | — | Partial Correlation (partial-r): 0.5799 [0.5692, 0.5903] | sex, age, birth date, deprivation index, 16 PCs | — |
| PPM012296 | PGS002181 (portability-ldpred2_log_lipoA) |
PSS009226| European Ancestry| 3,133 individuals |
PGP000263 | Privé F et al. Am J Hum Genet (2022) |
Reported Trait: Lipoprotein A | — | — | Partial Correlation (partial-r): 0.5522 [0.5273, 0.5761] | sex, age, birth date, deprivation index, 16 PCs | — |
| PPM012297 | PGS002181 (portability-ldpred2_log_lipoA) |
PSS008780| European Ancestry| 5,176 individuals |
PGP000263 | Privé F et al. Am J Hum Genet (2022) |
Reported Trait: Lipoprotein A | — | — | Partial Correlation (partial-r): 0.4499 [0.4278, 0.4714] | sex, age, birth date, deprivation index, 16 PCs | — |
| PPM012298 | PGS002181 (portability-ldpred2_log_lipoA) |
PSS008554| Greater Middle Eastern Ancestry| 925 individuals |
PGP000263 | Privé F et al. Am J Hum Genet (2022) |
Reported Trait: Lipoprotein A | — | — | Partial Correlation (partial-r): 0.2534 [0.1913, 0.3133] | sex, age, birth date, deprivation index, 16 PCs | — |
| PPM012299 | PGS002181 (portability-ldpred2_log_lipoA) |
PSS008332| South Asian Ancestry| 5,230 individuals |
PGP000263 | Privé F et al. Am J Hum Genet (2022) |
Reported Trait: Lipoprotein A | — | — | Partial Correlation (partial-r): 0.2953 [0.2703, 0.3199] | sex, age, birth date, deprivation index, 16 PCs | — |
| PPM012301 | PGS002181 (portability-ldpred2_log_lipoA) |
PSS007896| African Ancestry| 1,926 individuals |
PGP000263 | Privé F et al. Am J Hum Genet (2022) |
Reported Trait: Lipoprotein A | — | — | Partial Correlation (partial-r): 0.0348 [-0.0101, 0.0796] | sex, age, birth date, deprivation index, 16 PCs | — |
| PPM012302 | PGS002181 (portability-ldpred2_log_lipoA) |
PSS009000| African Ancestry| 3,050 individuals |
PGP000263 | Privé F et al. Am J Hum Genet (2022) |
Reported Trait: Lipoprotein A | — | — | Partial Correlation (partial-r): 0.0087 [-0.0269, 0.0443] | sex, age, birth date, deprivation index, 16 PCs | — |
| PPM012300 | PGS002181 (portability-ldpred2_log_lipoA) |
PSS008109| East Asian Ancestry| 1,541 individuals |
PGP000263 | Privé F et al. Am J Hum Genet (2022) |
Reported Trait: Lipoprotein A | — | — | Partial Correlation (partial-r): 0.1432 [0.0936, 0.192] | sex, age, birth date, deprivation index, 16 PCs | — |
| PPM013026 | PGS002297 (GRS48_lpa) |
PSS009655| Ancestry Not Reported| 22 individuals |
PGP000327 | Coassin S et al. Circ Genom Precis Med (2022) |
Reported Trait: Lipoprotein (a) levels | — | — | R²: 0.53 | — | — |
| PPM017470 | PGS003542 (cont-decay-log_lipoA) |
PSS010907| European Ancestry| 15,302 individuals |
PGP000457 | Ding Y et al. bioRxiv (2022) |Pre |
Reported Trait: Lipoprotein A | — | — | partial-R2: 0.34 | sex, age, deprivation index, PC1-16 | — |
| PPM017554 | PGS003542 (cont-decay-log_lipoA) |
PSS010823| European Ancestry| 3,124 individuals |
PGP000457 | Ding Y et al. bioRxiv (2022) |Pre |
Reported Trait: Lipoprotein A | — | — | partial-R2: 0.29 | sex, age, deprivation index, PC1-16 | — |
| PPM017638 | PGS003542 (cont-decay-log_lipoA) |
PSS010655| European Ancestry| 5,045 individuals |
PGP000457 | Ding Y et al. bioRxiv (2022) |Pre |
Reported Trait: Lipoprotein A | — | — | partial-R2: 0.2 | sex, age, deprivation index, PC1-16 | — |
| PPM017722 | PGS003542 (cont-decay-log_lipoA) |
PSS010571| Greater Middle Eastern Ancestry| 899 individuals |
PGP000457 | Ding Y et al. bioRxiv (2022) |Pre |
Reported Trait: Lipoprotein A | — | — | partial-R2: 0.07 | sex, age, deprivation index, PC1-16 | — |
| PPM017806 | PGS003542 (cont-decay-log_lipoA) |
PSS010235| European Ancestry| 1,954 individuals |
PGP000457 | Ding Y et al. bioRxiv (2022) |Pre |
Reported Trait: Lipoprotein A | — | — | partial-R2: 0.14 | sex, age, deprivation index, PC1-16 | — |
| PPM017890 | PGS003542 (cont-decay-log_lipoA) |
PSS010487| South Asian Ancestry| 5,181 individuals |
PGP000457 | Ding Y et al. bioRxiv (2022) |Pre |
Reported Trait: Lipoprotein A | — | — | partial-R2: 0.09 | sex, age, deprivation index, PC1-16 | — |
| PPM017974 | PGS003542 (cont-decay-log_lipoA) |
PSS010403| East Asian Ancestry| 1,532 individuals |
PGP000457 | Ding Y et al. bioRxiv (2022) |Pre |
Reported Trait: Lipoprotein A | — | — | partial-R2: 0.02 | sex, age, deprivation index, PC1-16 | — |
| PPM018058 | PGS003542 (cont-decay-log_lipoA) |
PSS010319| African Ancestry| 1,916 individuals |
PGP000457 | Ding Y et al. bioRxiv (2022) |Pre |
Reported Trait: Lipoprotein A | — | — | partial-R2: 0.0 | sex, age, deprivation index, PC1-16 | — |
| PPM018142 | PGS003542 (cont-decay-log_lipoA) |
PSS010739| African Ancestry| 3,027 individuals |
PGP000457 | Ding Y et al. bioRxiv (2022) |Pre |
Reported Trait: Lipoprotein A | — | — | partial-R2: 0.0 | sex, age, deprivation index, PC1-16 | — |
| PPM020135 | PGS004202 (lpa_2) |
PSS011296| European Ancestry| 45,334 individuals |
PGP000520 | Raben TG et al. Sci Rep (2023) |
Reported Trait: Lipoprotein A | — | — | R²: 0.577 | year of birth, sex | — |
| PPM020136 | PGS004203 (lpa_3) |
PSS011296| European Ancestry| 45,334 individuals |
PGP000520 | Raben TG et al. Sci Rep (2023) |
Reported Trait: Lipoprotein A | — | — | R²: 0.577 | year of birth, sex | — |
| PPM020137 | PGS004204 (lpa_4) |
PSS011296| European Ancestry| 45,334 individuals |
PGP000520 | Raben TG et al. Sci Rep (2023) |
Reported Trait: Lipoprotein A | — | — | R²: 0.577 | year of birth, sex | — |
| PPM020138 | PGS004205 (lpa_5) |
PSS011296| European Ancestry| 45,334 individuals |
PGP000520 | Raben TG et al. Sci Rep (2023) |
Reported Trait: Lipoprotein A | — | — | R²: 0.576 | year of birth, sex | — |
|
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 |
|---|---|---|---|---|---|---|---|---|
| PSS010655 | — | — | 5,045 individuals, 44.0 % Male samples |
Mean = 54.4 years Sd = 8.4 years |
European | Italian | UKB | — |
| PSS010403 | — | — | 1,532 individuals, 33.0 % Male samples |
Mean = 52.5 years Sd = 7.8 years |
East Asian | Chinese | UKB | — |
| PSS008780 | — | — | 5,176 individuals | — | European | Italy (South Europe) | UKB | — |
| PSS007896 | — | — | 1,926 individuals | — | African American or Afro-Caribbean | Carribean | UKB | — |
| PSS000954 | — | — | 43,071 individuals | — | European | — | UKB | — |
| PSS011441 | — | — | [ ,
82.0 % Male samples |
Mean = 27.5 years | African unspecified | — | PDAY | — |
| PSS011442 | — | — | [ ,
77.0 % Male samples |
Mean = 26.7 years | European | — | PDAY | — |
| PSS008554 | — | — | 925 individuals | — | Greater Middle Eastern (Middle Eastern, North African or Persian) | Iran (Middle East) | UKB | — |
| PSS011296 | 22,667 sibling pairs | — | 45,334 individuals | — | European | — | UKB | — |
| PSS000719 | — | — | 5,018 individuals | — | African unspecified | — | UKB | — |
| PSS000720 | — | — | 980 individuals | — | East Asian | — | UKB | — |
| PSS000721 | — | — | 19,003 individuals | — | European | Non-British White | UKB | — |
| PSS000722 | — | — | 6,453 individuals | — | South Asian | — | UKB | — |
| PSS000723 | — | — | 50,709 individuals | — | European (British) |
— | UKB | — |
| PSS009452 | — | — | 15,154 individuals | — | European | UK (+ Ireland) | UKB | — |
| PSS008109 | — | — | 1,541 individuals | — | East Asian | China (East Asia) | UKB | — |
| PSS010823 | — | — | 3,124 individuals, 38.0 % Male samples |
Mean = 54.4 years Sd = 7.5 years |
European | Polish | UKB | — |
| PSS010571 | — | — | 899 individuals, 60.0 % Male samples |
Mean = 51.7 years Sd = 7.9 years |
Greater Middle Eastern (Middle Eastern, North African or Persian) | Iranian | UKB | — |
| PSS010319 | — | — | 1,916 individuals, 38.0 % Male samples |
Mean = 52.4 years Sd = 8.1 years |
African American or Afro-Caribbean | Caribbean | UKB | — |
| PSS000376 | We measured weight and height using regularly calibrated equipment (scales and stadiometer models 770 and 214, respectively; Seca, Hamburg, Germany). Body mass index (BMI; in kg/m2) was also calculated. We measured waist circumference at the midpoint between the lower costal margin and the iliac crest. The hip circumference was measured over both trochanter majores (tangible bone on the outside of the hip joint). Waist to hip ratio was also calculated. We performed all measurements in duplicate, and, if the difference between these measurements exceeded a predefined value, a third measurement was performed. All available measurements were used to calculate means. Heart rate, systolic (SBP) and diastolic (DBP) blood pressure were measured in duplicate with a Dinamap Critikon 1846SX (Critikon Inc, Tampa, FL), from which we calculated means. At the third visit, fasting blood sample of participants were drawn for the measurement of glucose (Roche Diagnostics, Basel, Switzerland), insulin (Diagnostic Systems Laboratories Inc, Webster, TX), HbA1c (high performance liquid chromatography, Variant, Bio-Rad), triglycerides, total cholesterol, HDL cholesterol (Roche Diagnostics) and LDL cholesterol (calculated according to Friedewald’s equation5), as well as alanine transaminase (Photometric determination according to the reference method of the International Federation of Clinical Chemistry (IFCC)6) and lipoprotein(a) (Nephelometric method, BN2, DadeBehring). Serum creatinine was measured by photometric determination with the Jaffé method without deproteinisation (Ecoline® MEGA, DiaSys Diagnostic Systems GmbH. Merck). eGFR for adolescents who were younger than 18 years old was calculated using the Schwartz formula.7 High‐sensitivity C‐reactive protein (hsCRP) was determined using an immunonephelometric method, BN2 (CardioPhase hsCRP, Siemens) with a lower detection limit of 0.175 mg/L. Total IgE measurements were performed using the Phadia Immunocap 100 system with fluoroenzyme immunoassay (FEIA). | — | 1,354 individuals, 47.56 % Male samples |
Mean = 16.22 years Sd = 0.66 years |
European | — | TRAILS | — |
| PSS009226 | — | — | 3,133 individuals | — | European | Poland (NE Europe) | UKB | — |
| PSS008332 | — | — | 5,230 individuals | — | South Asian | India (South Asia) | UKB | — |
| PSS007176 | — | — | 5,086 individuals | — | African unspecified | — | UKB | — |
| PSS007177 | — | — | 1,452 individuals | — | East Asian | — | UKB | — |
| PSS007178 | — | — | 19,197 individuals | — | European | non-white British ancestry | UKB | — |
| PSS007179 | — | — | 6,542 individuals | — | South Asian | — | UKB | — |
| PSS007180 | — | — | 51,385 individuals | — | European | white British ancestry | UKB | Testing cohort (heldout set) |
| PSS010739 | — | — | 3,027 individuals, 48.0 % Male samples |
Mean = 51.8 years Sd = 8.1 years |
African unspecified | Nigerian | UKB | — |
| PSS009655 | — | — | 22 individuals, 50.0 % Male samples |
— | Not reported | — | NR | — |
| PSS010487 | — | — | 5,181 individuals, 55.0 % Male samples |
Mean = 53.3 years Sd = 8.4 years |
South Asian | Indian | UKB | — |
| PSS010235 | — | — | 1,954 individuals, 46.0 % Male samples |
Mean = 58.0 years Sd = 7.1 years |
European | Ashkenazi | UKB | — |
| PSS011311 | — | — | 12,815 individuals, 45.1 % Male samples |
Median = 75.1 years | European | — | ASPREE | — |
| PSS009000 | — | — | 3,050 individuals | — | African unspecified | Nigeria (West Africa) | UKB | — |
| 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 | — |
| PSS010907 | — | — | 15,302 individuals, 46.0 % Male samples |
Mean = 56.8 years Sd = 7.9 years |
European | white British | UKB | — |