| Experimental Factor Ontology (EFO) Information | |
| Identifier | EFO_0004612 |
| Description | The measurement of HDL cholesterol in blood used as a risk indicator for heart disease. | Trait category |
Lipid or lipoprotein measurement
|
| Synonym | HDL measurement |
| Mapped terms |
3 mapped terms
|
| Polygenic Score ID & Name | PGS Publication ID (PGP) | Reported Trait | Mapped Trait(s) (Ontology) | Number of Variants | Ancestry distribution | Scoring File (FTP Link) |
|---|---|---|---|---|---|---|
| PGS000060 (GRS_HDL) |
PGP000045 | Johnson L et al. PLoS One (2015) |
high-density lipoprotein (HDL) cholesterol | high density lipoprotein cholesterol measurement | 46 | - |
https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS000060/ScoringFiles/PGS000060.txt.gz |
| PGS000064 (GLGC2017_HDL) |
PGP000046 | Kuchenbaecker K et al. Nat Commun (2019) |
High density lipoprotein (HDL) cholesterol | high density lipoprotein cholesterol measurement | 120 | - |
https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS000064/ScoringFiles/PGS000064.txt.gz |
| PGS000192 (GS9) |
PGP000079 | Kathiresan S et al. N Engl J Med (2008) |
Cholesterol | low density lipoprotein cholesterol measurement, high density lipoprotein cholesterol measurement |
9 | - |
https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS000192/ScoringFiles/PGS000192.txt.gz |
| PGS000309 (GRS247_HDL) |
PGP000092 | Xie T et al. Circ Genom Precis Med (2020) |
High-density lipoprotein | high density lipoprotein cholesterol measurement | 247 | - |
https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS000309/ScoringFiles/PGS000309.txt.gz |
| PGS000660 (PRS-HDL) |
PGP000121 | Tam CHT et al. Genome Med (2021) |
HDL cholesterol | high density lipoprotein cholesterol measurement | 549 | https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS000660/ScoringFiles/PGS000660.txt.gz | |
| PGS000686 (snpnet.HDL_cholesterol) |
PGP000128 | Sinnott-Armstrong N et al. Nat Genet (2021) |
HDL cholesterol [mmol/L] | high density lipoprotein cholesterol measurement | 25,069 | - |
https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS000686/ScoringFiles/PGS000686.txt.gz |
| PGS000825 (HDL-C_PGS) |
PGP000210 | Zubair N et al. Sci Rep (2019) |
High-density lipoprotein cholesterol | high density lipoprotein cholesterol measurement | 883 | - |
https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS000825/ScoringFiles/PGS000825.txt.gz |
| PGS000845 (HDL) |
PGP000211 | Aly DM et al. Nat Genet (2021) |
High density lipoprotein (HDL) | high density lipoprotein cholesterol measurement | 303 | - |
https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS000845/ScoringFiles/PGS000845.txt.gz |
| PGS001954 (portability-PLR_log_HDL) |
PGP000263 | Privé F et al. Am J Hum Genet (2022) |
HDL cholesterol | high density lipoprotein cholesterol measurement | 85,429 | - |
https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS001954/ScoringFiles/PGS001954.txt.gz |
| PGS002172 (portability-ldpred2_log_HDL) |
PGP000263 | Privé F et al. Am J Hum Genet (2022) |
HDL cholesterol | high density lipoprotein cholesterol measurement | 732,902 | - |
https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS002172/ScoringFiles/PGS002172.txt.gz |
| PGS002284 (GRS_286_HDL) |
PGP000313 | Kamiza AB et al. Nat Med (2022) |
High density lipoprotein cholesterol | high density lipoprotein cholesterol measurement | 286 | https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS002284/ScoringFiles/PGS002284.txt.gz | |
| PGS002329 (biochemistry_HDLcholesterol.BOLT-LMM) |
PGP000332 | Weissbrod O et al. Nat Genet (2022) |
HDL Cholesterol | high density lipoprotein cholesterol measurement | 1,109,311 | - |
https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS002329/ScoringFiles/PGS002329.txt.gz |
| PGS002366 (biochemistry_HDLcholesterol.BOLT-LMM-BBJ) |
PGP000332 | Weissbrod O et al. Nat Genet (2022) |
HDL Cholesterol | high density lipoprotein cholesterol measurement | 920,924 | - |
https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS002366/ScoringFiles/PGS002366.txt.gz |
| PGS002401 (biochemistry_HDLcholesterol.P+T.0.0001) |
PGP000332 | Weissbrod O et al. Nat Genet (2022) |
HDL Cholesterol | high density lipoprotein cholesterol measurement | 15,141 | - |
https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS002401/ScoringFiles/PGS002401.txt.gz |
| PGS002450 (biochemistry_HDLcholesterol.P+T.0.001) |
PGP000332 | Weissbrod O et al. Nat Genet (2022) |
HDL Cholesterol | high density lipoprotein cholesterol measurement | 35,979 | - |
https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS002450/ScoringFiles/PGS002450.txt.gz |
| PGS002499 (biochemistry_HDLcholesterol.P+T.0.01) |
PGP000332 | Weissbrod O et al. Nat Genet (2022) |
HDL Cholesterol | high density lipoprotein cholesterol measurement | 141,710 | - |
https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS002499/ScoringFiles/PGS002499.txt.gz |
| PGS002548 (biochemistry_HDLcholesterol.P+T.1e-06) |
PGP000332 | Weissbrod O et al. Nat Genet (2022) |
HDL Cholesterol | high density lipoprotein cholesterol measurement | 6,518 | - |
https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS002548/ScoringFiles/PGS002548.txt.gz |
| PGS002597 (biochemistry_HDLcholesterol.P+T.5e-08) |
PGP000332 | Weissbrod O et al. Nat Genet (2022) |
HDL Cholesterol | high density lipoprotein cholesterol measurement | 4,738 | - |
https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS002597/ScoringFiles/PGS002597.txt.gz |
| PGS002646 (biochemistry_HDLcholesterol.PolyFun-pred) |
PGP000332 | Weissbrod O et al. Nat Genet (2022) |
HDL Cholesterol | high density lipoprotein cholesterol measurement | 402,183 | - |
https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS002646/ScoringFiles/PGS002646.txt.gz |
| PGS002695 (biochemistry_HDLcholesterol.SBayesR) |
PGP000332 | Weissbrod O et al. Nat Genet (2022) |
HDL Cholesterol | high density lipoprotein cholesterol measurement | 971,682 | - |
https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS002695/ScoringFiles/PGS002695.txt.gz |
| PGS002781 (GLGC_2021_ALL_HDL_PRS_weights_PRS-CS) |
PGP000366 | Kanoni S et al. medRxiv (2021) |Pre |
HDL Cholesterol | high density lipoprotein cholesterol measurement | 1,239,184 | - |
https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS002781/ScoringFiles/PGS002781.txt.gz |
| PGS002954 (ExPRSweb_HDL_30760-irnt_LASSOSUM_MGI_20211120) |
PGP000393 | Ma Y et al. Am J Hum Genet (2022) |
HDL | high density lipoprotein cholesterol measurement | 815,573 | https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS002954/ScoringFiles/PGS002954.txt.gz | |
| PGS002955 (ExPRSweb_HDL_30760-irnt_PT_MGI_20211120) |
PGP000393 | Ma Y et al. Am J Hum Genet (2022) |
HDL | high density lipoprotein cholesterol measurement | 16,393 | https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS002955/ScoringFiles/PGS002955.txt.gz | |
| PGS002956 (ExPRSweb_HDL_30760-irnt_PLINK_MGI_20211120) |
PGP000393 | Ma Y et al. Am J Hum Genet (2022) |
HDL | high density lipoprotein cholesterol measurement | 25,134 | https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS002956/ScoringFiles/PGS002956.txt.gz | |
| PGS002957 (ExPRSweb_HDL_30760-irnt_DBSLMM_MGI_20211120) |
PGP000393 | Ma Y et al. Am J Hum Genet (2022) |
HDL | high density lipoprotein cholesterol measurement | 7,449,065 | https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS002957/ScoringFiles/PGS002957.txt.gz | |
| PGS002958 (ExPRSweb_HDL_30760-irnt_PRSCS_MGI_20211120) |
PGP000393 | Ma Y et al. Am J Hum Genet (2022) |
HDL | high density lipoprotein cholesterol measurement | 1,113,830 | https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS002958/ScoringFiles/PGS002958.txt.gz | |
| PGS002959 (ExPRSweb_HDL_30760-raw_LASSOSUM_MGI_20211120) |
PGP000393 | Ma Y et al. Am J Hum Genet (2022) |
HDL | high density lipoprotein cholesterol measurement | 799,981 | https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS002959/ScoringFiles/PGS002959.txt.gz | |
| PGS002960 (ExPRSweb_HDL_30760-raw_PT_MGI_20211120) |
PGP000393 | Ma Y et al. Am J Hum Genet (2022) |
HDL | high density lipoprotein cholesterol measurement | 17,935 | https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS002960/ScoringFiles/PGS002960.txt.gz | |
| PGS002961 (ExPRSweb_HDL_30760-raw_PLINK_MGI_20211120) |
PGP000393 | Ma Y et al. Am J Hum Genet (2022) |
HDL | high density lipoprotein cholesterol measurement | 28,354 | https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS002961/ScoringFiles/PGS002961.txt.gz | |
| PGS002962 (ExPRSweb_HDL_30760-raw_DBSLMM_MGI_20211120) |
PGP000393 | Ma Y et al. Am J Hum Genet (2022) |
HDL | high density lipoprotein cholesterol measurement | 7,449,036 | https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS002962/ScoringFiles/PGS002962.txt.gz | |
| PGS002963 (ExPRSweb_HDL_30760-raw_PRSCS_MGI_20211120) |
PGP000393 | Ma Y et al. Am J Hum Genet (2022) |
HDL | high density lipoprotein cholesterol measurement | 1,113,830 | https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS002963/ScoringFiles/PGS002963.txt.gz | |
| PGS003338 (CVGRS_HDL) |
PGP000405 | Kim YJ et al. Nat Commun (2022) |
HDL cholesterol level | high density lipoprotein cholesterol measurement | 79 | - |
https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS003338/ScoringFiles/PGS003338.txt.gz |
| PGS003347 (ALLGRS_HDL) |
PGP000405 | Kim YJ et al. Nat Commun (2022) |
HDL cholesterol level | high density lipoprotein cholesterol measurement | 92 | - |
https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS003347/ScoringFiles/PGS003347.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 |
|---|---|---|---|---|---|---|---|---|---|
| PPM000151 | PGS000060 (GRS_HDL) |
PSS000098| European Ancestry| 2,063 individuals |
PGP000045 | Johnson L et al. PLoS One (2015) |
Reported Trait: Serum high-density lipoprotein (HDL) levels | β: 8.39 | — | Beta (p-value): 2.76e-06 | age, age^2, sex, GRS_LDL, GRS_TC, GRS_TG | Association (p-value; unadjusted for covariates) < 0.001 |
| PPM000152 | PGS000060 (GRS_HDL) |
PSS000097| East Asian Ancestry| 666 individuals |
PGP000045 | Johnson L et al. PLoS One (2015) |
Reported Trait: Serum high-density lipoprotein (HDL) levels | β: 15.58 | — | Beta (p-value): 2.17e-07 | age, age^2, sex, GRS_LDL, GRS_TC, GRS_TG | Association (p-value; unadjusted for covariates) < 0.001 |
| PPM000153 | PGS000060 (GRS_HDL) |
PSS000096| African Ancestry| 1,355 individuals |
PGP000045 | Johnson L et al. PLoS One (2015) |
Reported Trait: Serum high-density lipoprotein (HDL) levels | β: 7.99 | — | Beta (p-value): 0.00036 | age, age^2, sex, GRS_LDL, GRS_TC, GRS_TG | Association (p-value; unadjusted for covariates) < 0.001 |
| PPM000154 | PGS000060 (GRS_HDL) |
PSS000099| Hispanic or Latin American Ancestry| 1,256 individuals |
PGP000045 | Johnson L et al. PLoS One (2015) |
Reported Trait: Serum high-density lipoprotein (HDL) levels | β: 10.97 | — | Beta (p-value): 6.48e-10 | age, age^2, sex, GRS_LDL, GRS_TC, GRS_TG | Association (p-value; unadjusted for covariates) < 0.001 |
| PPM000167 | PGS000064 (GLGC2017_HDL) |
PSS000104| European Ancestry| 9,962 individuals |
PGP000046 | Kuchenbaecker K et al. Nat Commun (2019) |
Reported Trait: Serum high-density lipoprotein (HDL) levels | — | — | correlation (r): 0.285 [0.265, 0.305] | age, sex | Relatedness and population structure were accounted for using a linear mixed model with random polygenic effect implemented in GEMMA |
| PPM000170 | PGS000064 (GLGC2017_HDL) |
PSS000102| European Ancestry| 1,641 individuals |
PGP000046 | Kuchenbaecker K et al. Nat Commun (2019) |
Reported Trait: Serum high-density lipoprotein (HDL) levels | — | — | correlation (r): 0.279 [0.222, 0.336] | age, sex | Relatedness and population structure were accounted for using a linear mixed model with random polygenic effect implemented in GEMMA |
| PPM000173 | PGS000064 (GLGC2017_HDL) |
PSS000103| European Ancestry| 1,945 individuals |
PGP000046 | Kuchenbaecker K et al. Nat Commun (2019) |
Reported Trait: Serum high-density lipoprotein (HDL) levels | — | — | correlation (r): 0.268 [0.209, 0.327] | age, sex | Relatedness and population structure were accounted for using a linear mixed model with random polygenic effect implemented in GEMMA |
| PPM000176 | PGS000064 (GLGC2017_HDL) |
PSS000100| African Ancestry| 6,407 individuals |
PGP000046 | Kuchenbaecker K et al. Nat Commun (2019) |
Reported Trait: Serum high-density lipoprotein (HDL) levels | — | — | correlation (r): 0.121 [0.098, 0.145] | age, sex | Relatedness and population structure were accounted for using a linear mixed model with random polygenic effect implemented in GEMMA |
| PPM000179 | PGS000064 (GLGC2017_HDL) |
PSS000101| East Asian Ancestry| 21,295 individuals |
PGP000046 | Kuchenbaecker K et al. Nat Commun (2019) |
Reported Trait: Serum high-density lipoprotein (HDL) levels | — | — | correlation (r): 0.18 [0.145, 0.215] | age, sex, region, 20 PCs of genetic ancestry | Relatedness and population structure were accounted for using a linear mixed model with random polygenic effect implemented in GEMMA |
| PPM000563 | PGS000192 (GS9) |
PSS000292| European Ancestry| 4,232 individuals |
PGP000079 | Kathiresan S et al. N Engl J Med (2008) |
Reported Trait: Incident cardiovascular event | — | AUROC: 0.8 | Hazard Ratio (HR; per allele): 1.15 [1.07, 1.24] | age, sex, family history of MI, LDL cholesterol, HDL cholesterol, triglycerides, blood pressure, body mass index, diabetes status, smoking status, CRP, lipid lowering medication | — |
| PPM000562 | PGS000192 (GS9) |
PSS000292| European Ancestry| 4,232 individuals |
PGP000079 | Kathiresan S et al. N Engl J Med (2008) |
Reported Trait: High-density lipoprotein (HDL) levels | — | — | Association p-value: 2.00e-18 | — | — |
| PPM000561 | PGS000192 (GS9) |
PSS000292| European Ancestry| 4,232 individuals |
PGP000079 | Kathiresan S et al. N Engl J Med (2008) |
Reported Trait: Low-density lipoprotein (LDL) levels | — | — | Association p-value: 3.00e-24 | — | — |
| PPM000779 | PGS000309 (GRS247_HDL) |
PSS000376| European Ancestry| 1,354 individuals |
PGP000092 | Xie T et al. Circ Genom Precis Med (2020) |
Reported Trait: High-density lipoprotein (mmol/l) | — | — | R²: 0.1149 | Sex, age, age^2 | — |
| PPM001357 | PGS000660 (PRS-HDL) |
PSS000587| East Asian Ancestry| 426 individuals |
PGP000121 | Tam CHT et al. Genome Med (2021) |
Reported Trait: HDL cholesterol at baseline (log transformed) | β: 0.066 (0.012) | — | Pearson Correlation Coefficient (r): 0.272 Incremental R² (PRS and covariates vs. covariates-alone): 0.0558 |
age, sex, BMI, PCs | — |
| PPM001358 | PGS000660 (PRS-HDL) |
PSS000593| East Asian Ancestry| 4,917 individuals |
PGP000121 | Tam CHT et al. Genome Med (2021) |
Reported Trait: HDL cholesterol at baseline (log transformed) | β: 0.064 (0.004) | — | Pearson Correlation Coefficient (r): 0.222 Incremental R² (PRS and covariates vs. covariates-alone): 0.0524 |
age, sex, BMI, PCs | — |
| PPM001359 | PGS000660 (PRS-HDL) |
PSS000589| East Asian Ancestry| 1,941 individuals |
PGP000121 | Tam CHT et al. Genome Med (2021) |
Reported Trait: HDL cholesterol at baseline (log transformed) | β: 0.073 (0.006) | — | Pearson Correlation Coefficient (r): 0.239 Incremental R² (PRS and covariates vs. covariates-alone): 0.0606 |
age, sex, BMI, PCs | — |
| PPM001360 | PGS000660 (PRS-HDL) |
PSS000591| East Asian Ancestry| 865 individuals |
PGP000121 | Tam CHT et al. Genome Med (2021) |
Reported Trait: HDL cholesterol at baseline (log transformed) | β: 0.077 (0.008) | — | Pearson Correlation Coefficient (r): 0.267 Incremental R² (PRS and covariates vs. covariates-alone): 0.0827 |
age, sex, BMI, PCs | — |
| PPM001519 | PGS000686 (snpnet.HDL_cholesterol) |
PSS000702| South Asian Ancestry| 6,689 individuals |
PGP000128 | Sinnott-Armstrong N et al. Nat Genet (2021) |
Reported Trait: HDL cholesterol [mmol/L] | — | — | Spearman's ρ: 0.39 R²: 0.30375 |
Age, sex, PCs(1-40) | — |
| PPM001554 | PGS000686 (snpnet.HDL_cholesterol) |
PSS000703| European Ancestry| 58,251 individuals |
PGP000128 | Sinnott-Armstrong N et al. Nat Genet (2021) |
Reported Trait: HDL cholesterol [mmol/L] | — | — | R²: 0.35648 Spearman's ρ: 0.438 |
Age, sex, PCs(1-40) | — |
| PPM001577 | PGS000686 (snpnet.HDL_cholesterol) |
PSS000818| European Ancestry| 2,127 individuals |
PGP000128 | Sinnott-Armstrong N et al. Nat Genet (2021) |
Reported Trait: HDL cholesterol [mmol/L] | — | — | Spearman's ρ: 0.301 | Age, sex | — |
| PPM001578 | PGS000686 (snpnet.HDL_cholesterol) |
PSS000819| European Ancestry| 2,002 individuals |
PGP000128 | Sinnott-Armstrong N et al. Nat Genet (2021) |
Reported Trait: HDL cholesterol [mmol/L] | — | — | Spearman's ρ: 0.305 | Age, sex | — |
| PPM001414 | PGS000686 (snpnet.HDL_cholesterol) |
PSS000699| African Ancestry| 5,573 individuals |
PGP000128 | Sinnott-Armstrong N et al. Nat Genet (2021) |
Reported Trait: HDL cholesterol [mmol/L] | — | — | R²: 0.17487 Spearman's ρ: 0.241 |
Age, sex, PCs(1-40) | — |
| PPM001449 | PGS000686 (snpnet.HDL_cholesterol) |
PSS000700| East Asian Ancestry| 986 individuals |
PGP000128 | Sinnott-Armstrong N et al. Nat Genet (2021) |
Reported Trait: HDL cholesterol [mmol/L] | — | — | R²: 0.31466 Spearman's ρ: 0.326 |
Age, sex, PCs(1-40) | — |
| PPM001484 | PGS000686 (snpnet.HDL_cholesterol) |
PSS000701| European Ancestry| 21,542 individuals |
PGP000128 | Sinnott-Armstrong N et al. Nat Genet (2021) |
Reported Trait: HDL cholesterol [mmol/L] | — | — | R²: 0.36109 Spearman's ρ: 0.422 |
Age, sex, PCs(1-40) | — |
| PPM007355 | PGS000686 (snpnet.HDL_cholesterol) |
PSS007161| African Ancestry| 5,656 individuals |
PGP000244 | Tanigawa Y et al. PLoS Genet (2022) |Ext. |
Reported Trait: HDL cholesterol | — | — | R²: 0.17012 [0.15349, 0.18676] Incremental R2 (full-covars): 0.05232 PGS R2 (no covariates): 0.05099 [0.04058, 0.06141] |
age, sex, UKB array type, Genotype PCs | — |
| PPM007356 | PGS000686 (snpnet.HDL_cholesterol) |
PSS007162| East Asian Ancestry| 1,475 individuals |
PGP000244 | Tanigawa Y et al. PLoS Genet (2022) |Ext. |
Reported Trait: HDL cholesterol | — | — | R²: 0.29075 [0.25451, 0.32699] Incremental R2 (full-covars): 0.07379 PGS R2 (no covariates): 0.07936 [0.05478, 0.10393] |
age, sex, UKB array type, Genotype PCs | — |
| PPM007357 | PGS000686 (snpnet.HDL_cholesterol) |
PSS007163| European Ancestry| 21,750 individuals |
PGP000244 | Tanigawa Y et al. PLoS Genet (2022) |Ext. |
Reported Trait: HDL cholesterol | — | — | R²: 0.32462 [0.31507, 0.33418] Incremental R2 (full-covars): 0.13703 PGS R2 (no covariates): 0.14659 [0.13848, 0.15471] |
age, sex, UKB array type, Genotype PCs | — |
| PPM007358 | PGS000686 (snpnet.HDL_cholesterol) |
PSS007164| South Asian Ancestry| 6,782 individuals |
PGP000244 | Tanigawa Y et al. PLoS Genet (2022) |Ext. |
Reported Trait: HDL cholesterol | — | — | R²: 0.27847 [0.26161, 0.29532] Incremental R2 (full-covars): 0.12939 PGS R2 (no covariates): 0.13685 [0.12272, 0.15099] |
age, sex, UKB array type, Genotype PCs | — |
| PPM007359 | PGS000686 (snpnet.HDL_cholesterol) |
PSS007165| European Ancestry| 59,060 individuals |
PGP000244 | Tanigawa Y et al. PLoS Genet (2022) |Ext. |
Reported Trait: HDL cholesterol | — | — | R²: 0.32153 [0.31572, 0.32734] Incremental R2 (full-covars): 0.14881 PGS R2 (no covariates): 0.16158 [0.15649, 0.16667] |
age, sex, UKB array type, Genotype PCs | — |
| PPM002231 | PGS000825 (HDL-C_PGS) |
PSS001083| Multi-ancestry (including European)| 2,531 individuals |
PGP000210 | Zubair N et al. Sci Rep (2019) |
Reported Trait: High density lipoprotein cholesterol | — | — | R²: 0.069 | Age at baseline, sex, enrollment channel, PCs(1-7), observation season, observation vendor | — |
| PPM002308 | PGS000845 (HDL) |
PSS001086| European Ancestry| 3,194 individuals |
PGP000211 | Aly DM et al. Nat Genet (2021) |
Reported Trait: Severe Autoimmune Diabetes | OR: 0.98 [0.89, 1.09] | — | — | PC1-10 | — |
| PPM002309 | PGS000845 (HDL) |
PSS001087| European Ancestry| 3,930 individuals |
PGP000211 | Aly DM et al. Nat Genet (2021) |
Reported Trait: Severe Insulin-Deficient Diabetes | OR: 0.97 [0.9, 1.04] | — | — | PC1-10 | — |
| PPM002310 | PGS000845 (HDL) |
PSS001088| European Ancestry| 3,869 individuals |
PGP000211 | Aly DM et al. Nat Genet (2021) |
Reported Trait: Severe Insulin-Resistant Diabetes | OR: 0.91 [0.84, 0.97] | — | — | PC1-10 | — |
| PPM002311 | PGS000845 (HDL) |
PSS001085| European Ancestry| 4,116 individuals |
PGP000211 | Aly DM et al. Nat Genet (2021) |
Reported Trait: Moderate Obesity-related Diabetes | OR: 0.94 [0.88, 1.0] | — | — | PC1-10 | — |
| PPM002312 | PGS000845 (HDL) |
PSS001084| European Ancestry| 5,597 individuals |
PGP000211 | Aly DM et al. Nat Genet (2021) |
Reported Trait: Moderate Age-Related Diabetes | OR: 1.0 [0.95, 1.05] | — | — | PC1-10 | — |
| PPM010507 | PGS001954 (portability-PLR_log_HDL) |
PSS009432| European Ancestry| 17,454 individuals |
PGP000263 | Privé F et al. Am J Hum Genet (2022) |
Reported Trait: HDL cholesterol | — | — | Partial Correlation (partial-r): 0.4605 [0.4488, 0.4721] | sex, age, birth date, deprivation index, 16 PCs | — |
| PPM010508 | PGS001954 (portability-PLR_log_HDL) |
PSS009206| European Ancestry| 3,590 individuals |
PGP000263 | Privé F et al. Am J Hum Genet (2022) |
Reported Trait: HDL cholesterol | — | — | Partial Correlation (partial-r): 0.4525 [0.4261, 0.4782] | sex, age, birth date, deprivation index, 16 PCs | — |
| PPM010509 | PGS001954 (portability-PLR_log_HDL) |
PSS008760| European Ancestry| 5,800 individuals |
PGP000263 | Privé F et al. Am J Hum Genet (2022) |
Reported Trait: HDL cholesterol | — | — | Partial Correlation (partial-r): 0.4564 [0.4357, 0.4765] | sex, age, birth date, deprivation index, 16 PCs | — |
| PPM010510 | PGS001954 (portability-PLR_log_HDL) |
PSS008534| Greater Middle Eastern Ancestry| 1,034 individuals |
PGP000263 | Privé F et al. Am J Hum Genet (2022) |
Reported Trait: HDL cholesterol | — | — | Partial Correlation (partial-r): 0.4038 [0.351, 0.4541] | sex, age, birth date, deprivation index, 16 PCs | — |
| PPM010511 | PGS001954 (portability-PLR_log_HDL) |
PSS008312| South Asian Ancestry| 5,476 individuals |
PGP000263 | Privé F et al. Am J Hum Genet (2022) |
Reported Trait: HDL cholesterol | — | — | Partial Correlation (partial-r): 0.409 [0.3867, 0.4309] | sex, age, birth date, deprivation index, 16 PCs | — |
| PPM010513 | PGS001954 (portability-PLR_log_HDL) |
PSS007876| African Ancestry| 2,160 individuals |
PGP000263 | Privé F et al. Am J Hum Genet (2022) |
Reported Trait: HDL cholesterol | — | — | Partial Correlation (partial-r): 0.3126 [0.2739, 0.3504] | sex, age, birth date, deprivation index, 16 PCs | — |
| PPM010514 | PGS001954 (portability-PLR_log_HDL) |
PSS008980| African Ancestry| 3,401 individuals |
PGP000263 | Privé F et al. Am J Hum Genet (2022) |
Reported Trait: HDL cholesterol | — | — | Partial Correlation (partial-r): 0.2509 [0.219, 0.2822] | sex, age, birth date, deprivation index, 16 PCs | — |
| PPM010512 | PGS001954 (portability-PLR_log_HDL) |
PSS008089| East Asian Ancestry| 1,562 individuals |
PGP000263 | Privé F et al. Am J Hum Genet (2022) |
Reported Trait: HDL cholesterol | — | — | Partial Correlation (partial-r): 0.3656 [0.3215, 0.408] | sex, age, birth date, deprivation index, 16 PCs | — |
| PPM012223 | PGS002172 (portability-ldpred2_log_HDL) |
PSS009432| European Ancestry| 17,454 individuals |
PGP000263 | Privé F et al. Am J Hum Genet (2022) |
Reported Trait: HDL cholesterol | — | — | Partial Correlation (partial-r): 0.4488 [0.4369, 0.4606] | sex, age, birth date, deprivation index, 16 PCs | — |
| PPM012224 | PGS002172 (portability-ldpred2_log_HDL) |
PSS009206| European Ancestry| 3,590 individuals |
PGP000263 | Privé F et al. Am J Hum Genet (2022) |
Reported Trait: HDL cholesterol | — | — | Partial Correlation (partial-r): 0.4312 [0.4041, 0.4575] | sex, age, birth date, deprivation index, 16 PCs | — |
| PPM012225 | PGS002172 (portability-ldpred2_log_HDL) |
PSS008760| European Ancestry| 5,800 individuals |
PGP000263 | Privé F et al. Am J Hum Genet (2022) |
Reported Trait: HDL cholesterol | — | — | Partial Correlation (partial-r): 0.4468 [0.426, 0.4672] | sex, age, birth date, deprivation index, 16 PCs | — |
| PPM012226 | PGS002172 (portability-ldpred2_log_HDL) |
PSS008534| Greater Middle Eastern Ancestry| 1,034 individuals |
PGP000263 | Privé F et al. Am J Hum Genet (2022) |
Reported Trait: HDL cholesterol | — | — | Partial Correlation (partial-r): 0.3881 [0.3345, 0.4391] | sex, age, birth date, deprivation index, 16 PCs | — |
| PPM012227 | PGS002172 (portability-ldpred2_log_HDL) |
PSS008312| South Asian Ancestry| 5,476 individuals |
PGP000263 | Privé F et al. Am J Hum Genet (2022) |
Reported Trait: HDL cholesterol | — | — | Partial Correlation (partial-r): 0.4033 [0.3808, 0.4253] | sex, age, birth date, deprivation index, 16 PCs | — |
| PPM012228 | PGS002172 (portability-ldpred2_log_HDL) |
PSS008089| East Asian Ancestry| 1,562 individuals |
PGP000263 | Privé F et al. Am J Hum Genet (2022) |
Reported Trait: HDL cholesterol | — | — | Partial Correlation (partial-r): 0.3613 [0.3171, 0.404] | sex, age, birth date, deprivation index, 16 PCs | — |
| PPM012230 | PGS002172 (portability-ldpred2_log_HDL) |
PSS008980| African Ancestry| 3,401 individuals |
PGP000263 | Privé F et al. Am J Hum Genet (2022) |
Reported Trait: HDL cholesterol | — | — | Partial Correlation (partial-r): 0.2397 [0.2077, 0.2713] | sex, age, birth date, deprivation index, 16 PCs | — |
| PPM012229 | PGS002172 (portability-ldpred2_log_HDL) |
PSS007876| African Ancestry| 2,160 individuals |
PGP000263 | Privé F et al. Am J Hum Genet (2022) |
Reported Trait: HDL cholesterol | — | — | Partial Correlation (partial-r): 0.2789 [0.2393, 0.3175] | sex, age, birth date, deprivation index, 16 PCs | — |
| PPM012982 | PGS002284 (GRS_286_HDL) |
PSS009639| African Ancestry| 2,569 individuals |
PGP000313 | Kamiza AB et al. Nat Med (2022) |
Reported Trait: High density lipoprotein cholesterol levels | — | — | R²: 0.0213 | age, sex, type 2 diabetes, PC1, PC2, PC3, PC4, PC5 | Nagelkerke’s R2 (estimate of variance explained by the PGS after covariate adjustment) |
| PPM013094 | PGS002329 (biochemistry_HDLcholesterol.BOLT-LMM) |
PSS009759| African Ancestry| 5,619 individuals |
PGP000332 | Weissbrod O et al. Nat Genet (2022) |
Reported Trait: HDL Cholesterol | — | — | Incremental R2 (full model vs. covariates alone): 0.0518 | age, sex, age*sex, assessment center, genotyping array, 10 PCs | — |
| PPM013143 | PGS002329 (biochemistry_HDLcholesterol.BOLT-LMM) |
PSS009760| East Asian Ancestry| 797 individuals |
PGP000332 | Weissbrod O et al. Nat Genet (2022) |
Reported Trait: HDL Cholesterol | — | — | Incremental R2 (full model vs. covariates alone): 0.0918 | age, sex, age*sex, assessment center, genotyping array, 10 PCs | — |
| PPM013192 | PGS002329 (biochemistry_HDLcholesterol.BOLT-LMM) |
PSS009761| European Ancestry| 37,633 individuals |
PGP000332 | Weissbrod O et al. Nat Genet (2022) |
Reported Trait: HDL Cholesterol | — | — | Incremental R2 (full model vs. covariates alone): 0.1578 | age, sex, age*sex, assessment center, genotyping array, 10 PCs | — |
| PPM013241 | PGS002329 (biochemistry_HDLcholesterol.BOLT-LMM) |
PSS009762| South Asian Ancestry| 6,980 individuals |
PGP000332 | Weissbrod O et al. Nat Genet (2022) |
Reported Trait: HDL Cholesterol | — | — | Incremental R2 (full model vs. covariates alone): 0.1256 | age, sex, age*sex, assessment center, genotyping array, 10 PCs | — |
| PPM013301 | PGS002366 (biochemistry_HDLcholesterol.BOLT-LMM-BBJ) |
PSS009760| East Asian Ancestry| 797 individuals |
PGP000332 | Weissbrod O et al. Nat Genet (2022) |
Reported Trait: HDL Cholesterol | — | — | Incremental R2 (full model vs. covariates alone): 0.087 | age, sex, age*sex, assessment center, genotyping array, 10 PCs | — |
| PPM013324 | PGS002366 (biochemistry_HDLcholesterol.BOLT-LMM-BBJ) |
PSS009761| European Ancestry| 37,633 individuals |
PGP000332 | Weissbrod O et al. Nat Genet (2022) |
Reported Trait: HDL Cholesterol | — | — | Incremental R2 (full model vs. covariates alone): 0.0175 | age, sex, age*sex, assessment center, genotyping array, 10 PCs | — |
| PPM013347 | PGS002366 (biochemistry_HDLcholesterol.BOLT-LMM-BBJ) |
PSS009762| South Asian Ancestry| 6,980 individuals |
PGP000332 | Weissbrod O et al. Nat Genet (2022) |
Reported Trait: HDL Cholesterol | — | — | Incremental R2 (full model vs. covariates alone): 0.0352 | age, sex, age*sex, assessment center, genotyping array, 10 PCs | — |
| PPM013278 | PGS002366 (biochemistry_HDLcholesterol.BOLT-LMM-BBJ) |
PSS009759| African Ancestry| 5,619 individuals |
PGP000332 | Weissbrod O et al. Nat Genet (2022) |
Reported Trait: HDL Cholesterol | — | — | Incremental R2 (full model vs. covariates alone): 0.0132 | age, sex, age*sex, assessment center, genotyping array, 10 PCs | — |
| PPM013382 | PGS002401 (biochemistry_HDLcholesterol.P+T.0.0001) |
PSS009759| African Ancestry| 5,619 individuals |
PGP000332 | Weissbrod O et al. Nat Genet (2022) |
Reported Trait: HDL Cholesterol | — | — | Incremental R2 (full model vs. covariates alone): 0.0065 | age, sex, age*sex, assessment center, genotyping array, 10 PCs | — |
| PPM013480 | PGS002401 (biochemistry_HDLcholesterol.P+T.0.0001) |
PSS009761| European Ancestry| 37,633 individuals |
PGP000332 | Weissbrod O et al. Nat Genet (2022) |
Reported Trait: HDL Cholesterol | — | — | Incremental R2 (full model vs. covariates alone): 0.0831 | age, sex, age*sex, assessment center, genotyping array, 10 PCs | — |
| PPM013529 | PGS002401 (biochemistry_HDLcholesterol.P+T.0.0001) |
PSS009762| South Asian Ancestry| 6,980 individuals |
PGP000332 | Weissbrod O et al. Nat Genet (2022) |
Reported Trait: HDL Cholesterol | — | — | Incremental R2 (full model vs. covariates alone): 0.062 | age, sex, age*sex, assessment center, genotyping array, 10 PCs | — |
| PPM013431 | PGS002401 (biochemistry_HDLcholesterol.P+T.0.0001) |
PSS009760| East Asian Ancestry| 797 individuals |
PGP000332 | Weissbrod O et al. Nat Genet (2022) |
Reported Trait: HDL Cholesterol | — | — | Incremental R2 (full model vs. covariates alone): 0.0511 | age, sex, age*sex, assessment center, genotyping array, 10 PCs | — |
| PPM013578 | PGS002450 (biochemistry_HDLcholesterol.P+T.0.001) |
PSS009759| African Ancestry| 5,619 individuals |
PGP000332 | Weissbrod O et al. Nat Genet (2022) |
Reported Trait: HDL Cholesterol | — | — | Incremental R2 (full model vs. covariates alone): 0.0003 | age, sex, age*sex, assessment center, genotyping array, 10 PCs | — |
| PPM013627 | PGS002450 (biochemistry_HDLcholesterol.P+T.0.001) |
PSS009760| East Asian Ancestry| 797 individuals |
PGP000332 | Weissbrod O et al. Nat Genet (2022) |
Reported Trait: HDL Cholesterol | — | — | Incremental R2 (full model vs. covariates alone): 0.0372 | age, sex, age*sex, assessment center, genotyping array, 10 PCs | — |
| PPM013676 | PGS002450 (biochemistry_HDLcholesterol.P+T.0.001) |
PSS009761| European Ancestry| 37,633 individuals |
PGP000332 | Weissbrod O et al. Nat Genet (2022) |
Reported Trait: HDL Cholesterol | — | — | Incremental R2 (full model vs. covariates alone): 0.0866 | age, sex, age*sex, assessment center, genotyping array, 10 PCs | — |
| PPM013725 | PGS002450 (biochemistry_HDLcholesterol.P+T.0.001) |
PSS009762| South Asian Ancestry| 6,980 individuals |
PGP000332 | Weissbrod O et al. Nat Genet (2022) |
Reported Trait: HDL Cholesterol | — | — | Incremental R2 (full model vs. covariates alone): 0.052 | age, sex, age*sex, assessment center, genotyping array, 10 PCs | — |
| PPM013823 | PGS002499 (biochemistry_HDLcholesterol.P+T.0.01) |
PSS009760| East Asian Ancestry| 797 individuals |
PGP000332 | Weissbrod O et al. Nat Genet (2022) |
Reported Trait: HDL Cholesterol | — | — | Incremental R2 (full model vs. covariates alone): 0.0015 | age, sex, age*sex, assessment center, genotyping array, 10 PCs | — |
| PPM013872 | PGS002499 (biochemistry_HDLcholesterol.P+T.0.01) |
PSS009761| European Ancestry| 37,633 individuals |
PGP000332 | Weissbrod O et al. Nat Genet (2022) |
Reported Trait: HDL Cholesterol | — | — | Incremental R2 (full model vs. covariates alone): 0.0649 | age, sex, age*sex, assessment center, genotyping array, 10 PCs | — |
| PPM013774 | PGS002499 (biochemistry_HDLcholesterol.P+T.0.01) |
PSS009759| African Ancestry| 5,619 individuals |
PGP000332 | Weissbrod O et al. Nat Genet (2022) |
Reported Trait: HDL Cholesterol | — | — | Incremental R2 (full model vs. covariates alone): 0.0 | age, sex, age*sex, assessment center, genotyping array, 10 PCs | — |
| PPM013921 | PGS002499 (biochemistry_HDLcholesterol.P+T.0.01) |
PSS009762| South Asian Ancestry| 6,980 individuals |
PGP000332 | Weissbrod O et al. Nat Genet (2022) |
Reported Trait: HDL Cholesterol | — | — | Incremental R2 (full model vs. covariates alone): 0.0142 | age, sex, age*sex, assessment center, genotyping array, 10 PCs | — |
| PPM013970 | PGS002548 (biochemistry_HDLcholesterol.P+T.1e-06) |
PSS009759| African Ancestry| 5,619 individuals |
PGP000332 | Weissbrod O et al. Nat Genet (2022) |
Reported Trait: HDL Cholesterol | — | — | Incremental R2 (full model vs. covariates alone): 0.0317 | age, sex, age*sex, assessment center, genotyping array, 10 PCs | — |
| PPM014019 | PGS002548 (biochemistry_HDLcholesterol.P+T.1e-06) |
PSS009760| East Asian Ancestry| 797 individuals |
PGP000332 | Weissbrod O et al. Nat Genet (2022) |
Reported Trait: HDL Cholesterol | — | — | Incremental R2 (full model vs. covariates alone): 0.0456 | age, sex, age*sex, assessment center, genotyping array, 10 PCs | — |
| PPM014117 | PGS002548 (biochemistry_HDLcholesterol.P+T.1e-06) |
PSS009762| South Asian Ancestry| 6,980 individuals |
PGP000332 | Weissbrod O et al. Nat Genet (2022) |
Reported Trait: HDL Cholesterol | — | — | Incremental R2 (full model vs. covariates alone): 0.0643 | age, sex, age*sex, assessment center, genotyping array, 10 PCs | — |
| PPM014068 | PGS002548 (biochemistry_HDLcholesterol.P+T.1e-06) |
PSS009761| European Ancestry| 37,633 individuals |
PGP000332 | Weissbrod O et al. Nat Genet (2022) |
Reported Trait: HDL Cholesterol | — | — | Incremental R2 (full model vs. covariates alone): 0.0746 | age, sex, age*sex, assessment center, genotyping array, 10 PCs | — |
| PPM014166 | PGS002597 (biochemistry_HDLcholesterol.P+T.5e-08) |
PSS009759| African Ancestry| 5,619 individuals |
PGP000332 | Weissbrod O et al. Nat Genet (2022) |
Reported Trait: HDL Cholesterol | — | — | Incremental R2 (full model vs. covariates alone): 0.0309 | age, sex, age*sex, assessment center, genotyping array, 10 PCs | — |
| PPM014215 | PGS002597 (biochemistry_HDLcholesterol.P+T.5e-08) |
PSS009760| East Asian Ancestry| 797 individuals |
PGP000332 | Weissbrod O et al. Nat Genet (2022) |
Reported Trait: HDL Cholesterol | — | — | Incremental R2 (full model vs. covariates alone): 0.044 | age, sex, age*sex, assessment center, genotyping array, 10 PCs | — |
| PPM014264 | PGS002597 (biochemistry_HDLcholesterol.P+T.5e-08) |
PSS009761| European Ancestry| 37,633 individuals |
PGP000332 | Weissbrod O et al. Nat Genet (2022) |
Reported Trait: HDL Cholesterol | — | — | Incremental R2 (full model vs. covariates alone): 0.0717 | age, sex, age*sex, assessment center, genotyping array, 10 PCs | — |
| PPM014313 | PGS002597 (biochemistry_HDLcholesterol.P+T.5e-08) |
PSS009762| South Asian Ancestry| 6,980 individuals |
PGP000332 | Weissbrod O et al. Nat Genet (2022) |
Reported Trait: HDL Cholesterol | — | — | Incremental R2 (full model vs. covariates alone): 0.0625 | age, sex, age*sex, assessment center, genotyping array, 10 PCs | — |
| PPM014362 | PGS002646 (biochemistry_HDLcholesterol.PolyFun-pred) |
PSS009759| African Ancestry| 5,619 individuals |
PGP000332 | Weissbrod O et al. Nat Genet (2022) |
Reported Trait: HDL Cholesterol | — | — | Incremental R2 (full model when combined with BOLT-LMM vs. covariates alone): 0.071 | age, sex, age*sex, assessment center, genotyping array, 10 PCs | See biochemistry_HDLcholesterol.mixweights file at http://data.broadinstitute.org/alkesgroup/polypred_results for combination weights |
| PPM014411 | PGS002646 (biochemistry_HDLcholesterol.PolyFun-pred) |
PSS009760| East Asian Ancestry| 797 individuals |
PGP000332 | Weissbrod O et al. Nat Genet (2022) |
Reported Trait: HDL Cholesterol | — | — | Incremental R2 (full model when combined with BOLT-LMM vs. covariates alone): 0.1071 | age, sex, age*sex, assessment center, genotyping array, 10 PCs | See biochemistry_HDLcholesterol.mixweights file at http://data.broadinstitute.org/alkesgroup/polypred_results for combination weights |
| PPM014460 | PGS002646 (biochemistry_HDLcholesterol.PolyFun-pred) |
PSS009761| European Ancestry| 37,633 individuals |
PGP000332 | Weissbrod O et al. Nat Genet (2022) |
Reported Trait: HDL Cholesterol | — | — | Incremental R2 (full model when combined with BOLT-LMM vs. covariates alone): 0.1701 | age, sex, age*sex, assessment center, genotyping array, 10 PCs | See biochemistry_HDLcholesterol.mixweights file at http://data.broadinstitute.org/alkesgroup/polypred_results for combination weights |
| PPM014509 | PGS002646 (biochemistry_HDLcholesterol.PolyFun-pred) |
PSS009762| South Asian Ancestry| 6,980 individuals |
PGP000332 | Weissbrod O et al. Nat Genet (2022) |
Reported Trait: HDL Cholesterol | — | — | Incremental R2 (full model when combined with BOLT-LMM vs. covariates alone): 0.1352 | age, sex, age*sex, assessment center, genotyping array, 10 PCs | See biochemistry_HDLcholesterol.mixweights file at http://data.broadinstitute.org/alkesgroup/polypred_results for combination weights |
| PPM014705 | PGS002695 (biochemistry_HDLcholesterol.SBayesR) |
PSS009762| South Asian Ancestry| 6,980 individuals |
PGP000332 | Weissbrod O et al. Nat Genet (2022) |
Reported Trait: HDL Cholesterol | — | — | Incremental R2 (full model vs. covariates alone): 0.1219 | age, sex, age*sex, assessment center, genotyping array, 10 PCs | — |
| PPM014558 | PGS002695 (biochemistry_HDLcholesterol.SBayesR) |
PSS009759| African Ancestry| 5,619 individuals |
PGP000332 | Weissbrod O et al. Nat Genet (2022) |
Reported Trait: HDL Cholesterol | — | — | Incremental R2 (full model vs. covariates alone): 0.046 | age, sex, age*sex, assessment center, genotyping array, 10 PCs | — |
| PPM014607 | PGS002695 (biochemistry_HDLcholesterol.SBayesR) |
PSS009760| East Asian Ancestry| 797 individuals |
PGP000332 | Weissbrod O et al. Nat Genet (2022) |
Reported Trait: HDL Cholesterol | — | — | Incremental R2 (full model vs. covariates alone): 0.1017 | age, sex, age*sex, assessment center, genotyping array, 10 PCs | — |
| PPM014656 | PGS002695 (biochemistry_HDLcholesterol.SBayesR) |
PSS009761| European Ancestry| 37,633 individuals |
PGP000332 | Weissbrod O et al. Nat Genet (2022) |
Reported Trait: HDL Cholesterol | — | — | Incremental R2 (full model vs. covariates alone): 0.1543 | age, sex, age*sex, assessment center, genotyping array, 10 PCs | — |
| PPM016161 | PGS002781 (GLGC_2021_ALL_HDL_PRS_weights_PRS-CS) |
PSS010052| Multi-ancestry (including European)| 461,918 individuals |
PGP000366 | Kanoni S et al. medRxiv (2021) |Pre |
Reported Trait: Baseline HDL cholesterol | — | — | R²: 0.13 | sex, batch, age at initial assessment, PCs1-4 | — |
| PPM015833 | PGS002954 (ExPRSweb_HDL_30760-irnt_LASSOSUM_MGI_20211120) |
PSS010006| European Ancestry| 9,320 individuals |
PGP000393 | Ma Y et al. Am J Hum Genet (2022) |
Reported Trait: HDL | β: 4.29 (0.128) | — | R²: 0.0815 | SEX,AGE,Batch,PC1,PC2,PC3,PC4 | — |
| PPM015836 | PGS002955 (ExPRSweb_HDL_30760-irnt_PT_MGI_20211120) |
PSS010006| European Ancestry| 9,320 individuals |
PGP000393 | Ma Y et al. Am J Hum Genet (2022) |
Reported Trait: HDL | β: 4.39 (0.127) | — | R²: 0.0903 | SEX,AGE,Batch,PC1,PC2,PC3,PC4 | — |
| PPM015834 | PGS002956 (ExPRSweb_HDL_30760-irnt_PLINK_MGI_20211120) |
PSS010006| European Ancestry| 9,320 individuals |
PGP000393 | Ma Y et al. Am J Hum Genet (2022) |
Reported Trait: HDL | β: 4.34 (0.127) | — | R²: 0.0883 | SEX,AGE,Batch,PC1,PC2,PC3,PC4 | — |
| PPM015832 | PGS002957 (ExPRSweb_HDL_30760-irnt_DBSLMM_MGI_20211120) |
PSS010006| European Ancestry| 9,320 individuals |
PGP000393 | Ma Y et al. Am J Hum Genet (2022) |
Reported Trait: HDL | β: 4.49 (0.125) | — | R²: 0.0956 | SEX,AGE,Batch,PC1,PC2,PC3,PC4 | — |
| PPM015835 | PGS002958 (ExPRSweb_HDL_30760-irnt_PRSCS_MGI_20211120) |
PSS010006| European Ancestry| 9,320 individuals |
PGP000393 | Ma Y et al. Am J Hum Genet (2022) |
Reported Trait: HDL | β: 4.68 (0.128) | — | R²: 0.0965 | SEX,AGE,Batch,PC1,PC2,PC3,PC4 | — |
| PPM015838 | PGS002959 (ExPRSweb_HDL_30760-raw_LASSOSUM_MGI_20211120) |
PSS010006| European Ancestry| 9,320 individuals |
PGP000393 | Ma Y et al. Am J Hum Genet (2022) |
Reported Trait: HDL | β: 4.28 (0.129) | — | R²: 0.0812 | SEX,AGE,Batch,PC1,PC2,PC3,PC4 | — |
| PPM015841 | PGS002960 (ExPRSweb_HDL_30760-raw_PT_MGI_20211120) |
PSS010006| European Ancestry| 9,320 individuals |
PGP000393 | Ma Y et al. Am J Hum Genet (2022) |
Reported Trait: HDL | β: 4.35 (0.127) | — | R²: 0.0885 | SEX,AGE,Batch,PC1,PC2,PC3,PC4 | — |
| PPM015839 | PGS002961 (ExPRSweb_HDL_30760-raw_PLINK_MGI_20211120) |
PSS010006| European Ancestry| 9,320 individuals |
PGP000393 | Ma Y et al. Am J Hum Genet (2022) |
Reported Trait: HDL | β: 4.31 (0.128) | — | R²: 0.0863 | SEX,AGE,Batch,PC1,PC2,PC3,PC4 | — |
| PPM015837 | PGS002962 (ExPRSweb_HDL_30760-raw_DBSLMM_MGI_20211120) |
PSS010006| European Ancestry| 9,320 individuals |
PGP000393 | Ma Y et al. Am J Hum Genet (2022) |
Reported Trait: HDL | β: 4.4 (0.126) | — | R²: 0.0921 | SEX,AGE,Batch,PC1,PC2,PC3,PC4 | — |
| PPM015840 | PGS002963 (ExPRSweb_HDL_30760-raw_PRSCS_MGI_20211120) |
PSS010006| European Ancestry| 9,320 individuals |
PGP000393 | Ma Y et al. Am J Hum Genet (2022) |
Reported Trait: HDL | β: 4.65 (0.127) | — | R²: 0.0955 | SEX,AGE,Batch,PC1,PC2,PC3,PC4 | — |
| PPM016177 | PGS003338 (CVGRS_HDL) |
PSS010055| East Asian Ancestry| 22,608 individuals |
PGP000405 | Kim YJ et al. Nat Commun (2022) |
Reported Trait: HDL cholesterol level | β: 0.32033 | — | — | — | — |
| PPM016194 | PGS003338 (CVGRS_HDL) |
PSS010055| East Asian Ancestry| 22,608 individuals |
PGP000405 | Kim YJ et al. Nat Commun (2022) |
Reported Trait: Type 2 diabetes | OR: 1.03795 | — | — | — | — |
| PPM016186 | PGS003347 (ALLGRS_HDL) |
PSS010055| East Asian Ancestry| 22,608 individuals |
PGP000405 | Kim YJ et al. Nat Commun (2022) |
Reported Trait: HDL cholesterol level | β: 0.32811 | — | — | — | — |
|
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 |
|---|---|---|---|---|---|---|---|---|
| PSS007876 | — | — | 2,160 individuals | — | African American or Afro-Caribbean | Carribean | UKB | — |
| PSS010052 | — | — | 461,918 individuals | — | European, African unspecified, East Asian, South Asian | — | UKB | — |
| PSS000818 | — | — | 2,127 individuals | — | European | Participants self-identifying as white | MESA | — |
| PSS000819 | — | — | 2,002 individuals | — | European | Participants self-identifying as white | MESA | — |
| PSS010055 | — | — | 22,608 individuals | — | East Asian | — | KBA, KoGES | — |
| PSS008534 | — | — | 1,034 individuals | — | Greater Middle Eastern (Middle Eastern, North African or Persian) | Iran (Middle East) | UKB | — |
| PSS009759 | — | — | 5,619 individuals | — | African unspecified | — | UKB | — |
| PSS000699 | — | — | 5,573 individuals | — | African unspecified | — | UKB | — |
| PSS000700 | — | — | 986 individuals | — | East Asian | — | UKB | — |
| PSS000701 | — | — | 21,542 individuals | — | European | Non-British White | UKB | — |
| PSS000702 | — | — | 6,689 individuals | — | South Asian | — | UKB | — |
| PSS000703 | — | — | 58,251 individuals | — | European (British) |
— | UKB | — |
| PSS009432 | — | — | 17,454 individuals | — | European | UK (+ Ireland) | UKB | — |
| PSS009760 | — | — | 797 individuals | — | East Asian | — | UKB | — |
| PSS009761 | — | — | 37,633 individuals | — | European | Non-British European | UKB | — |
| PSS009762 | — | — | 6,980 individuals | — | South Asian | — | UKB | — |
| PSS001083 | Of the 2,531 participants, 1,809 had longitudinal observations for total cholesterol (mg/dL), high density lipoprotein cholesterol (mg/dL) and trigycerides (mg/dL), 1,801 had longitudinal observations for low density lipoprotein cholesterol (mg/dL), 1,325 had longitudinal observations for waist circumference (inches), 2,355 had longitudinal observations for body mass index (kg/m^2) and 1,572 had longitudinal observations for homocysteine (μmol/L). | — | 2,531 individuals, 40.0 % Male samples |
Mean = 48.0 years Sd = 12.0 years |
European, Asian unspecified, Hispanic or Latin American, African unspecified, NR | European = 1,999, Asian unspecified = 228, Hispanic or Latin American = 101, African unspecified = 51, Not reported = 152 | NR | Participants were obtained from the Scientific Wellness Program. |
| PSS000292 | Composite end point of cardiovascular events was defined as myocardial infarction, ischemic stroke, and death from coronary heart disease. Death from coronary heart disease was defined on the basis of codes 412 and 414 (ICD-9) or I22–I23 and I25 (ICD-10) in the Swedish Cause of Death Register. Myocardial infarction was defined on the basis of codes 410 and I21 in the International Classification of Diseases, 9th Revision and 10th Revision (ICD-9 and ICD-10), respectively. Ischemic stroke was defined on the basis of codes 434 or 436 (ICD-9) and I63 or I64 (ICD-10). | Median = 10.6 years | [
|
— | European | — | MDC | — |
| PSS009206 | — | — | 3,590 individuals | — | European | Poland (NE Europe) | 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 | — |
| PSS008312 | — | — | 5,476 individuals | — | South Asian | India (South Asia) | UKB | — |
| PSS009639 | Non-fasting serum lipid levels were measured using the Cobas Integra 400 Plus Chemistry analyser, an automated analyser that employs four different technologies: absorption photometry, fluorescence polarization immunoassay, immune-turbidimetry, and potentiometry for accurate analysis. LDL-C were measured using the homogeneous enzymatic colorimetric assays | — | 2,569 individuals, 42.9 % Male samples |
Mean = 33.1 years Ci = [18.0, 48.2] years |
Sub-Saharan African (South Africans) |
— | SAZ | — |
| PSS001084 | Moderate Age-Related Diabetes (MARD) vs. controls | — | [
|
— | European | Swedish | ANDIS | — |
| PSS001085 | Moderate Obesity-related Diabetes (MOD) vs. controls | — | [
|
— | European | Swedish | ANDIS | — |
| PSS001086 | Severe Autoimmune Diabetes (SAID) vs. controls | — | [
|
— | European | Swedish | ANDIS | — |
| PSS001087 | Severe Insulin-Deficient Diabetes (SIDD) vs. controls | — | [
|
— | European | Swedish | ANDIS | — |
| PSS001088 | Severe Insulin-Resistant Diabetes (SIRD) vs. controls | — | [
|
— | European | Swedish | ANDIS | — |
| PSS010006 | HIGH DENSITY LIPOPROTEIN CHOL (LOINC: 2085-9); Quantitative | — | 9,320 individuals | — | European | — | MGI | — |
| PSS000587 | Measured using fasting blood samples | — | 426 individuals, 46.0 % Male samples |
Mean = 43.3 years Sd = 11.4 years |
East Asian (Chinese) |
— | NR | Adults |
| PSS007161 | — | — | 5,656 individuals | — | African unspecified | — | UKB | — |
| PSS000589 | Measured using fasting blood samples | — | 1,941 individuals, 57.7 % Male samples |
Mean = 58.2 years Sd = 12.34 years |
East Asian (Chinese) |
— | HKDB | — |
| PSS007162 | — | — | 1,475 individuals | — | East Asian | — | UKB | — |
| PSS000591 | Measured using fasting blood samples | — | 865 individuals, 57.6 % Male samples |
Mean = 57.0 years Sd = 12.08 years |
East Asian (Chinese) |
— | HKDB | — |
| PSS007163 | — | — | 21,750 individuals | — | European | non-white British ancestry | UKB | — |
| PSS000593 | Measured using fasting blood samples | — | 4,917 individuals, 44.9 % Male samples |
Mean = 56.3 years Sd = 13.5 years |
East Asian (Chinese) |
— | HKDR | — |
| PSS007164 | — | — | 6,782 individuals | — | South Asian | — | UKB | — |
| PSS007165 | — | — | 59,060 individuals | — | European | white British ancestry | UKB | Testing cohort (heldout set) |
| PSS000096 | Lipid levels are represented in mg/dL, individuals on any lipid-lowering medication (n = 1,018) were omitted from all analyses. | — | 1,355 individuals, 46.2 % Male samples |
Mean = 61.68 years | African American or Afro-Caribbean | — | MESA | MESA Classic Cohort |
| PSS000097 | Lipid levels are represented in mg/dL, individuals on any lipid-lowering medication (n = 1,018) were omitted from all analyses. | — | 666 individuals, 50.15 % Male samples |
Mean = 61.5 years | East Asian | — | MESA | MESA Classic Cohort |
| PSS000098 | Lipid levels are represented in mg/dL, individuals on any lipid-lowering medication (n = 1,018) were omitted from all analyses. | — | 2,063 individuals, 46.78 % Male samples |
Mean = 62.09 years | European | — | MESA | MESA Classic Cohort |
| PSS000099 | Lipid levels are represented in mg/dL, individuals on any lipid-lowering medication (n = 1,018) were omitted from all analyses. | — | 1,256 individuals, 48.89 % Male samples |
Mean = 60.65 years | Hispanic or Latin American | — | MESA | MESA Classic Cohort |
| PSS008980 | — | — | 3,401 individuals | — | African unspecified | Nigeria (West Africa) | UKB | — |
| PSS008089 | — | — | 1,562 individuals | — | East Asian | China (East Asia) | UKB | — |
| PSS000100 | Serum levels of high-density lipoprotein (HDL), low-density lipoprotein (LDL) cholesterol and triglycerides (TG) | — | 6,407 individuals, 44.0 % Male samples |
Mean = 34.0 years | Sub-Saharan African | — | APCDR | APCDR-Uganda study |
| PSS000101 | Serum levels of high-density lipoprotein (HDL), low-density lipoprotein (LDL) cholesterol and triglycerides (TG) | — | 21,295 individuals, 38.0 % Male samples |
Mean = 60.0 years | East Asian (Chinese) |
— | CKB | - 20810 samples had HDL measurements - 17662 samples had LDL measurements - 20222 samples had triglyceride measurements |
| PSS000102 | Serum levels of high-density lipoprotein (HDL), low-density lipoprotein (LDL) cholesterol and triglycerides (TG) | — | 1,641 individuals, 58.0 % Male samples |
Mean = 62.0 years | European (Greek) |
Population isolate from the Pomak villages in the North of Greece | HELIC | - 1186 samples had HDL measurements - 1186 samples had LDL measurements - 1176 samples had triglyceride measurements |
| PSS000103 | Serum levels of high-density lipoprotein (HDL), low-density lipoprotein (LDL) cholesterol and triglycerides (TG) | — | 1,945 individuals, 66.0 % Male samples |
Mean = 45.0 years | European (Greek) |
Population isolate from the Mylopotamos villages in Crete | HELIC | - 1078 samples had HDL measurements - 1075 samples had LDL measurements - 1066 samples had triglyceride measurements |
| PSS000104 | Serum levels of high-density lipoprotein (HDL), low-density lipoprotein (LDL) cholesterol and triglycerides (TG) | — | 9,962 individuals, 56.0 % Male samples |
Mean = 52.0 years | European | — | UKHLS | - 9706 samples had HDL measurements - 9767 samples had LDL measurements - 9635 samples had triglyceride measurements |
| PSS008760 | — | — | 5,800 individuals | — | European | Italy (South Europe) | UKB | — |