Trait: high density lipoprotein cholesterol measurement

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
Synonyms HDL measurement
Mapped term(s) 2 mapped terms
  • NCIt:C105587
  • SNOMEDCT:28036006

Associated Polygenic Score(s)

Filter PGS by Participant Ancestry
Individuals included in:
G - Source of Variant Associations (GWAS)
D - Score Development/Training
E - PGS Evaluation
List of ancestries includes:
Display options:
Ancestry legend
Multi-ancestry (including European)
Multi-ancestry (excluding European)
African
East Asian
South Asian
Additional Asian Ancestries
European
Greater Middle Eastern
Hispanic or Latin American
Additional Diverse Ancestries
Not Reported
Polygenic Score ID & Name PGS Publication ID (PGP) Reported Trait Mapped Trait(s) (Ontology) Number of Variants Ancestry distribution PGS 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
-
http://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
-
http://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
-
http://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
-
http://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
http://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
-
http://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS000686/ScoringFiles/PGS000686.txt.gz - Check Terms/Licenses

Performance Metrics

Disclaimer: The performance metrics are displayed as reported by the source studies. It is important to note that metrics are not necessarily comparable with each other. For example, metrics depend on the sample characteristics (described by the PGS Catalog Sample Set [PSS] ID), phenotyping, and statistical modelling. Please refer to the source publication for additional guidance on performance.

PGS Performance
Metric ID (PPM)
Evaluated Score PGS Sample Set ID
(PSS)
Performance Source Trait PGS Effect Sizes
(per SD change)
Classification Metrics Other Metrics Covariates Included in the Model PGS Performance:
Other Relevant Information
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
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) : 0.1149 Sex, age, age^2
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
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] : 0.30375
Spearman's ρ: 0.39
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] : 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] : 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] : 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] : 0.36109
Spearman's ρ: 0.422
Age, sex, PCs(1-40)

Evaluated Samples

PGS Sample Set ID
(PSS)
Phenotype Definitions and Methods Participant Follow-up Time Sample Numbers Age of Study Participants Sample Ancestry Additional Ancestry Description Cohort(s) Additional Sample/Cohort Information
PSS000818 2,127 individuals European Participants self-identifying as white MESA
PSS000819 2,002 individuals European Participants self-identifying as white MESA
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
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
[
  • 238 cases
  • , 3,994 controls
]
European MDC
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
PSS000587 Measured using fasting blood samples 426 individuals,
46.0 % Male samples
Mean = 43.3 years
Sd = 11.4 years
East Asian
(Chinese)
Adults
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
PSS000591 Measured using fasting blood samples 865 individuals,
57.6 % Male samples
Mean = 57.0 years
Sd = 12.08 years
East Asian
(Chinese)
HKDB
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
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
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