Trait: total cholesterol measurement

Experimental Factor Ontology (EFO) Information
Identifier EFO_0004574
Description A total cholesterol measurement is the quantification of cholesterol in blood, total cholesterol is defined as the sum of HDL, LDL, and VLDL.
Trait category
Lipid or lipoprotein measurement
Synonyms 2 synonyms
  • cholesterol, total
  • total cholesterol levels
Mapped term(s) SNOMEDCT:121868005

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 Scoring File (FTP Link)
PGS000062
(GRS_TC)
PGP000045 |
Johnson L et al. PLoS One (2015)
total cholesterol total cholesterol measurement 52
-
http://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS000062/ScoringFiles/PGS000062.txt.gz
PGS000311
(GRS234_TC)
PGP000092 |
Xie T et al. Circ Genom Precis Med (2020)
Total cholesterol total cholesterol measurement 234
-
http://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS000311/ScoringFiles/PGS000311.txt.gz
PGS000658
(PRS-TC)
PGP000121 |
Tam CHT et al. Genome Med (2021)
Total cholesterol total cholesterol measurement 229
http://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS000658/ScoringFiles/PGS000658.txt.gz
PGS000677
(snpnet.Cholesterol_adjstatins)
PGP000128 |
Sinnott-Armstrong N et al. Nat Genet (2021)
Cholesterol [mmol/L] (statin adjusted) total cholesterol measurement 17,204
-
http://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS000677/ScoringFiles/PGS000677.txt.gz - Check Terms/Licenses
PGS000831
(Total_cholesterol_PGS)
PGP000210 |
Zubair N et al. Sci Rep (2019)
Total cholesterol total cholesterol measurement 1,032
-
http://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS000831/ScoringFiles/PGS000831.txt.gz - Check Terms/Licenses
PGS001201
(GBE_INI20030690)
PGP000244 |
Tanigawa Y et al. medRxiv (2021)
|Pre
Cholesterol total cholesterol measurement 14,403
-
http://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS001201/ScoringFiles/PGS001201.txt.gz
PGS001202
(GBE_INI30690)
PGP000244 |
Tanigawa Y et al. medRxiv (2021)
|Pre
Total cholesterol total cholesterol measurement 7,517
-
http://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS001202/ScoringFiles/PGS001202.txt.gz

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
PPM000159 PGS000062
(GRS_TC)
PSS000098|
European Ancestry|
2,063 individuals
PGP000045 |
Johnson L et al. PLoS One (2015)
Reported Trait: Serum total cholesterol (TC) levels β: 20.69 Beta (p-value): 0.0108 age, age^2, sex, GRS_HDL, GRS_LDL, GRS_TG Association (p-value; unadjusted for covariates) < 0.001
PPM000160 PGS000062
(GRS_TC)
PSS000097|
East Asian Ancestry|
666 individuals
PGP000045 |
Johnson L et al. PLoS One (2015)
Reported Trait: Serum total cholesterol (TC) levels β: 8.57 Beta (p-value): 0.583 age, age^2, sex, GRS_HDL, GRS_LDL, GRS_TG Association (p-value; unadjusted for covariates) < 0.001
PPM000161 PGS000062
(GRS_TC)
PSS000096|
African Ancestry|
1,355 individuals
PGP000045 |
Johnson L et al. PLoS One (2015)
Reported Trait: Serum total cholesterol (TC) levels β: 1.99 Beta (p-value): 0.852 age, age^2, sex, GRS_HDL, GRS_LDL, GRS_TG Association (p-value; unadjusted for covariates) < 0.001
PPM000162 PGS000062
(GRS_TC)
PSS000099|
Hispanic or Latin American Ancestry|
1,256 individuals
PGP000045 |
Johnson L et al. PLoS One (2015)
Reported Trait: Serum total cholesterol (TC) levels β: -2.62 Beta (p-value): 0.815 age, age^2, sex, GRS_HDL, GRS_LDL, GRS_TG Association (p-value; unadjusted for covariates) < 0.001
PPM000781 PGS000311
(GRS234_TC)
PSS000376|
European Ancestry|
1,354 individuals
PGP000092 |
Xie T et al. Circ Genom Precis Med (2020)
Reported Trait: Total cholesterol (mmol/l) : 0.1295 Sex, age, age^2
PPM001350 PGS000658
(PRS-TC)
PSS000593|
East Asian Ancestry|
4,917 individuals
PGP000121 |
Tam CHT et al. Genome Med (2021)
Reported Trait: Total cholesterol at baseline (log transformed) β: 0.042 (0.003) Pearson Correlation Coefficient (r): 0.186
Incremental R² (PRS and covariates vs. covariates-alone): 0.0393
age, sex, BMI, PCs
PPM001351 PGS000658
(PRS-TC)
PSS000589|
East Asian Ancestry|
1,941 individuals
PGP000121 |
Tam CHT et al. Genome Med (2021)
Reported Trait: Total cholesterol at baseline (log transformed) β: 0.036 (0.004) Pearson Correlation Coefficient (r): 0.187
Incremental R² (PRS and covariates vs. covariates-alone): 0.0332
age, sex, BMI, PCs
PPM001349 PGS000658
(PRS-TC)
PSS000587|
East Asian Ancestry|
426 individuals
PGP000121 |
Tam CHT et al. Genome Med (2021)
Reported Trait: Total cholesterol at baseline (log transformed) β: 0.043 (0.008) Pearson Correlation Coefficient (r): 0.251
Incremental R² (PRS and covariates vs. covariates-alone): 0.0506
age, sex, BMI, PCs
PPM001352 PGS000658
(PRS-TC)
PSS000591|
East Asian Ancestry|
865 individuals
PGP000121 |
Tam CHT et al. Genome Med (2021)
Reported Trait: Total cholesterol at baseline (log transformed) β: 0.034 (0.006) Pearson Correlation Coefficient (r): 0.173
Incremental R² (PRS and covariates vs. covariates-alone): 0.0298
age, sex, BMI, PCs
PPM001405 PGS000677
(snpnet.Cholesterol_adjstatins)
PSS000662|
African Ancestry|
6,014 individuals
PGP000128 |
Sinnott-Armstrong N et al. Nat Genet (2021)
Reported Trait: Cholesterol [mmol/L] (statin adjusted) : 0.1282
Spearman's ρ: 0.26
Age, sex, PCs(1-40)
PPM001440 PGS000677
(snpnet.Cholesterol_adjstatins)
PSS000663|
East Asian Ancestry|
1,082 individuals
PGP000128 |
Sinnott-Armstrong N et al. Nat Genet (2021)
Reported Trait: Cholesterol [mmol/L] (statin adjusted) : 0.17187
Spearman's ρ: 0.314
Age, sex, PCs(1-40)
PPM001475 PGS000677
(snpnet.Cholesterol_adjstatins)
PSS000664|
European Ancestry|
23,581 individuals
PGP000128 |
Sinnott-Armstrong N et al. Nat Genet (2021)
Reported Trait: Cholesterol [mmol/L] (statin adjusted) : 0.26423
Spearman's ρ: 0.421
Age, sex, PCs(1-40)
PPM001510 PGS000677
(snpnet.Cholesterol_adjstatins)
PSS000665|
South Asian Ancestry|
7,336 individuals
PGP000128 |
Sinnott-Armstrong N et al. Nat Genet (2021)
Reported Trait: Cholesterol [mmol/L] (statin adjusted) : 0.1266
Spearman's ρ: 0.3
Age, sex, PCs(1-40)
PPM001545 PGS000677
(snpnet.Cholesterol_adjstatins)
PSS000666|
European Ancestry|
63,794 individuals
PGP000128 |
Sinnott-Armstrong N et al. Nat Genet (2021)
Reported Trait: Cholesterol [mmol/L] (statin adjusted) : 0.26395
Spearman's ρ: 0.429
Age, sex, PCs(1-40)
PPM001574 PGS000677
(snpnet.Cholesterol_adjstatins)
PSS000798|
European Ancestry|
2,004 individuals
PGP000128 |
Sinnott-Armstrong N et al. Nat Genet (2021)
Reported Trait: Cholesterol [mmol/L] (statin adjusted) Spearman's ρ: 0.173 Age, sex
PPM001573 PGS000677
(snpnet.Cholesterol_adjstatins)
PSS000797|
European Ancestry|
2,129 individuals
PGP000128 |
Sinnott-Armstrong N et al. Nat Genet (2021)
Reported Trait: Cholesterol [mmol/L] (statin adjusted) Spearman's ρ: 0.184 Age, sex
PPM002237 PGS000831
(Total_cholesterol_PGS)
PSS001083|
Multi-ancestry (including European)|
2,531 individuals
PGP000210 |
Zubair N et al. Sci Rep (2019)
Reported Trait: Total cholesterol : 0.087 Age at baseline, sex, enrollment channel, PCs(1-7), observation season, observation vendor
PPM004378 PGS001201
(GBE_INI20030690)
PSS002841|
African Ancestry|
6,014 individuals
PGP000244 |
Tanigawa Y et al. medRxiv (2021)
|Pre
Reported Trait: Cholesterol : 0.07899
Incremental R2 (full-covars): 0.07608
PGS R2 (no covariates): 0.07703
age, sex Genotype PCs
PPM004379 PGS001201
(GBE_INI20030690)
PSS002842|
East Asian Ancestry|
1,579 individuals
PGP000244 |
Tanigawa Y et al. medRxiv (2021)
|Pre
Reported Trait: Cholesterol : 0.12715
Incremental R2 (full-covars): 0.11704
PGS R2 (no covariates): 0.12031
age, sex Genotype PCs
PPM004380 PGS001201
(GBE_INI20030690)
PSS002843|
European Ancestry|
23,579 individuals
PGP000244 |
Tanigawa Y et al. medRxiv (2021)
|Pre
Reported Trait: Cholesterol : 0.18581
Incremental R2 (full-covars): 0.18504
PGS R2 (no covariates): 0.18559
age, sex Genotype PCs
PPM004381 PGS001201
(GBE_INI20030690)
PSS002844|
South Asian Ancestry|
7,285 individuals
PGP000244 |
Tanigawa Y et al. medRxiv (2021)
|Pre
Reported Trait: Cholesterol : 0.11567
Incremental R2 (full-covars): 0.09371
PGS R2 (no covariates): 0.09595
age, sex Genotype PCs
PPM004382 PGS001201
(GBE_INI20030690)
PSS002845|
European Ancestry|
63,789 individuals
PGP000244 |
Tanigawa Y et al. medRxiv (2021)
|Pre
Reported Trait: Cholesterol : 0.19731
Incremental R2 (full-covars): 0.1973
PGS R2 (no covariates): 0.19718
age, sex Genotype PCs
PPM004768 PGS001202
(GBE_INI30690)
PSS003231|
African Ancestry|
6,097 individuals
PGP000244 |
Tanigawa Y et al. medRxiv (2021)
|Pre
Reported Trait: Cholesterol : 0.05843
Incremental R2 (full-covars): 0.04634
PGS R2 (no covariates): 0.05088
age, sex Genotype PCs
PPM004769 PGS001202
(GBE_INI30690)
PSS003232|
East Asian Ancestry|
1,616 individuals
PGP000244 |
Tanigawa Y et al. medRxiv (2021)
|Pre
Reported Trait: Cholesterol : 0.10583
Incremental R2 (full-covars): 0.07236
PGS R2 (no covariates): 0.07434
age, sex Genotype PCs
PPM004770 PGS001202
(GBE_INI30690)
PSS003233|
European Ancestry|
23,774 individuals
PGP000244 |
Tanigawa Y et al. medRxiv (2021)
|Pre
Reported Trait: Cholesterol : 0.13064
Incremental R2 (full-covars): 0.0977
PGS R2 (no covariates): 0.10022
age, sex Genotype PCs
PPM004771 PGS001202
(GBE_INI30690)
PSS003234|
South Asian Ancestry|
7,426 individuals
PGP000244 |
Tanigawa Y et al. medRxiv (2021)
|Pre
Reported Trait: Cholesterol : 0.07555
Incremental R2 (full-covars): 0.03907
PGS R2 (no covariates): 0.04215
age, sex Genotype PCs
PPM004772 PGS001202
(GBE_INI30690)
PSS003235|
European Ancestry|
64,473 individuals
PGP000244 |
Tanigawa Y et al. medRxiv (2021)
|Pre
Reported Trait: Cholesterol : 0.12915
Incremental R2 (full-covars): 0.09358
PGS R2 (no covariates): 0.09426
age, sex Genotype PCs

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
PSS002841 6,014 individuals African unspecified UKB
PSS002842 1,579 individuals East Asian UKB
PSS002843 23,579 individuals European non-white British ancestry UKB
PSS002844 7,285 individuals South Asian UKB
PSS002845 63,789 individuals European white British ancestry UKB
PSS003231 6,097 individuals African unspecified UKB
PSS003232 1,616 individuals East Asian UKB
PSS003233 23,774 individuals European non-white British ancestry UKB
PSS003234 7,426 individuals South Asian UKB
PSS003235 64,473 individuals European white British ancestry 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.
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)
NR 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
PSS000662 6,014 individuals African unspecified UKB
PSS000663 1,082 individuals East Asian UKB
PSS000664 23,581 individuals European Non-British White UKB
PSS000665 7,336 individuals South Asian UKB
PSS000666 63,794 individuals European
(British)
UKB
PSS000797 2,129 individuals European Participants self-identifying as white MESA
PSS000798 2,004 individuals European Participants self-identifying as white MESA