PGS Publication: PGP000121

Publication Information (EuropePMC)
Title Development of genome-wide polygenic risk scores for lipid traits and clinical applications for dyslipidemia, subclinical atherosclerosis, and diabetes cardiovascular complications among East Asians.
PubMed ID 33608049(Europe PMC)
doi 10.1186/s13073-021-00831-z
Publication Date Feb. 19, 2021
Journal Genome Med
Author(s) Tam CHT, Lim CKP, Luk AOY, Ng ACW, Lee HM, Jiang G, Lau ESH, Fan B, Wan R, Kong APS, Tam WH, Ozaki R, Chow EYK, Lee KF, Siu SC, Hui G, Tsang CC, Lau KP, Leung JYY, Tsang MW, Kam G, Lau IT, Li JKY, Yeung VTF, Lau E, Lo S, Fung S, Cheng YL, Chow CC, Hu M, Yu W, Tsui SKW, Huang Y, Lan H, Szeto CC, Tang NLS, Ng MCY, So WY, Tomlinson B, Chan JCN, Ma RCW, Hong Kong Diabetes Register TRS Study Group, Hong Kong Diabetes Biobank Study Group.
Released in PGS Catalog: Feb. 23, 2021

Associated Polygenic Score(s)

PGS Developed By This Publication

Polygenic Score (PGS) ID PGS Name PGS Publication (PGP) ID Reported Trait Mapped Trait(s) (Ontology) Number of Variants PGS Scoring File (FTP Link)
PGS000659 PRS-TG PGP000121
Tam CHT et al. Genome Med (2021)
Triglycerides triglyceride measurement 142 http://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS000659/ScoringFiles/PGS000659.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
PGS000661 PRS-LDL PGP000121
Tam CHT et al. Genome Med (2021)
LDL choldesterol low density lipoprotein cholesterol measurement 84 http://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS000661/ScoringFiles/PGS000661.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

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 ID)
Evaluated Score PGS Sample Set ID
(PSS ID)
Performance Source Trait PGS Effect Sizes
(per SD change)
PGS Classification Metrics Other Metrics Covariates Included in the Model PGS Performance: Other Relevant Information
PPM001362 PGS000661
(PRS-LDL)
PSS000594 PGP000121
Tam CHT et al. Genome Med (2021)
Reported Trait: LDL choldesterol at baseline (log transformed) β: 0.059 (0.004) Pearson Correlation Coefficient (r): 0.178
Incremental R² (PRS and covariates vs. covariates-alone): 0.0351
age, sex, BMI, PCs
PPM001356 PGS000659
(PRS-TG)
PSS000591 PGP000121
Tam CHT et al. Genome Med (2021)
Reported Trait: Triglycerides at baseline (log transformed) β: 0.14 (0.019) Pearson Correlation Coefficient (r): 0.231
Incremental R² (PRS and covariates vs. covariates-alone): 0.0558
age, sex, BMI, PCs
PPM001357 PGS000660
(PRS-HDL)
PSS000587 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 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 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 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
PPM001361 PGS000661
(PRS-LDL)
PSS000588 PGP000121
Tam CHT et al. Genome Med (2021)
Reported Trait: LDL choldesterol at baseline (log transformed) β: 0.072 (0.012) Pearson Correlation Coefficient (r): 0.255
Incremental R² (PRS and covariates vs. covariates-alone): 0.0672
age, sex, BMI, PCs
PPM001350 PGS000658
(PRS-TC)
PSS000593 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 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
PPM001353 PGS000659
(PRS-TG)
PSS000587 PGP000121
Tam CHT et al. Genome Med (2021)
Reported Trait: Triglycerides at baseline (log transformed) β: 0.133 (0.023) Pearson Correlation Coefficient (r): 0.251
Incremental R² (PRS and covariates vs. covariates-alone): 0.0514
age, sex, BMI, PCs
PPM001354 PGS000659
(PRS-TG)
PSS000593 PGP000121
Tam CHT et al. Genome Med (2021)
Reported Trait: Triglycerides at baseline (log transformed) β: 0.165 (0.008) Pearson Correlation Coefficient (r): 0.2
Incremental R² (PRS and covariates vs. covariates-alone): 0.0731
age, sex, BMI, PCs
PPM001355 PGS000659
(PRS-TG)
PSS000589 PGP000121
Tam CHT et al. Genome Med (2021)
Reported Trait: Triglycerides at baseline (log transformed) β: 0.133 (0.013) Pearson Correlation Coefficient (r): 0.209
Incremental R² (PRS and covariates vs. covariates-alone): 0.05
age, sex, BMI, PCs
PPM001363 PGS000661
(PRS-LDL)
PSS000590 PGP000121
Tam CHT et al. Genome Med (2021)
Reported Trait: LDL choldesterol at baseline (log transformed) β: 0.054 (0.006) Pearson Correlation Coefficient (r): 0.19
Incremental R² (PRS and covariates vs. covariates-alone): 0.036
age, sex, BMI, PCs
PPM001364 PGS000661
(PRS-LDL)
PSS000592 PGP000121
Tam CHT et al. Genome Med (2021)
Reported Trait: LDL choldesterol at baseline (log transformed) β: 0.058 (0.01) Pearson Correlation Coefficient (r): 0.195
Incremental R² (PRS and covariates vs. covariates-alone): 0.0374
age, sex, BMI, PCs
PPM001349 PGS000658
(PRS-TC)
PSS000587 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 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

Evaluated Samples

PGS Sample Set ID
(PSS ID)
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
PSS000590 Derived from the Friedewald’s formula 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
PSS000592 Derived from the Friedewald’s formula 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
PSS000594 Derived from the Friedewald’s formula 4,917 individuals,
44.9 % Male samples
Mean = 56.3 years
Sd = 13.5 years
East Asian
(Chinese)
HKDR
PSS000587 Measured using fasting blood samples 426 individuals,
46.0 % Male samples
Mean = 43.3 years
Sd = 11.4 years
East Asian
(Chinese)
Adults
PSS000588 Derived from the Friedewald’s formula 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