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)

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

PGS Developed By This Publication

Polygenic Score ID & Name PGS Publication ID (PGP) Reported Trait Mapped Trait(s) (Ontology) Number of Variants Ancestry distribution
GWAS
Dev
Eval
 Scoring File (FTP Link)
PGS000658
(PRS-TC)
 PGP000121 |
Tam CHT et al. Genome Med (2021)
 Total cholesterol total cholesterol measurement 229
https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS000658/ScoringFiles/PGS000658.txt.gz
PGS000661
(PRS-LDL)
 PGP000121 |
Tam CHT et al. Genome Med (2021)
 LDL cholesterol low density lipoprotein cholesterol measurement 84
https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS000661/ScoringFiles/PGS000661.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
PGS000659
(PRS-TG)
 PGP000121 |
Tam CHT et al. Genome Med (2021)
 Triglycerides triglyceride measurement 142
https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS000659/ScoringFiles/PGS000659.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
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 —
PPM001353 PGS000659
(PRS-TG)
 PSS000587|
East Asian Ancestry|
426 individuals
 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|
East Asian Ancestry|
4,917 individuals
 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|
East Asian Ancestry|
1,941 individuals
 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 —
PPM001356 PGS000659
(PRS-TG)
 PSS000591|
East Asian Ancestry|
865 individuals
 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|
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 —
PPM001361 PGS000661
(PRS-LDL)
 PSS000588|
East Asian Ancestry|
426 individuals
 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 —
PPM001362 PGS000661
(PRS-LDL)
 PSS000594|
East Asian Ancestry|
4,917 individuals
 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 —
PPM001363 PGS000661
(PRS-LDL)
 PSS000590|
East Asian Ancestry|
1,941 individuals
 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|
East Asian Ancestry|
865 individuals
 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|
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 —

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
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)		 — NR 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)		 — 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 —