Polygenic Score (PGS) ID: PGS000660

Predicted Trait
Reported Trait HDL cholesterol
Mapped Trait(s) high density lipoprotein cholesterol measurement (EFO_0004612)
Released in PGS Catalog: Feb. 23, 2021
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Score Details

Score Construction
PGS Name PRS-HDL
Development Method
Name LD-pruning and p-value thresholding
Parameters r2 = 0.2 and p = 1.0E-04
Variants
Original Genome Build GRCh37
Number of Variants 549
Effect Weight Type beta
PGS Source
PGS Catalog Publication (PGP) ID PGP000121
Citation (link to publication) Tam CHT et al. Genome Med (2021)
Ancestry Distribution
Source of Variant
Associations (GWAS)
East Asian: 100%
70,657 individuals (100%)
Score Development/Training
East Asian: 100%
4,271 individuals (100%)
PGS Evaluation
East Asian: 100%
4 Sample Sets

Development Samples

Source of Variant Associations (GWAS)
Study Identifiers Sample Numbers Sample Ancestry Cohort(s)
GWAS Catalog: GCST006005
Europe PMC: 29403010
70,657 individuals,
57.4 % Male samples
East Asian BBJ
Score Development/Training
Study Identifiers Sample Numbers Sample Ancestry Cohort(s) Phenotype Definitions & Methods Age of Study Participants Participant Follow-up Time Additional Ancestry Description Additional Sample/Cohort Information
Europe PMC: 28279981
909 individuals,
51.9 % Male samples
East Asian
(Chinese)
HAPO Measured using fasting blood samples Mean = 6.96 years
Sd = 0.44 years
HAPO HK Offspring
Europe PMC: 17088339
1,973 individuals,
45.0 % Male samples
East Asian
(Chinese)
NR Measured using fasting blood samples Mean = 15.6 years
Sd = 2.04 years
Adolescent cohort
Europe PMC: 16718283
441 individuals,
49.7 % Male samples
East Asian
(Chinese)
NR Measured using fasting blood samples Mean = 44.9 years
Sd = 9.8 years
Adults
Europe PMC: 28279981
948 individuals,
0.0 % Male samples
East Asian
(Chinese)
HAPO Measured using fasting blood samples Mean = 37.7 years
Sd = 4.64 years
HAPO Mothers

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)
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
PPM001357 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 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 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 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

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
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
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