PGS Catalog - PGS000660 / HDL cholesterol (Polygenic Score)

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	—