PGS Catalog - PGS000661 / LDL cholesterol (Polygenic Score)

Polygenic Score (PGS) ID: PGS000661

Predicted Trait
Reported Trait	LDL cholesterol
Mapped Trait(s)	low density lipoprotein cholesterol measurement (EFO_0004611)

Released in PGS Catalog: Feb. 23, 2021

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Score Details

Score Construction
PGS Name	PRS-LDL
Development Method
Name	LD-pruning and p-value thresholding
Parameters	r2 = 0.2 and p = 5.0E-08
Variants
Original Genome Build	GRCh37
Number of Variants	84
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% 72,866 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: GCST006004 Europe PMC: 29403010	72,866 individuals, 57.2 % 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	Derived from the Friedewald’s formula	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	Derived from the Friedewald’s formula	Mean = 15.6 years Sd = 2.04 years	—	—	Adolescent cohort
Europe PMC: 16718283	441 individuals, 49.7 % Male samples	East Asian (Chinese)	NR	Derived from the Friedewald’s formula	Mean = 44.9 years Sd = 9.8 years	—	—	Adults
Europe PMC: 28279981	948 individuals, 0.0 % Male samples	East Asian (Chinese)	HAPO	Derived from the Friedewald’s formula	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
PPM001361	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	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	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	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	—

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	—
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	—
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	—
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