Polygenic Score (PGS) ID: PGS000115

Predicted Trait
Reported Trait low density lipoprotein cholesterol
Mapped Trait(s) low density lipoprotein cholesterol measurement (EFO_0004611)
Released in PGS: March 4, 2020

Score Details

Score Construction
PGS Name LDL-C_20
Variants
Original Genome Build hg38
Number of Variants 223
Development Method
Name Established lipid loci
Parameters Independent GWAS-significant SNVs
PGS Source
PGS Catalog Publication (PGP) ID PGP000053
Citation (link to publication) Trinder M et al. JAMA Cardiol (2020)

Contributing Samples

Source of Variant Associations (GWAS)
Study Identifiers Sample Numbers Sample Ancestry
GWAS Catalog: GCST006612
PubMed: 30275531
24,743 individuals Hispanic or Latin American
GWAS Catalog: GCST006612
PubMed: 30275531
57,332 individuals African American or Afro-Caribbean
GWAS Catalog: GCST006612
PubMed: 30275531
215,551 individuals European

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)
PGS Sample Set ID
(PSS ID)
Performance Source Trait PGS Effect Sizes
(per SD change)
PGS Classification Metrics Other Metrics Covariates Included in PGS Model PGS Performance: Other Relevant Information
PPM000264 PSS000184 PGP000053
Trinder M et al. (2020)
Reported Trait: Serum low density lipoprotein cholesterol (LDL-C) levels β: 28.01 : 0.09 age, sex, 4 PCs of genetic ancestry, genotyping method (array and batch)
PPM000265 PSS000183 PGP000053
Trinder M et al. (2020)
Reported Trait: Serum low density lipoprotein cholesterol (LDL-C) levels β: 21.73 : 0.06 age, sex, 4 PCs of genetic ancestry, genotyping method (array and batch)
PPM000266 PSS000181 PGP000053
Trinder M et al. (2020)
Reported Trait: Serum low density lipoprotein cholesterol (LDL-C) levels β: 17.4 : 0.04 age, sex, 4 PCs of genetic ancestry, genotyping method (array and batch)
PPM000267 PSS000185 PGP000053
Trinder M et al. (2020)
Reported Trait: Serum low density lipoprotein cholesterol (LDL-C) levels β: 27.78 : 0.09 age, sex, 4 PCs of genetic ancestry, genotyping method (array and batch)
PPM000268 PSS000182 PGP000053
Trinder M et al. (2020)
Reported Trait: Cardiovascular disease events Hazard Ratio (HR; top vs. bottom decile of risk): 1.35[1.3, 1.4] age, sex, 4 PCs of genetic ancestry, genotyping method (array and batch)

Evaluated Samples

PGS Sample Set ID
(PSS ID)
Detailed Phenotype Description Participant Follow-up Time Sample Numbers Age of Study Participants Sample Ancestry Additional Ancestry Description Cohort(s) Additional Sample/Cohort Information
PSS000181 LDL-C serum biochemistry was desribed previously (http://biobank.ndph.ox.ac.uk/showcase/showcase/docs/serum_biochemistry.pdf). 4,680 individuals,
45.8 % Male samples
Mean = 56.6 years
Sd = 8.1 years
African unspecified UKB Genotyping Array Cohort
PSS000182 Cardiovascular disease events were defined as coronary and carotid revascularization, myocardial infarction, ischemic stroke, and all-cause mortality. The CVD events occurring before and after enrollment were included. Events occurring prior to enrollment were identified by either self-reported medical history and/or previous hospital admission documented in an electronic health record.
[
  • 5,397 cases
  • , 42,448 controls
]
,
43.36 % Male samples
Mean = 56.64 years
Sd = 7.99 years
Other Combined analysis of European, East Asian and African unspecified  UKB Genotyping Array & Exome Sequencing Cohort
PSS000183 LDL-C serum biochemistry was desribed previously (http://biobank.ndph.ox.ac.uk/showcase/showcase/docs/serum_biochemistry.pdf). 10,640 individuals,
45.8 % Male samples
Mean = 56.6 years
Sd = 8.1 years
East Asian UKB Genotyping Array Cohort
PSS000184 LDL-C serum biochemistry was desribed previously (http://biobank.ndph.ox.ac.uk/showcase/showcase/docs/serum_biochemistry.pdf). 439,871 individuals,
45.8 % Male samples
Mean = 56.6 years
Sd = 8.1 years
European UKB Genotyping Array Cohort
PSS000185 LDL-C serum biochemistry was desribed previously (http://biobank.ndph.ox.ac.uk/showcase/showcase/docs/serum_biochemistry.pdf). 439,871 individuals,
45.8 % Male samples
Mean = 56.6 years
Sd = 8.1 years
European UKB Genotyping Array Cohort
PSS000185 LDL-C serum biochemistry was desribed previously (http://biobank.ndph.ox.ac.uk/showcase/showcase/docs/serum_biochemistry.pdf). 10,640 individuals,
45.8 % Male samples
Mean = 56.6 years
Sd = 8.1 years
East Asian UKB Genotyping Array Cohort
PSS000185 LDL-C serum biochemistry was desribed previously (http://biobank.ndph.ox.ac.uk/showcase/showcase/docs/serum_biochemistry.pdf). 4,680 individuals,
45.8 % Male samples
Mean = 56.6 years
Sd = 8.1 years
African unspecified UKB Genotyping Array Cohort