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 Catalog: March 4, 2020
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Score Details

Score Construction
PGS Name LDL-C_20
Development Method
Name Established lipid loci
Parameters Independent GWAS-significant SNVs
Variants
Original Genome Build GRCh37
Number of Variants 223
Effect Weight Type NR
PGS Source
PGS Catalog Publication (PGP) ID PGP000053
Citation (link to publication) Trinder M et al. JAMA Cardiol (2020)
Ancestry Distribution
Source of Variant
Associations (GWAS)
European: 72.4%
African: 19.3%
Hispanic or Latin American: 8.3%
297,626 individuals (100%)
PGS Evaluation
European: 55.6%
Multi-ancestry (including European): 22.2%
  • European
  • East Asian
  • African
African: 11.1%
East Asian: 11.1%
9 Sample Sets

Development Samples

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

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
PPM000268 PSS000182|
Multi-ancestry (including European)|
47,845 individuals
PGP000053 |
Trinder M et al. JAMA Cardiol (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)
PPM000267 PSS000185|
Multi-ancestry (including European)|
455,191 individuals
PGP000053 |
Trinder M et al. JAMA Cardiol (2020)
Reported Trait: Serum low density lipoprotein cholesterol (LDL-C) levels β: 27.78 (0.18) : 0.09 age, sex, 4 PCs of genetic ancestry, genotyping method (array and batch)
PPM000266 PSS000181|
African Ancestry|
4,680 individuals
PGP000053 |
Trinder M et al. JAMA Cardiol (2020)
Reported Trait: Serum low density lipoprotein cholesterol (LDL-C) levels β: 17.4 (1.91) : 0.04 age, sex, 4 PCs of genetic ancestry, genotyping method (array and batch)
PPM000265 PSS000183|
East Asian Ancestry|
10,640 individuals
PGP000053 |
Trinder M et al. JAMA Cardiol (2020)
Reported Trait: Serum low density lipoprotein cholesterol (LDL-C) levels β: 21.73 (1.25) : 0.06 age, sex, 4 PCs of genetic ancestry, genotyping method (array and batch)
PPM000264 PSS000184|
European Ancestry|
439,871 individuals
PGP000053 |
Trinder M et al. JAMA Cardiol (2020)
Reported Trait: Serum low density lipoprotein cholesterol (LDL-C) levels β: 28.01 (0.18) : 0.09 age, sex, 4 PCs of genetic ancestry, genotyping method (array and batch)
PPM012862 PSS009579|
European Ancestry|
33,787 individuals
PGP000284 |
Tapela NM et al. Eur J Prev Cardiol (2021)
|Ext.
Reported Trait: Incident stroke in statin treatment Hazard Ratio (HR, top vs. bottom quintile): 0.93 [0.77, 1.12] age, sex, socioeconomic characteristics (education, occupation, Townsend deprivation score, and country of residence), metabolic and lifestyle CVD risk factors (smoking status, body mass index, physical activity in METS, and weekly alcohol consumption), family history of CVD (diagnosis at any age), and the first four principal components of genetic ancestry, genotyping array and systolic blood pressure at baseline 218 SNPs remained after QC
PPM012861 PSS009578|
European Ancestry|
33,787 individuals
PGP000284 |
Tapela NM et al. Eur J Prev Cardiol (2021)
|Ext.
Reported Trait: Incident myocardial infarction in statin treatment Hazard Ratio (HR, top vs. bottom quintile): 1.08 [0.95, 1.23] age, sex, socioeconomic characteristics (education, occupation, Townsend deprivation score, and country of residence), metabolic and lifestyle CVD risk factors (smoking status, body mass index, physical activity in METS, and weekly alcohol consumption), family history of CVD (diagnosis at any age), and the first four principal components of genetic ancestry, genotyping array and systolic blood pressure at baseline 218 SNPs remained after QC
PPM012860 PSS009577|
European Ancestry|
33,787 individuals
PGP000284 |
Tapela NM et al. Eur J Prev Cardiol (2021)
|Ext.
Reported Trait: Incident major adverse cardiovascular events in statin treatment Hazard Ratio (HR, top vs. bottom quintile): 1.03 [0.92, 1.14] age, sex, socioeconomic characteristics (education, occupation, Townsend deprivation score, and country of residence), metabolic and lifestyle CVD risk factors (smoking status, body mass index, physical activity in METS, and weekly alcohol consumption), family history of CVD (diagnosis at any age), and the first four principal components of genetic ancestry, genotyping array and systolic blood pressure at baseline 218 SNPs remained after QC
PPM012859 PSS009580|
European Ancestry|
33,787 individuals
PGP000284 |
Tapela NM et al. Eur J Prev Cardiol (2021)
|Ext.
Reported Trait: Uncontrolled hypercholesterolaemia Odds Ratio (OR, top vs. bottom quintile): 2.78 [2.58, 3.0] age, sex, socioeconomic characteristics (education, occupation, Townsend deprivation score, and country of residence), metabolic and lifestyle CVD risk factors (smoking status, body mass index, physical activity in METS, and weekly alcohol consumption), family history of CVD (diagnosis at any age), and the first four principal components of genetic ancestry, genotyping array and systolic blood pressure at baseline 218 SNPs remained after QC

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
PSS009577 Self-reported statin-use. Uncontrolled hypercholesterolaemia was defined as having baseline LDL-cholesterol >_3 mmol/L, among individuals in the treated hypercholesterolaemia sub-cohort. We used prospective follow-up data to assess the composite outcome of incident major adverse cardiovascular events (MACE), which we defined as the first non-fatal stroke (ischaemic or haemorrhagic), non-fatal myocardial infarction, or fatal cardiovascular events, or disease-modifying cardiovascular procedures. We identified MACE components using International Classification of Diseases (ICD-9 and ICD-10) and the Office of Population Censuses and Surveys Classification of Interventions and Procedures version 4 (OPCS-4) codes from Hospital Episodes Statistics (HES) data, and death registries data. Median = 11.4 years
[
  • 3,565 cases
  • , 30,222 controls
]
,
58.5 % Male samples
Mean = 61.7 years European
(white British)
UKB
PSS009578 Self-reported statin-use. Uncontrolled hypercholesterolaemia was defined as having baseline LDL-cholesterol >_3 mmol/L, among individuals in the treated hypercholesterolaemia sub-cohort. We used prospective follow-up data to assess the composite outcome of incident major adverse cardiovascular events (MACE), which we defined as the first non-fatal stroke (ischaemic or haemorrhagic), non-fatal myocardial infarction, or fatal cardiovascular events, or disease-modifying cardiovascular procedures. We identified MACE components using International Classification of Diseases (ICD-9 and ICD-10) and the Office of Population Censuses and Surveys Classification of Interventions and Procedures version 4 (OPCS-4) codes from Hospital Episodes Statistics (HES) data, and death registries data. Median = 11.4 years
[
  • 2,358 cases
  • , 31,429 controls
]
,
58.5 % Male samples
Mean = 61.7 years European
(white British)
UKB
PSS009579 Self-reported statin-use. Uncontrolled hypercholesterolaemia was defined as having baseline LDL-cholesterol >_3 mmol/L, among individuals in the treated hypercholesterolaemia sub-cohort. We used prospective follow-up data to assess the composite outcome of incident major adverse cardiovascular events (MACE), which we defined as the first non-fatal stroke (ischaemic or haemorrhagic), non-fatal myocardial infarction, or fatal cardiovascular events, or disease-modifying cardiovascular procedures. We identified MACE components using International Classification of Diseases (ICD-9 and ICD-10) and the Office of Population Censuses and Surveys Classification of Interventions and Procedures version 4 (OPCS-4) codes from Hospital Episodes Statistics (HES) data, and death registries data. Median = 11.4 years
[
  • 1,207 cases
  • , 32,580 controls
]
,
58.5 % Male samples
Mean = 61.7 years European
(white British)
UKB
PSS009580 Self-reported statin-use. Uncontrolled hypercholesterolaemia was defined as having baseline LDL-cholesterol >_3 mmol/L, among individuals in the treated hypercholesterolaemia sub-cohort. We used prospective follow-up data to assess the composite outcome of incident major adverse cardiovascular events (MACE), which we defined as the first non-fatal stroke (ischaemic or haemorrhagic), non-fatal myocardial infarction, or fatal cardiovascular events, or disease-modifying cardiovascular procedures. We identified MACE components using International Classification of Diseases (ICD-9 and ICD-10) and the Office of Population Censuses and Surveys Classification of Interventions and Procedures version 4 (OPCS-4) codes from Hospital Episodes Statistics (HES) data, and death registries data. Median = 11.4 years
[
  • 11,767 cases
  • , 22,020 controls
]
,
58.5 % Male samples
Mean = 61.7 years European
(white British)
UKB
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
European, East Asian, 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