| Predicted Trait | |
| Reported Trait | LDL cholesterol |
| Mapped Trait(s) | low density lipoprotein cholesterol measurement (EFO_0004611) |
| 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 | |
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 |
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 |
|---|---|---|---|---|---|---|---|---|
| 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) | — | R²: 0.09 | 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) | — | R²: 0.06 | 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) | — | R²: 0.04 | 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) | — | R²: 0.09 | age, sex, 4 PCs of genetic ancestry, genotyping method (array and batch) | — |
| 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) | — |
| 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 coun... try 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 baselineShow more | 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 coun... try 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 baselineShow more | 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 coun... try 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 baselineShow more | 218 SNPs remained after QC |
| 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 coun... try 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 baselineShow more | 218 SNPs remained after QC |
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
|
|---|---|---|---|---|---|---|---|---|
| PSS000181 | LDL-C serum biochemistry was desribed previously (http://biobank.ndph.ox.ac.uk/showcase/showcase/doc... s/serum_biochemistry.pdf).Show more | — | 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 inf... arction, 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.Show more | — | [ ,
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/doc... s/serum_biochemistry.pdf).Show more | — | 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/doc... s/serum_biochemistry.pdf).Show more | — | 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/doc... s/serum_biochemistry.pdf).Show more | — | 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/doc... s/serum_biochemistry.pdf).Show more | — | 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/doc... s/serum_biochemistry.pdf).Show more | — | 4,680 individuals, 45.8 % Male samples | Mean = 56.6 years Sd = 8.1 years | African unspecified | — | UKB | Genotyping Array Cohort |
| PSS009577 | Self-reported statin-use. Uncontrolled hypercholesterolaemia was defined as having baseline LDL-chol... esterol >_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.Show more | Median = 11.4 years | [ ,
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-chol... esterol >_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.Show more | Median = 11.4 years | [ ,
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-chol... esterol >_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.Show more | Median = 11.4 years | [ ,
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-chol... esterol >_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.Show more | Median = 11.4 years | [ ,
58.5 % Male samples | Mean = 61.7 years | European (white British) | — | UKB | — |