Polygenic Score (PGS) ID: PGS000887

Predicted Trait
Reported Trait LDL cholesterol
Mapped Trait(s) low density lipoprotein cholesterol measurement (EFO_0004611)
Released in PGS Catalog: Dec. 10, 2021
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Score Details

Score Construction
PGS Name GLGC_2021_AFR_LDL_PRS_weights_PT
Development Method
Name Pruning and Thresholding (P+T)
Parameters r2=0.1 distance=250kb p=5e-9
Variants
Original Genome Build hg19
Number of Variants 295
Effect Weight Type beta
PGS Source
PGS Catalog Publication (PGP) ID PGP000230
Citation (link to publication) Graham SE et al. Nature (2021)
Ancestry Distribution
Source of Variant
Associations (GWAS)
African: 100%
87,760 individuals (100%)
PGS Evaluation
African: 62.5%
European: 12.5%
Hispanic or Latin American: 6.2%
Additional Asian Ancestries: 6.2%
East Asian: 6.2%
South Asian: 6.2%
16 Sample Sets

Development Samples

Source of Variant Associations (GWAS)
Study Identifiers Sample Numbers Sample Ancestry Cohort(s)
GWAS Catalog: GLGC2021
 87,760 individuals African unspecified 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
PPM002545 PSS001146|
African Ancestry|
3,566 individuals
 PGP000230 |
Graham SE et al. Nature (2021)
 Reported Trait: Baseline LDL cholesterol — — R²: 0.125 age, sex, PC1-3 —
PPM002557 PSS001149|
African Ancestry|
4,972 individuals
 PGP000230 |
Graham SE et al. Nature (2021)
 Reported Trait: Baseline LDL cholesterol — — R²: 0.128 age, sex, PC1-6 —
PPM002560 PSS001150|
African Ancestry|
3,743 individuals
 PGP000230 |
Graham SE et al. Nature (2021)
 Reported Trait: Baseline LDL cholesterol — — R²: 0.076 age, sex, and PC1-4 —
PPM002563 PSS001151|
South Asian Ancestry|
15,242 individuals
 PGP000230 |
Graham SE et al. Nature (2021)
 Reported Trait: Max LDL cholesterol — — R²: 0.069 age, sex, and PC1-10 —
PPM002568 PSS001152|
East Asian Ancestry|
118,260 individuals
 PGP000230 |
Graham SE et al. Nature (2021)
 Reported Trait: Baseline LDL cholesterol — — R²: 0.051 age, sex, and recruitment area —
PPM002574 PSS001153|
African Ancestry|
1,341 individuals
 PGP000230 |
Graham SE et al. Nature (2021)
 Reported Trait: Mean LDL cholesterol — — R²: 0.115 sex, batch, PC1-4, and birth year —
PPM002575 PSS001154|
European Ancestry|
17,190 individuals
 PGP000230 |
Graham SE et al. Nature (2021)
 Reported Trait: Mean LDL cholesterol — — R²: 0.074 sex, batch, PC1-4, and birth year —
PPM002584 PSS001156|
African Ancestry|
18,251 individuals
 PGP000230 |
Graham SE et al. Nature (2021)
 Reported Trait: Mean LDL cholesterol — — R²: 0.148 sex, PC1-4, birth year, and mean age —
PPM002585 PSS001157|
Additional Asian Ancestries|
4,155 individuals
 PGP000230 |
Graham SE et al. Nature (2021)
 Reported Trait: Mean LDL cholesterol — — R²: 0.063 sex, PC1-4, birth year, and mean age —
PPM002587 PSS001159|
Hispanic or Latin American Ancestry|
7,669 individuals
 PGP000230 |
Graham SE et al. Nature (2021)
 Reported Trait: Mean LDL cholesterol — — R²: 0.071 sex, PC1-4, birth year, and mean age —
PPM002616 PSS001160|
African Ancestry|
2,138 individuals
 PGP000230 |
Graham SE et al. Nature (2021)
 Reported Trait: Mean LDL cholesterol — — R²: 0.129 birth year, sex, and PC1-4 —
PPM002629 PSS001163|
African Ancestry|
6,863 individuals
 PGP000230 |
Graham SE et al. Nature (2021)
 Reported Trait: Baseline LDL cholesterol — — R²: 0.175 sex, batch, age at initial assessment, PCs1-4 —
PPM002543 PSS001144|
African Ancestry|
4,273 individuals
 PGP000230 |
Graham SE et al. Nature (2021)
 Reported Trait: Baseline LDL cholesterol — — R²: 0.118 age, sex, PC1-3 —
PPM002544 PSS001145|
African Ancestry|
707 individuals
 PGP000230 |
Graham SE et al. Nature (2021)
 Reported Trait: Baseline LDL cholesterol — — R²: 0.101 age, sex, PC1-3 —
PPM002554 PSS001148|
African Ancestry|
1,745 individuals
 PGP000230 |
Graham SE et al. Nature (2021)
 Reported Trait: Baseline LDL cholesterol — — R²: 0.085 age, sex, PC1-6 —
PPM002586 PSS001158|
European Ancestry|
68,381 individuals
 PGP000230 |
Graham SE et al. Nature (2021)
 Reported Trait: Mean LDL cholesterol — — R²: 0.103 sex, PC1-4, birth year, and mean age —

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
PSS001144 — — 4,273 individuals — African unspecified — AADM —
PSS001145 — — 707 individuals — African unspecified — AADM —
PSS001146 — — 3,566 individuals — African unspecified — AADM —
PSS001148 — — 1,745 individuals — African unspecified — AWI-Gen —
PSS001149 — — 4,972 individuals — Sub-Saharan African — AWI-Gen —
PSS001150 — — 3,743 individuals — African unspecified — AWI-Gen —
PSS001151 — — 15,242 individuals — South Asian — G&H —
PSS001152 — — 118,260 individuals — East Asian — KoGES —
PSS001153 — — 1,341 individuals — African American or Afro-Caribbean — MGI —
PSS001154 — — 17,190 individuals — European — MGI —
PSS001156 — — 18,251 individuals — African American or Afro-Caribbean — MVP Subset not used in discovery dataset
PSS001157 — — 4,155 individuals — Asian unspecified — MVP Subset not used in discovery dataset
PSS001158 — — 68,381 individuals — European — MVP Subset not used in discovery dataset
PSS001159 — — 7,669 individuals — Hispanic or Latin American — MVP Subset not used in discovery dataset
PSS001160 — — 2,138 individuals — African American or Afro-Caribbean — PMB —
PSS001163 — — 6,863 individuals — African unspecified — UKB —