Polygenic Score (PGS) ID: PGS000889

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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Terms and Licenses
PGS obtained from the Catalog should be cited appropriately, and used in accordance with any licensing restrictions set by the authors. See EBI Terms of Use (https://www.ebi.ac.uk/about/terms-of-use/) for additional details.

Score Details

Score Construction
PGS Name GLGC_2021_ALL_LDL_PRS_weights_PT
Development Method
Name Pruning and Thresholding (P+T)
Parameters r2=0.1 distance=500kb p=5e-4
Variants
Original Genome Build hg19
Number of Variants 9,009
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)
Multi-ancestry (including European): 100%
  • African
  • East Asian
  • European
  • Hispanic or Latin American
  • South Asian
1,088,526 individuals (100%)
PGS Evaluation
African: 55%
European: 15%
East Asian: 10%
Hispanic or Latin American: 5%
Additional Asian Ancestries: 5%
Multi-ancestry (including European): 5%
  • European
  • African
  • East Asian
  • South Asian
South Asian: 5%
20 Sample Sets

Development Samples

Source of Variant Associations (GWAS)
Study Identifiers Sample Numbers Sample Ancestry Cohort(s)
GWAS Catalog: GLGC2021
 1,088,526 individuals African unspecified, East Asian, European, Hispanic or Latin American, South Asian 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
PPM002588 PSS001156|
African Ancestry|
18,251 individuals
 PGP000230 |
Graham SE et al. Nature (2021)
 Reported Trait: Mean LDL cholesterol — — R²: 0.162 sex, PC1-4, birth year, and mean age —
PPM002589 PSS001157|
Additional Asian Ancestries|
4,155 individuals
 PGP000230 |
Graham SE et al. Nature (2021)
 Reported Trait: Mean LDL cholesterol — — R²: 0.1 sex, PC1-4, birth year, and mean age —
PPM002590 PSS001158|
European Ancestry|
68,381 individuals
 PGP000230 |
Graham SE et al. Nature (2021)
 Reported Trait: Mean LDL cholesterol — — R²: 0.158 sex, PC1-4, birth year, and mean age —
PPM002546 PSS001144|
African Ancestry|
4,273 individuals
 PGP000230 |
Graham SE et al. Nature (2021)
 Reported Trait: Baseline LDL cholesterol — — R²: 0.114 age, sex, PC1-3 —
PPM002547 PSS001145|
African Ancestry|
707 individuals
 PGP000230 |
Graham SE et al. Nature (2021)
 Reported Trait: Baseline LDL cholesterol — — R²: 0.067 age, sex, PC1-3 —
PPM002548 PSS001146|
African Ancestry|
3,566 individuals
 PGP000230 |
Graham SE et al. Nature (2021)
 Reported Trait: Baseline LDL cholesterol — — R²: 0.123 age, sex, PC1-3 —
PPM002552 PSS001147|
African Ancestry|
10,460 individuals
 PGP000230 |
Graham SE et al. Nature (2021)
 Reported Trait: Baseline LDL cholesterol — — R²: 0.173 age, sex, PC1-6 —
PPM002555 PSS001148|
African Ancestry|
1,745 individuals
 PGP000230 |
Graham SE et al. Nature (2021)
 Reported Trait: Baseline LDL cholesterol — — R²: 0.069 age, sex, PC1-6 —
PPM002558 PSS001149|
African Ancestry|
4,972 individuals
 PGP000230 |
Graham SE et al. Nature (2021)
 Reported Trait: Baseline LDL cholesterol — — R²: 0.108 age, sex, PC1-6 —
PPM002561 PSS001150|
African Ancestry|
3,743 individuals
 PGP000230 |
Graham SE et al. Nature (2021)
 Reported Trait: Baseline LDL cholesterol — — R²: 0.075 age, sex, and PC1-4 —
PPM002569 PSS001152|
East Asian Ancestry|
118,260 individuals
 PGP000230 |
Graham SE et al. Nature (2021)
 Reported Trait: Baseline LDL cholesterol — — R²: 0.095 age, sex, and recruitment area —
PPM002578 PSS001153|
African Ancestry|
1,341 individuals
 PGP000230 |
Graham SE et al. Nature (2021)
 Reported Trait: Mean LDL cholesterol — — R²: 0.122 sex, batch, PC1-4, and birth year —
PPM002579 PSS001154|
European Ancestry|
17,190 individuals
 PGP000230 |
Graham SE et al. Nature (2021)
 Reported Trait: Mean LDL cholesterol — — R²: 0.13 sex, batch, PC1-4, and birth year —
PPM002591 PSS001159|
Hispanic or Latin American Ancestry|
7,669 individuals
 PGP000230 |
Graham SE et al. Nature (2021)
 Reported Trait: Mean LDL cholesterol — — R²: 0.134 sex, PC1-4, birth year, and mean age —
PPM002617 PSS001160|
African Ancestry|
2,138 individuals
 PGP000230 |
Graham SE et al. Nature (2021)
 Reported Trait: Mean LDL cholesterol — — R²: 0.132 birth year, sex, and PC1-4 —
PPM002625 PSS001162|
Multi-ancestry (including European)|
461,918 individuals
 PGP000230 |
Graham SE et al. Nature (2021)
 Reported Trait: Baseline LDL cholesterol — — R²: 0.182 sex, batch, age at initial assessment, PCs1-4 —
PPM002564 PSS001151|
South Asian Ancestry|
15,242 individuals
 PGP000230 |
Graham SE et al. Nature (2021)
 Reported Trait: Max LDL cholesterol — — R²: 0.105 age, sex, and PC1-10 —
PPM002619 PSS001161|
East Asian Ancestry|
28,217 individuals
 PGP000230 |
Graham SE et al. Nature (2021)
 Reported Trait: Baseline LDL cholesterol — — R²: 0.098 sex, age, recruitment method, and PC1-20 —
PPM020883 PSS011442|
European Ancestry|
564 individuals
 PGP000599 |
Guarischi-Sousa R et al. Circ Genom Precis Med (2023)
|Ext.		 Reported Trait: Raised coronary lesion OR: 1.42 [1.16, 1.73] — — — —
PPM020891 PSS011441|
African Ancestry|
504 individuals
 PGP000599 |
Guarischi-Sousa R et al. Circ Genom Precis Med (2023)
|Ext.		 Reported Trait: Raised coronary lesion OR: 1.18 [0.95, 1.47] — — — —

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
PSS011441 — —
[
  • 165 cases
  • , 339 controls
]
,
82.0 % Male samples
 Mean = 27.5 years African unspecified — PDAY —
PSS011442 — —
[
  • 181 cases
  • , 383 controls
]
,
77.0 % Male samples
 Mean = 26.7 years European — PDAY —
PSS001144 — — 4,273 individuals — African unspecified — AADM —
PSS001145 — — 707 individuals — African unspecified — AADM —
PSS001146 — — 3,566 individuals — African unspecified — AADM —
PSS001147 — — 10,460 individuals — African unspecified — AWI-Gen —
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 —
PSS001161 — — 28,217 individuals — East Asian — ToMMo Only participants from Miyagi Prefecture were included
PSS001162 — — 461,918 individuals — European, African unspecified, East Asian, South Asian — UKB —