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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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_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)
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Study Identifiers
Sample Numbers
Sample Ancestry
Cohort(s)
GWAS Catalog: GLGC2021
87,760 individualsAfrican unspecifiedNR
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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.

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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
PPM002543PSS001144|
African Ancestry|
4,273 individuals
PGP000230 |
Graham SE et al. Nature (2021)
Reported Trait: Baseline LDL cholesterol: 0.118age, sex, PC1-3
PPM002544PSS001145|
African Ancestry|
707 individuals
PGP000230 |
Graham SE et al. Nature (2021)
Reported Trait: Baseline LDL cholesterol: 0.101age, sex, PC1-3
PPM002545PSS001146|
African Ancestry|
3,566 individuals
PGP000230 |
Graham SE et al. Nature (2021)
Reported Trait: Baseline LDL cholesterol: 0.125age, sex, PC1-3
PPM002554PSS001148|
African Ancestry|
1,745 individuals
PGP000230 |
Graham SE et al. Nature (2021)
Reported Trait: Baseline LDL cholesterol: 0.085age, sex, PC1-6
PPM002557PSS001149|
African Ancestry|
4,972 individuals
PGP000230 |
Graham SE et al. Nature (2021)
Reported Trait: Baseline LDL cholesterol: 0.128age, sex, PC1-6
PPM002560PSS001150|
African Ancestry|
3,743 individuals
PGP000230 |
Graham SE et al. Nature (2021)
Reported Trait: Baseline LDL cholesterol: 0.076age, sex, and PC1-4
PPM002563PSS001151|
South Asian Ancestry|
15,242 individuals
PGP000230 |
Graham SE et al. Nature (2021)
Reported Trait: Max LDL cholesterol: 0.069age, sex, and PC1-10
PPM002568PSS001152|
East Asian Ancestry|
118,260 individuals
PGP000230 |
Graham SE et al. Nature (2021)
Reported Trait: Baseline LDL cholesterol: 0.051age, sex, and recruitment area
PPM002574PSS001153|
African Ancestry|
1,341 individuals
PGP000230 |
Graham SE et al. Nature (2021)
Reported Trait: Mean LDL cholesterol: 0.115sex, batch, PC1-4, and birth year
PPM002575PSS001154|
European Ancestry|
17,190 individuals
PGP000230 |
Graham SE et al. Nature (2021)
Reported Trait: Mean LDL cholesterol: 0.074sex, batch, PC1-4, and birth year
PPM002584PSS001156|
African Ancestry|
18,251 individuals
PGP000230 |
Graham SE et al. Nature (2021)
Reported Trait: Mean LDL cholesterol: 0.148sex, PC1-4, birth year, and mean age
PPM002585PSS001157|
Additional Asian Ancestries|
4,155 individuals
PGP000230 |
Graham SE et al. Nature (2021)
Reported Trait: Mean LDL cholesterol: 0.063sex, PC1-4, birth year, and mean age
PPM002586PSS001158|
European Ancestry|
68,381 individuals
PGP000230 |
Graham SE et al. Nature (2021)
Reported Trait: Mean LDL cholesterol: 0.103sex, PC1-4, birth year, and mean age
PPM002587PSS001159|
Hispanic or Latin American Ancestry|
7,669 individuals
PGP000230 |
Graham SE et al. Nature (2021)
Reported Trait: Mean LDL cholesterol: 0.071sex, PC1-4, birth year, and mean age
PPM002616PSS001160|
African Ancestry|
2,138 individuals
PGP000230 |
Graham SE et al. Nature (2021)
Reported Trait: Mean LDL cholesterol: 0.129birth year, sex, and PC1-4
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Evaluated Samples

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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
PSS0011444,273 individualsAfrican unspecifiedAADM
PSS001145707 individualsAfrican unspecifiedAADM
PSS0011463,566 individualsAfrican unspecifiedAADM
PSS0011481,745 individualsAfrican unspecifiedAWI-Gen
PSS0011494,972 individualsSub-Saharan AfricanAWI-Gen
PSS0011503,743 individualsAfrican unspecifiedAWI-Gen
PSS00115115,242 individualsSouth AsianG&H
PSS001152118,260 individualsEast AsianKoGES
PSS0011531,341 individualsAfrican American or Afro-CaribbeanMGI
PSS00115417,190 individualsEuropeanMGI
PSS00115618,251 individualsAfrican American or Afro-CaribbeanMVPSubset not used in discovery dataset
PSS0011574,155 individualsAsian unspecifiedMVPSubset not used in discovery dataset
PSS00115868,381 individualsEuropeanMVPSubset not used in discovery dataset
PSS0011597,669 individualsHispanic or Latin AmericanMVPSubset not used in discovery dataset
PSS0011602,138 individualsAfrican American or Afro-CaribbeanPMB
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