Polygenic Score (PGS) ID: PGS000892

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_EUR_LDL_PRS_weights_PRS-CS
Development Method
Name PRS-CS
Parameters 1000Genomes reference panel
Variants
Original Genome Build hg19
Number of Variants 1,119,211
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)
European: 100%
831,666 individuals (100%)
PGS Evaluation
African: 55.6%
European: 16.7%
East Asian: 11.1%
Hispanic or Latin American: 5.6%
Additional Asian Ancestries: 5.6%
South Asian: 5.6%
18 Sample Sets

Development Samples

Source of Variant Associations (GWAS)
Study Identifiers Sample Numbers Sample Ancestry Cohort(s)
GWAS Catalog: GLGC2021
 831,666 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
PPM002549 PSS001144|
African Ancestry|
4,273 individuals
 PGP000230 |
Graham SE et al. Nature (2021)
 Reported Trait: Baseline LDL cholesterol — — R²: 0.052 age, sex, PC1-3 —
PPM002550 PSS001145|
African Ancestry|
707 individuals
 PGP000230 |
Graham SE et al. Nature (2021)
 Reported Trait: Baseline LDL cholesterol — — R²: 0.063 age, sex, PC1-3 —
PPM002551 PSS001146|
African Ancestry|
3,566 individuals
 PGP000230 |
Graham SE et al. Nature (2021)
 Reported Trait: Baseline LDL cholesterol — — R²: 0.055 age, sex, PC1-3 —
PPM002553 PSS001147|
African Ancestry|
10,460 individuals
 PGP000230 |
Graham SE et al. Nature (2021)
 Reported Trait: Baseline LDL cholesterol — — R²: 0.122 age, sex, PC1-6 —
PPM002556 PSS001148|
African Ancestry|
1,745 individuals
 PGP000230 |
Graham SE et al. Nature (2021)
 Reported Trait: Baseline LDL cholesterol — — R²: 0.041 age, sex, PC1-6 —
PPM002559 PSS001149|
African Ancestry|
4,972 individuals
 PGP000230 |
Graham SE et al. Nature (2021)
 Reported Trait: Baseline LDL cholesterol — — R²: 0.04 age, sex, PC1-6 —
PPM002562 PSS001150|
African Ancestry|
3,743 individuals
 PGP000230 |
Graham SE et al. Nature (2021)
 Reported Trait: Baseline LDL cholesterol — — R²: 0.022 age, sex, and PC1-4 —
PPM002566 PSS001151|
South Asian Ancestry|
15,242 individuals
 PGP000230 |
Graham SE et al. Nature (2021)
 Reported Trait: Max LDL cholesterol — — R²: 0.088 age, sex, and PC1-10 —
PPM002573 PSS001152|
East Asian Ancestry|
118,260 individuals
 PGP000230 |
Graham SE et al. Nature (2021)
 Reported Trait: Baseline LDL cholesterol — — R²: 0.064 age, sex, and recruitment area —
PPM002582 PSS001153|
African Ancestry|
1,341 individuals
 PGP000230 |
Graham SE et al. Nature (2021)
 Reported Trait: Mean LDL cholesterol — — R²: 0.062 sex, batch, PC1-4, and birth year —
PPM002583 PSS001154|
European Ancestry|
17,190 individuals
 PGP000230 |
Graham SE et al. Nature (2021)
 Reported Trait: Mean LDL cholesterol — — R²: 0.129 sex, batch, PC1-4, and birth year —
PPM002604 PSS001156|
African Ancestry|
18,251 individuals
 PGP000230 |
Graham SE et al. Nature (2021)
 Reported Trait: Mean LDL cholesterol — — R²: 0.04 sex, PC1-4, birth year, and mean age —
PPM002605 PSS001157|
Additional Asian Ancestries|
4,155 individuals
 PGP000230 |
Graham SE et al. Nature (2021)
 Reported Trait: Mean LDL cholesterol — — R²: 0.067 sex, PC1-4, birth year, and mean age —
PPM002606 PSS001158|
European Ancestry|
68,381 individuals
 PGP000230 |
Graham SE et al. Nature (2021)
 Reported Trait: Mean LDL cholesterol — — R²: 0.153 sex, PC1-4, birth year, and mean age —
PPM002607 PSS001159|
Hispanic or Latin American Ancestry|
7,669 individuals
 PGP000230 |
Graham SE et al. Nature (2021)
 Reported Trait: Mean LDL cholesterol — — R²: 0.114 sex, PC1-4, birth year, and mean age —
PPM002618 PSS001160|
African Ancestry|
2,138 individuals
 PGP000230 |
Graham SE et al. Nature (2021)
 Reported Trait: Mean LDL cholesterol — — R²: 0.069 birth year, sex, and PC1-4 —
PPM002621 PSS001161|
East Asian Ancestry|
28,217 individuals
 PGP000230 |
Graham SE et al. Nature (2021)
 Reported Trait: Baseline LDL cholesterol — — R²: 0.074 sex, age, recruitment method, and PC1-20 —
PPM002622 PSS001165|
European Ancestry|
389,158 individuals
 PGP000230 |
Graham SE et al. Nature (2021)
 Reported Trait: Baseline LDL cholesterol — — R²: 0.182 sex, batch, age at initial assessment, PCs1-4 —

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 —
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
PSS001165 — — 389,158 individuals — European — UKB —