Polygenic Score (PGS) ID: PGS002669

Predicted Trait
Reported Trait Total cholesterol
Mapped Trait(s) total cholesterol measurement (EFO_0004574)
Released in PGS Catalog: June 9, 2022
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Score Details

Score Construction
PGS Name biochemistry_Cholesterol.PolyFun-pred
Development Method
Name PolyFun-pred
Parameters NR
Variants
Original Genome Build GRCh37
Number of Variants 309,475
Effect Weight Type beta
PGS Source
PGS Catalog Publication (PGP) ID PGP000332
Citation (link to publication) Weissbrod O et al. Nat Genet (2022)
Ancestry Distribution
Source of Variant
Associations (GWAS)
European: 100%
321,595 individuals (100%)
PGS Evaluation
African: 25%
East Asian: 25%
European: 25%
South Asian: 25%
4 Sample Sets

Development Samples

Source of Variant Associations (GWAS)
Study Identifiers Sample Numbers Sample Ancestry Cohort(s)
— 321,595 individuals European UKB

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
PPM014385 PSS009851|
African Ancestry|
6,080 individuals
 PGP000332 |
Weissbrod O et al. Nat Genet (2022)
 Reported Trait: Total cholesterol — — Incremental R2 (full model when combined with BOLT-LMM vs. covariates alone): 0.0835 age, sex, age*sex, assessment center, genotyping array, 10 PCs See biochemistry_Cholesterol.mixweights file at http://data.broadinstitute.org/alkesgroup/polypred_results for combination weights
PPM014483 PSS009853|
European Ancestry|
41,214 individuals
 PGP000332 |
Weissbrod O et al. Nat Genet (2022)
 Reported Trait: Total cholesterol — — Incremental R2 (full model when combined with BOLT-LMM vs. covariates alone): 0.1127 age, sex, age*sex, assessment center, genotyping array, 10 PCs See biochemistry_Cholesterol.mixweights file at http://data.broadinstitute.org/alkesgroup/polypred_results for combination weights
PPM014532 PSS009854|
South Asian Ancestry|
7,655 individuals
 PGP000332 |
Weissbrod O et al. Nat Genet (2022)
 Reported Trait: Total cholesterol — — Incremental R2 (full model when combined with BOLT-LMM vs. covariates alone): 0.0526 age, sex, age*sex, assessment center, genotyping array, 10 PCs See biochemistry_Cholesterol.mixweights file at http://data.broadinstitute.org/alkesgroup/polypred_results for combination weights
PPM014434 PSS009852|
East Asian Ancestry|
877 individuals
 PGP000332 |
Weissbrod O et al. Nat Genet (2022)
 Reported Trait: Total cholesterol — — Incremental R2 (full model when combined with BOLT-LMM vs. covariates alone): 0.0838 age, sex, age*sex, assessment center, genotyping array, 10 PCs See biochemistry_Cholesterol.mixweights file at http://data.broadinstitute.org/alkesgroup/polypred_results for combination weights

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
PSS009852 — — 877 individuals — East Asian — UKB —
PSS009853 — — 41,214 individuals — European Non-British European UKB —
PSS009854 — — 7,655 individuals — South Asian — UKB —
PSS009851 — — 6,080 individuals — African unspecified — UKB —