Polygenic Score (PGS) ID: PGS002646

Predicted Trait
Reported Trait HDL cholesterol
Mapped Trait(s) high density lipoprotein cholesterol measurement (EFO_0004612)
Released in PGS Catalog: June 9, 2022
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Score Details

Score Construction
PGS Name biochemistry_HDLcholesterol.PolyFun-pred
Development Method
Name PolyFun-pred
Parameters NR
Variants
Original Genome Build GRCh37
Number of Variants 402,183
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%
294,075 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)
— 294,075 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
PPM014362 PSS009759|
African Ancestry|
5,619 individuals
 PGP000332 |
Weissbrod O et al. Nat Genet (2022)
 Reported Trait: HDL Cholesterol — — Incremental R2 (full model when combined with BOLT-LMM vs. covariates alone): 0.071 age, sex, age*sex, assessment center, genotyping array, 10 PCs See biochemistry_HDLcholesterol.mixweights file at http://data.broadinstitute.org/alkesgroup/polypred_results for combination weights
PPM014411 PSS009760|
East Asian Ancestry|
797 individuals
 PGP000332 |
Weissbrod O et al. Nat Genet (2022)
 Reported Trait: HDL Cholesterol — — Incremental R2 (full model when combined with BOLT-LMM vs. covariates alone): 0.1071 age, sex, age*sex, assessment center, genotyping array, 10 PCs See biochemistry_HDLcholesterol.mixweights file at http://data.broadinstitute.org/alkesgroup/polypred_results for combination weights
PPM014460 PSS009761|
European Ancestry|
37,633 individuals
 PGP000332 |
Weissbrod O et al. Nat Genet (2022)
 Reported Trait: HDL Cholesterol — — Incremental R2 (full model when combined with BOLT-LMM vs. covariates alone): 0.1701 age, sex, age*sex, assessment center, genotyping array, 10 PCs See biochemistry_HDLcholesterol.mixweights file at http://data.broadinstitute.org/alkesgroup/polypred_results for combination weights
PPM014509 PSS009762|
South Asian Ancestry|
6,980 individuals
 PGP000332 |
Weissbrod O et al. Nat Genet (2022)
 Reported Trait: HDL Cholesterol — — Incremental R2 (full model when combined with BOLT-LMM vs. covariates alone): 0.1352 age, sex, age*sex, assessment center, genotyping array, 10 PCs See biochemistry_HDLcholesterol.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
PSS009759 — — 5,619 individuals — African unspecified — UKB —
PSS009760 — — 797 individuals — East Asian — UKB —
PSS009761 — — 37,633 individuals — European Non-British European UKB —
PSS009762 — — 6,980 individuals — South Asian — UKB —