Polygenic Score (PGS) ID: PGS003517

Predicted Trait
Reported Trait LDL direct
Mapped Trait(s) low density lipoprotein cholesterol measurement (EFO_0004611)
Released in PGS Catalog: April 12, 2023
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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 cont-decay-LDL
Development Method
Name LDpred2-auto
Parameters vec_p_init = seq_log(1e-4, 0.9, length.out = 10), burn_in = 100, num_iter = 500, report_step = 5
Variants
Original Genome Build GRCh37
Number of Variants 979,739
Effect Weight Type beta
PGS Source
PGS Catalog Publication (PGP) ID PGP000457
Citation (link to publication) Ding Y et al. bioRxiv (2022) Preprint
Ancestry Distribution
Score Development/Training
European: 100%
352,884 individuals (100%)
PGS Evaluation
European: 44.4%
African: 22.2%
East Asian: 11.1%
Greater Middle Eastern: 11.1%
South Asian: 11.1%
9 Sample Sets

Development Samples

Score Development/Training
Study Identifiers Sample Numbers Sample Ancestry Cohort(s) Phenotype Definitions & Methods Age of Study Participants Participant Follow-up Time Additional Ancestry Description Additional Sample/Cohort Information
— 352,884 individuals,
0.46 % Male samples
 European UKB — Mean = 56.8 years
Sd = 8.0 years		 — white British —

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
PPM017445 PSS010879|
European Ancestry|
19,077 individuals
 PGP000457 |
Ding Y et al. bioRxiv (2022)
|Pre		 Reported Trait: LDL direct — — partial-R2: 0.11 sex, age, deprivation index, PC1-16 —
PPM017529 PSS010795|
European Ancestry|
3,935 individuals
 PGP000457 |
Ding Y et al. bioRxiv (2022)
|Pre		 Reported Trait: LDL direct — — partial-R2: 0.12 sex, age, deprivation index, PC1-16 —
PPM017697 PSS010543|
Greater Middle Eastern Ancestry|
1,093 individuals
 PGP000457 |
Ding Y et al. bioRxiv (2022)
|Pre		 Reported Trait: LDL direct — — partial-R2: 0.09 sex, age, deprivation index, PC1-16 —
PPM017781 PSS010207|
European Ancestry|
2,235 individuals
 PGP000457 |
Ding Y et al. bioRxiv (2022)
|Pre		 Reported Trait: LDL direct — — partial-R2: 0.07 sex, age, deprivation index, PC1-16 —
PPM017865 PSS010459|
South Asian Ancestry|
5,934 individuals
 PGP000457 |
Ding Y et al. bioRxiv (2022)
|Pre		 Reported Trait: LDL direct — — partial-R2: 0.04 sex, age, deprivation index, PC1-16 —
PPM017949 PSS010375|
East Asian Ancestry|
1,705 individuals
 PGP000457 |
Ding Y et al. bioRxiv (2022)
|Pre		 Reported Trait: LDL direct — — partial-R2: 0.06 sex, age, deprivation index, PC1-16 —
PPM018033 PSS010291|
African Ancestry|
2,326 individuals
 PGP000457 |
Ding Y et al. bioRxiv (2022)
|Pre		 Reported Trait: LDL direct — — partial-R2: 0.08 sex, age, deprivation index, PC1-16 —
PPM018117 PSS010711|
African Ancestry|
3,622 individuals
 PGP000457 |
Ding Y et al. bioRxiv (2022)
|Pre		 Reported Trait: LDL direct — — partial-R2: 0.05 sex, age, deprivation index, PC1-16 —
PPM017613 PSS010627|
European Ancestry|
6,160 individuals
 PGP000457 |
Ding Y et al. bioRxiv (2022)
|Pre		 Reported Trait: LDL direct — — partial-R2: 0.09 sex, age, deprivation index, PC1-16 —

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
PSS010207 — — 2,235 individuals,
45.0 % Male samples
 Mean = 58.1 years
Sd = 7.1 years		 European Ashkenazi UKB —
PSS010879 — — 19,077 individuals,
46.0 % Male samples
 Mean = 56.9 years
Sd = 7.9 years		 European white British UKB —
PSS010627 — — 6,160 individuals,
45.0 % Male samples
 Mean = 54.4 years
Sd = 8.4 years		 European Italian UKB —
PSS010375 — — 1,705 individuals,
33.0 % Male samples
 Mean = 52.4 years
Sd = 7.8 years		 East Asian Chinese UKB —
PSS010795 — — 3,935 individuals,
38.0 % Male samples
 Mean = 54.4 years
Sd = 7.5 years		 European Polish UKB —
PSS010543 — — 1,093 individuals,
60.0 % Male samples
 Mean = 51.9 years
Sd = 7.9 years		 Greater Middle Eastern (Middle Eastern, North African or Persian) Iranian UKB —
PSS010291 — — 2,326 individuals,
37.0 % Male samples
 Mean = 52.5 years
Sd = 8.1 years		 African American or Afro-Caribbean Caribbean UKB —
PSS010711 — — 3,622 individuals,
46.0 % Male samples
 Mean = 51.9 years
Sd = 8.1 years		 African unspecified Nigerian UKB —
PSS010459 — — 5,934 individuals,
54.0 % Male samples
 Mean = 53.3 years
Sd = 8.4 years		 South Asian Indian UKB —