Polygenic Score (PGS) ID: PGS003542

Predicted Trait
Reported Trait Lipoprotein A
Mapped Trait(s) lipoprotein A measurement (EFO_0006925)
Released in PGS Catalog: April 12, 2023
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Terms and Licenses
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Score Details

Score Construction
PGS Name cont-decay-log_lipoA
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%
281,256 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
— 281,256 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
PPM017470 PSS010907|
European Ancestry|
15,302 individuals
 PGP000457 |
Ding Y et al. bioRxiv (2022)
|Pre		 Reported Trait: Lipoprotein A — — partial-R2: 0.34 sex, age, deprivation index, PC1-16 —
PPM017554 PSS010823|
European Ancestry|
3,124 individuals
 PGP000457 |
Ding Y et al. bioRxiv (2022)
|Pre		 Reported Trait: Lipoprotein A — — partial-R2: 0.29 sex, age, deprivation index, PC1-16 —
PPM017638 PSS010655|
European Ancestry|
5,045 individuals
 PGP000457 |
Ding Y et al. bioRxiv (2022)
|Pre		 Reported Trait: Lipoprotein A — — partial-R2: 0.2 sex, age, deprivation index, PC1-16 —
PPM017722 PSS010571|
Greater Middle Eastern Ancestry|
899 individuals
 PGP000457 |
Ding Y et al. bioRxiv (2022)
|Pre		 Reported Trait: Lipoprotein A — — partial-R2: 0.07 sex, age, deprivation index, PC1-16 —
PPM017806 PSS010235|
European Ancestry|
1,954 individuals
 PGP000457 |
Ding Y et al. bioRxiv (2022)
|Pre		 Reported Trait: Lipoprotein A — — partial-R2: 0.14 sex, age, deprivation index, PC1-16 —
PPM017890 PSS010487|
South Asian Ancestry|
5,181 individuals
 PGP000457 |
Ding Y et al. bioRxiv (2022)
|Pre		 Reported Trait: Lipoprotein A — — partial-R2: 0.09 sex, age, deprivation index, PC1-16 —
PPM017974 PSS010403|
East Asian Ancestry|
1,532 individuals
 PGP000457 |
Ding Y et al. bioRxiv (2022)
|Pre		 Reported Trait: Lipoprotein A — — partial-R2: 0.02 sex, age, deprivation index, PC1-16 —
PPM018058 PSS010319|
African Ancestry|
1,916 individuals
 PGP000457 |
Ding Y et al. bioRxiv (2022)
|Pre		 Reported Trait: Lipoprotein A — — partial-R2: 0.0 sex, age, deprivation index, PC1-16 —
PPM018142 PSS010739|
African Ancestry|
3,027 individuals
 PGP000457 |
Ding Y et al. bioRxiv (2022)
|Pre		 Reported Trait: Lipoprotein A — — partial-R2: 0.0 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
PSS010655 — — 5,045 individuals,
44.0 % Male samples
 Mean = 54.4 years
Sd = 8.4 years		 European Italian UKB —
PSS010403 — — 1,532 individuals,
33.0 % Male samples
 Mean = 52.5 years
Sd = 7.8 years		 East Asian Chinese UKB —
PSS010823 — — 3,124 individuals,
38.0 % Male samples
 Mean = 54.4 years
Sd = 7.5 years		 European Polish UKB —
PSS010907 — — 15,302 individuals,
46.0 % Male samples
 Mean = 56.8 years
Sd = 7.9 years		 European white British UKB —
PSS010571 — — 899 individuals,
60.0 % Male samples
 Mean = 51.7 years
Sd = 7.9 years		 Greater Middle Eastern (Middle Eastern, North African or Persian) Iranian UKB —
PSS010319 — — 1,916 individuals,
38.0 % Male samples
 Mean = 52.4 years
Sd = 8.1 years		 African American or Afro-Caribbean Caribbean UKB —
PSS010739 — — 3,027 individuals,
48.0 % Male samples
 Mean = 51.8 years
Sd = 8.1 years		 African unspecified Nigerian UKB —
PSS010487 — — 5,181 individuals,
55.0 % Male samples
 Mean = 53.3 years
Sd = 8.4 years		 South Asian Indian UKB —
PSS010235 — — 1,954 individuals,
46.0 % Male samples
 Mean = 58.0 years
Sd = 7.1 years		 European Ashkenazi UKB —