Polygenic Score (PGS) ID: PGS003491

Predicted Trait
Reported Trait Apolipoprotein A
Mapped Trait(s) apolipoprotein A-IV measurement (EFO_0007848)
Released in PGS Catalog: April 12, 2023
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Score Details

Score Construction
PGS Name cont-decay-apoA
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%
321,783 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
— 321,783 individuals,
0.47 % Male samples
 European UKB — Mean = 56.9 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
PPM017419 PSS010870|
European Ancestry|
17,435 individuals
 PGP000457 |
Ding Y et al. bioRxiv (2022)
|Pre		 Reported Trait: Apolipoprotein A — — partial-R2: 0.15 sex, age, deprivation index, PC1-16 —
PPM017503 PSS010786|
European Ancestry|
3,551 individuals
 PGP000457 |
Ding Y et al. bioRxiv (2022)
|Pre		 Reported Trait: Apolipoprotein A — — partial-R2: 0.16 sex, age, deprivation index, PC1-16 —
PPM017587 PSS010618|
European Ancestry|
5,626 individuals
 PGP000457 |
Ding Y et al. bioRxiv (2022)
|Pre		 Reported Trait: Apolipoprotein A — — partial-R2: 0.16 sex, age, deprivation index, PC1-16 —
PPM017671 PSS010534|
Greater Middle Eastern Ancestry|
1,004 individuals
 PGP000457 |
Ding Y et al. bioRxiv (2022)
|Pre		 Reported Trait: Apolipoprotein A — — partial-R2: 0.12 sex, age, deprivation index, PC1-16 —
PPM017755 PSS010198|
European Ancestry|
2,045 individuals
 PGP000457 |
Ding Y et al. bioRxiv (2022)
|Pre		 Reported Trait: Apolipoprotein A — — partial-R2: 0.12 sex, age, deprivation index, PC1-16 —
PPM017839 PSS010450|
South Asian Ancestry|
5,419 individuals
 PGP000457 |
Ding Y et al. bioRxiv (2022)
|Pre		 Reported Trait: Apolipoprotein A — — partial-R2: 0.13 sex, age, deprivation index, PC1-16 —
PPM017923 PSS010366|
East Asian Ancestry|
1,533 individuals
 PGP000457 |
Ding Y et al. bioRxiv (2022)
|Pre		 Reported Trait: Apolipoprotein A — — partial-R2: 0.12 sex, age, deprivation index, PC1-16 —
PPM018007 PSS010282|
African Ancestry|
2,140 individuals
 PGP000457 |
Ding Y et al. bioRxiv (2022)
|Pre		 Reported Trait: Apolipoprotein A — — partial-R2: 0.06 sex, age, deprivation index, PC1-16 —
PPM018091 PSS010702|
African Ancestry|
3,363 individuals
 PGP000457 |
Ding Y et al. bioRxiv (2022)
|Pre		 Reported Trait: Apolipoprotein A — — partial-R2: 0.05 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
PSS010366 — — 1,533 individuals,
34.0 % Male samples
 Mean = 52.4 years
Sd = 7.8 years		 East Asian Chinese UKB —
PSS010786 — — 3,551 individuals,
39.0 % Male samples
 Mean = 54.4 years
Sd = 7.6 years		 European Polish UKB —
PSS010534 — — 1,004 individuals,
60.0 % Male samples
 Mean = 51.9 years
Sd = 7.9 years		 Greater Middle Eastern (Middle Eastern, North African or Persian) Iranian UKB —
PSS010282 — — 2,140 individuals,
37.0 % Male samples
 Mean = 52.5 years
Sd = 8.1 years		 African American or Afro-Caribbean Caribbean UKB —
PSS010702 — — 3,363 individuals,
47.0 % Male samples
 Mean = 51.9 years
Sd = 8.1 years		 African unspecified Nigerian UKB —
PSS010450 — — 5,419 individuals,
55.0 % Male samples
 Mean = 53.2 years
Sd = 8.4 years		 South Asian Indian UKB —
PSS010870 — — 17,435 individuals,
47.0 % Male samples
 Mean = 56.9 years
Sd = 7.9 years		 European white British UKB —
PSS010198 — — 2,045 individuals,
46.0 % Male samples
 Mean = 58.0 years
Sd = 7.1 years		 European Ashkenazi UKB —
PSS010618 — — 5,626 individuals,
46.0 % Male samples
 Mean = 54.5 years
Sd = 8.4 years		 European Italian UKB —