Polygenic Score (PGS) ID: PGS000671

Predicted Trait
Reported Trait Apolipoprotein A [g/L]
Mapped Trait(s) apolipoprotein A 1 measurement (EFO_0004614)
Released in PGS Catalog: Feb. 3, 2021
Download Score FTP directory
Terms and Licenses
Creative Commons Attribution 4.0 International (CC BY 4.0)

Score Details

Score Construction
PGS Name snpnet.Apolipoprotein_A
Development Method
Name snpnet
Parameters 1,080,968 variants as input (directly genotyped variants, imputed HLA allelotypes, and CNVs)
Variants
Original Genome Build hg19
Number of Variants 19,324
Effect Weight Type beta
PGS Source
PGS Catalog Publication (PGP) ID PGP000128
Citation (link to publication) Sinnott-Armstrong N et al. Nat Genet (2021)
Ancestry Distribution
Score Development/Training
European: 100%
255,256 individuals (100%)
PGS Evaluation
European: 45.5%
African: 18.2%
East Asian: 18.2%
South Asian: 18.2%
11 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
223,327 individuals European
(British)		 UKB — — — — Training
31,929 individuals European
(British)		 UKB — — — — Validation

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
PPM001434 PSS000638|
East Asian Ancestry|
974 individuals
 PGP000128 |
Sinnott-Armstrong N et al. Nat Genet (2021)
 Reported Trait: Apolipoprotein A [g/L] — — R²: 0.32046
Spearman's ρ: 0.329		 Age, sex, PCs(1-40) —
PPM001399 PSS000637|
African Ancestry|
5,550 individuals
 PGP000128 |
Sinnott-Armstrong N et al. Nat Genet (2021)
 Reported Trait: Apolipoprotein A [g/L] — — R²: 0.1486
Spearman's ρ: 0.213		 Age, sex, PCs(1-40) —
PPM001469 PSS000639|
European Ancestry|
21,403 individuals
 PGP000128 |
Sinnott-Armstrong N et al. Nat Genet (2021)
 Reported Trait: Apolipoprotein A [g/L] — — R²: 0.31504
Spearman's ρ: 0.385		 Age, sex, PCs(1-40) —
PPM001504 PSS000640|
South Asian Ancestry|
6,682 individuals
 PGP000128 |
Sinnott-Armstrong N et al. Nat Genet (2021)
 Reported Trait: Apolipoprotein A [g/L] — — R²: 0.29281
Spearman's ρ: 0.358		 Age, sex, PCs(1-40) —
PPM001539 PSS000641|
European Ancestry|
57,932 individuals
 PGP000128 |
Sinnott-Armstrong N et al. Nat Genet (2021)
 Reported Trait: Apolipoprotein A [g/L] — — R²: 0.30509
Spearman's ρ: 0.398		 Age, sex, PCs(1-40) —
PPM001580 PSS000795|
European Ancestry|
1,378 individuals
 PGP000128 |
Sinnott-Armstrong N et al. Nat Genet (2021)
 Reported Trait: Apolipoprotein A [g/L] — — Spearman's ρ: 0.241 Age, sex —
PPM007280 PSS007086|
African Ancestry|
5,632 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
|Ext.		 Reported Trait: Apolipoprotein A — — R²: 0.14722 [0.13131, 0.16312]
Incremental R2 (full-covars): 0.04255
PGS R2 (no covariates): 0.03865 [0.02947, 0.04784]		 age, sex, UKB array type, Genotype PCs —
PPM007281 PSS007087|
East Asian Ancestry|
1,462 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
|Ext.		 Reported Trait: Apolipoprotein A — — R²: 0.28691 [0.25071, 0.3231]
Incremental R2 (full-covars): 0.07041
PGS R2 (no covariates): 0.08155 [0.0567, 0.10641]		 age, sex, UKB array type, Genotype PCs —
PPM007282 PSS007088|
European Ancestry|
21,609 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
|Ext.		 Reported Trait: Apolipoprotein A — — R²: 0.28381 [0.27434, 0.29329]
Incremental R2 (full-covars): 0.11215
PGS R2 (no covariates): 0.12323 [0.11558, 0.13087]		 age, sex, UKB array type, Genotype PCs —
PPM007283 PSS007089|
South Asian Ancestry|
6,776 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
|Ext.		 Reported Trait: Apolipoprotein A — — R²: 0.26533 [0.24858, 0.28209]
Incremental R2 (full-covars): 0.1056
PGS R2 (no covariates): 0.11603 [0.1027, 0.12937]		 age, sex, UKB array type, Genotype PCs —
PPM007284 PSS007090|
European Ancestry|
58,749 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
|Ext.		 Reported Trait: Apolipoprotein A — — R²: 0.27548 [0.26974, 0.28122]
Incremental R2 (full-covars): 0.12135
PGS R2 (no covariates): 0.1349 [0.1301, 0.13969]		 age, sex, UKB array type, Genotype PCs —

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
PSS007086 — — 5,632 individuals — African unspecified — UKB —
PSS007087 — — 1,462 individuals — East Asian — UKB —
PSS000795 — — 1,378 individuals — European Participants self-identifying as white MESA —
PSS007088 — — 21,609 individuals — European non-white British ancestry UKB —
PSS000637 — — 5,550 individuals — African unspecified — UKB —
PSS000638 — — 974 individuals — East Asian — UKB —
PSS000639 — — 21,403 individuals — European Non-British White UKB —
PSS000640 — — 6,682 individuals — South Asian — UKB —
PSS000641 — — 57,932 individuals — European
(British)		 — UKB —
PSS007089 — — 6,776 individuals — South Asian — UKB —
PSS007090 — — 58,749 individuals — European white British ancestry UKB Testing cohort (heldout set)