Polygenic Score (PGS) ID: PGS000689

Predicted Trait
Reported Trait Lipoprotein A [nmol/L]
Mapped Trait(s) lipoprotein A measurement (EFO_0006925)
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.Lipoprotein_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 8,308
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: 40%
African: 20%
East Asian: 20%
South Asian: 20%
10 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
PPM001417 PSS000719|
African Ancestry|
5,018 individuals
 PGP000128 |
Sinnott-Armstrong N et al. Nat Genet (2021)
 Reported Trait: Lipoprotein A [nmol/L] — — R²: 0.00769
Spearman's ρ: 0.058		 Age, sex, PCs(1-40) —
PPM001452 PSS000720|
East Asian Ancestry|
980 individuals
 PGP000128 |
Sinnott-Armstrong N et al. Nat Genet (2021)
 Reported Trait: Lipoprotein A [nmol/L] — — R²: 0.06202
Spearman's ρ: 0.164		 Age, sex, PCs(1-40) —
PPM001487 PSS000721|
European Ancestry|
19,003 individuals
 PGP000128 |
Sinnott-Armstrong N et al. Nat Genet (2021)
 Reported Trait: Lipoprotein A [nmol/L] — — R²: 0.48522
Spearman's ρ: 0.663		 Age, sex, PCs(1-40) —
PPM001522 PSS000722|
South Asian Ancestry|
6,453 individuals
 PGP000128 |
Sinnott-Armstrong N et al. Nat Genet (2021)
 Reported Trait: Lipoprotein A [nmol/L] — — R²: 0.16668
Spearman's ρ: 0.375		 Age, sex, PCs(1-40) —
PPM001557 PSS000723|
European Ancestry|
50,709 individuals
 PGP000128 |
Sinnott-Armstrong N et al. Nat Genet (2021)
 Reported Trait: Lipoprotein A [nmol/L] — — R²: 0.51648
Spearman's ρ: 0.692		 Age, sex, PCs(1-40) —
PPM007370 PSS007176|
African Ancestry|
5,086 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
|Ext.		 Reported Trait: Lipoprotein A — — R²: 0.0174 [0.0111, 0.0237]
Incremental R2 (full-covars): 0.00171
PGS R2 (no covariates): 0.00657 [0.00266, 0.01049]		 age, sex, UKB array type, Genotype PCs —
PPM007371 PSS007177|
East Asian Ancestry|
1,452 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
|Ext.		 Reported Trait: Lipoprotein A — — R²: 0.01457 [0.0033, 0.02585]
Incremental R2 (full-covars): 0.00715
PGS R2 (no covariates): 0.05715 [0.03579, 0.07851]		 age, sex, UKB array type, Genotype PCs —
PPM007372 PSS007178|
European Ancestry|
19,197 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
|Ext.		 Reported Trait: Lipoprotein A — — R²: 0.04874 [0.04353, 0.05396]
Incremental R2 (full-covars): 0.04393
PGS R2 (no covariates): 0.49585 [0.48704, 0.50467]		 age, sex, UKB array type, Genotype PCs —
PPM007373 PSS007179|
South Asian Ancestry|
6,542 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
|Ext.		 Reported Trait: Lipoprotein A — — R²: 0.02102 [0.01474, 0.02731]
Incremental R2 (full-covars): 0.01343
PGS R2 (no covariates): 0.13628 [0.12216, 0.1504]		 age, sex, UKB array type, Genotype PCs —
PPM007374 PSS007180|
European Ancestry|
51,385 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
|Ext.		 Reported Trait: Lipoprotein A — — R²: 0.17636 [0.17114, 0.18158]
Incremental R2 (full-covars): 0.17582
PGS R2 (no covariates): 0.53443 [0.5293, 0.53957]		 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
PSS000719 — — 5,018 individuals — African unspecified — UKB —
PSS000720 — — 980 individuals — East Asian — UKB —
PSS000721 — — 19,003 individuals — European Non-British White UKB —
PSS000722 — — 6,453 individuals — South Asian — UKB —
PSS000723 — — 50,709 individuals — European
(British)		 — UKB —
PSS007176 — — 5,086 individuals — African unspecified — UKB —
PSS007177 — — 1,452 individuals — East Asian — UKB —
PSS007178 — — 19,197 individuals — European non-white British ancestry UKB —
PSS007179 — — 6,542 individuals — South Asian — UKB —
PSS007180 — — 51,385 individuals — European white British ancestry UKB Testing cohort (heldout set)