Polygenic Score (PGS) ID: PGS000672

Predicted Trait
Reported Trait Apolipoprotein B [g/L] (statin adjusted)
Mapped Trait(s) apolipoprotein B measurement (EFO_0004615)
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_B_adjstatins
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 18,666
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
PPM001400 PSS000642|
African Ancestry|
5,962 individuals
 PGP000128 |
Sinnott-Armstrong N et al. Nat Genet (2021)
 Reported Trait: Apolipoprotein B [g/L] (statin adjusted) — — R²: 0.15686
Spearman's ρ: 0.318		 Age, sex, PCs(1-40) —
PPM001470 PSS000644|
European Ancestry|
23,448 individuals
 PGP000128 |
Sinnott-Armstrong N et al. Nat Genet (2021)
 Reported Trait: Apolipoprotein B [g/L] (statin adjusted) — — R²: 0.29807
Spearman's ρ: 0.467		 Age, sex, PCs(1-40) —
PPM001540 PSS000646|
European Ancestry|
63,491 individuals
 PGP000128 |
Sinnott-Armstrong N et al. Nat Genet (2021)
 Reported Trait: Apolipoprotein B [g/L] (statin adjusted) — — R²: 0.30182
Spearman's ρ: 0.483		 Age, sex, PCs(1-40) —
PPM001435 PSS000643|
East Asian Ancestry|
1,074 individuals
 PGP000128 |
Sinnott-Armstrong N et al. Nat Genet (2021)
 Reported Trait: Apolipoprotein B [g/L] (statin adjusted) — — R²: 0.17749
Spearman's ρ: 0.346		 Age, sex, PCs(1-40) —
PPM001505 PSS000645|
South Asian Ancestry|
7,275 individuals
 PGP000128 |
Sinnott-Armstrong N et al. Nat Genet (2021)
 Reported Trait: Apolipoprotein B [g/L] (statin adjusted) — — R²: 0.15714
Spearman's ρ: 0.335		 Age, sex, PCs(1-40) —
PPM007285 PSS007096|
African Ancestry|
6,044 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
|Ext.		 Reported Trait: Apolipoprotein B — — R²: 0.09116 [0.07782, 0.1045]
Incremental R2 (full-covars): 0.08614
PGS R2 (no covariates): 0.08777 [0.07463, 0.10091]		 age, sex, UKB array type, Genotype PCs —
PPM007286 PSS007097|
East Asian Ancestry|
1,605 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
|Ext.		 Reported Trait: Apolipoprotein B — — R²: 0.11275 [0.08452, 0.14098]
Incremental R2 (full-covars): 0.09788
PGS R2 (no covariates): 0.09846 [0.07165, 0.12527]		 age, sex, UKB array type, Genotype PCs —
PPM007287 PSS007098|
European Ancestry|
23,638 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
|Ext.		 Reported Trait: Apolipoprotein B — — R²: 0.15705 [0.14875, 0.16535]
Incremental R2 (full-covars): 0.14836
PGS R2 (no covariates): 0.14904 [0.14088, 0.1572]		 age, sex, UKB array type, Genotype PCs —
PPM007288 PSS007099|
South Asian Ancestry|
7,362 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
|Ext.		 Reported Trait: Apolipoprotein B — — R²: 0.08178 [0.07015, 0.09341]
Incremental R2 (full-covars): 0.05616
PGS R2 (no covariates): 0.06062 [0.05038, 0.07086]		 age, sex, UKB array type, Genotype PCs —
PPM007289 PSS007100|
European Ancestry|
64,166 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
|Ext.		 Reported Trait: Apolipoprotein B — — R²: 0.15112 [0.14614, 0.1561]
Incremental R2 (full-covars): 0.14801
PGS R2 (no covariates): 0.14785 [0.1429, 0.15279]		 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
PSS007100 — — 64,166 individuals — European white British ancestry UKB Testing cohort (heldout set)
PSS007096 — — 6,044 individuals — African unspecified — UKB —
PSS007097 — — 1,605 individuals — East Asian — UKB —
PSS007098 — — 23,638 individuals — European non-white British ancestry UKB —
PSS007099 — — 7,362 individuals — South Asian — UKB —
PSS000642 — — 5,962 individuals — African unspecified — UKB —
PSS000643 — — 1,074 individuals — East Asian — UKB —
PSS000644 — — 23,448 individuals — European Non-British White UKB —
PSS000645 — — 7,275 individuals — South Asian — UKB —
PSS000646 — — 63,491 individuals — European
(British)		 — UKB —