Polygenic Score (PGS) ID: PGS000699

Predicted Trait
Reported Trait Triglycerides [mmol/L]
Mapped Trait(s) triglyceride measurement (EFO_0004530)
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.Triglycerides
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 16,003
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: 50%
African: 16.7%
East Asian: 16.7%
South Asian: 16.7%
12 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
PPM001427 PSS000772|
African Ancestry|
6,014 individuals
 PGP000128 |
Sinnott-Armstrong N et al. Nat Genet (2021)
 Reported Trait: Triglycerides [mmol/L] — — R²: 0.10632
Spearman's ρ: 0.169		 Age, sex, PCs(1-40) —
PPM001462 PSS000773|
East Asian Ancestry|
1,081 individuals
 PGP000128 |
Sinnott-Armstrong N et al. Nat Genet (2021)
 Reported Trait: Triglycerides [mmol/L] — — R²: 0.1757
Spearman's ρ: 0.256		 Age, sex, PCs(1-40) —
PPM001497 PSS000774|
European Ancestry|
23,559 individuals
 PGP000128 |
Sinnott-Armstrong N et al. Nat Genet (2021)
 Reported Trait: Triglycerides [mmol/L] — — R²: 0.23168
Spearman's ρ: 0.339		 Age, sex, PCs(1-40) —
PPM001532 PSS000775|
South Asian Ancestry|
7,330 individuals
 PGP000128 |
Sinnott-Armstrong N et al. Nat Genet (2021)
 Reported Trait: Triglycerides [mmol/L] — — R²: 0.16187
Spearman's ρ: 0.317		 Age, sex, PCs(1-40) —
PPM001567 PSS000776|
European Ancestry|
63,731 individuals
 PGP000128 |
Sinnott-Armstrong N et al. Nat Genet (2021)
 Reported Trait: Triglycerides [mmol/L] — — R²: 0.22344
Spearman's ρ: 0.352		 Age, sex, PCs(1-40) —
PPM001582 PSS000833|
European Ancestry|
2,004 individuals
 PGP000128 |
Sinnott-Armstrong N et al. Nat Genet (2021)
 Reported Trait: Triglycerides [mmol/L] — — Spearman's ρ: 0.29 Age, sex —
PPM001581 PSS000832|
European Ancestry|
2,129 individuals
 PGP000128 |
Sinnott-Armstrong N et al. Nat Genet (2021)
 Reported Trait: Triglycerides [mmol/L] — — Spearman's ρ: 0.258 Age, sex —
PPM007420 PSS007206|
African Ancestry|
6,096 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
|Ext.		 Reported Trait: Triglycerides — — R²: 0.07363 [0.06141, 0.08585]
Incremental R2 (full-covars): 0.02258
PGS R2 (no covariates): 0.02275 [0.01559, 0.02992]		 age, sex, UKB array type, Genotype PCs —
PPM007421 PSS007207|
East Asian Ancestry|
1,615 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
|Ext.		 Reported Trait: Triglycerides — — R²: 0.10923 [0.08133, 0.13713]
Incremental R2 (full-covars): 0.05029
PGS R2 (no covariates): 0.0596 [0.03784, 0.08136]		 age, sex, UKB array type, Genotype PCs —
PPM007422 PSS007208|
European Ancestry|
23,749 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
|Ext.		 Reported Trait: Triglycerides — — R²: 0.14451 [0.13643, 0.15258]
Incremental R2 (full-covars): 0.08283
PGS R2 (no covariates): 0.09525 [0.08831, 0.10218]		 age, sex, UKB array type, Genotype PCs —
PPM007423 PSS007209|
South Asian Ancestry|
7,419 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
|Ext.		 Reported Trait: Triglycerides — — R²: 0.11194 [0.09878, 0.12509]
Incremental R2 (full-covars): 0.08162
PGS R2 (no covariates): 0.09593 [0.08353, 0.10833]		 age, sex, UKB array type, Genotype PCs —
PPM007424 PSS007210|
European Ancestry|
64,410 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
|Ext.		 Reported Trait: Triglycerides — — R²: 0.13984 [0.13498, 0.14469]
Incremental R2 (full-covars): 0.09299
PGS R2 (no covariates): 0.10941 [0.10496, 0.11385]		 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
PSS000775 — — 7,330 individuals — South Asian — UKB —
PSS000776 — — 63,731 individuals — European
(British)		 — UKB —
PSS007206 — — 6,096 individuals — African unspecified — UKB —
PSS007207 — — 1,615 individuals — East Asian — UKB —
PSS007208 — — 23,749 individuals — European non-white British ancestry UKB —
PSS007209 — — 7,419 individuals — South Asian — UKB —
PSS007210 — — 64,410 individuals — European white British ancestry UKB Testing cohort (heldout set)
PSS000832 — — 2,129 individuals — European Participants self-identifying as white MESA —
PSS000833 — — 2,004 individuals — European Participants self-identifying as white MESA —
PSS000772 — — 6,014 individuals — African unspecified — UKB —
PSS000773 — — 1,081 individuals — East Asian — UKB —
PSS000774 — — 23,559 individuals — European Non-British White UKB —