Polygenic Score (PGS) ID: PGS000684

Predicted Trait
Reported Trait Glucose [mmol/L]
Mapped Trait(s) glucose measurement (EFO_0004468)
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.Glucose
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 3,313
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
PPM001447 PSS000695|
East Asian Ancestry|
60 individuals
 PGP000128 |
Sinnott-Armstrong N et al. Nat Genet (2021)
 Reported Trait: Glucose [mmol/L] — — R²: 0.08219
Spearman's ρ: 0.178		 Age, sex, PCs(1-40) —
PPM001482 PSS000696|
European Ancestry|
986 individuals
 PGP000128 |
Sinnott-Armstrong N et al. Nat Genet (2021)
 Reported Trait: Glucose [mmol/L] — — R²: 0.06962
Spearman's ρ: 0.242		 Age, sex, PCs(1-40) —
PPM001517 PSS000697|
South Asian Ancestry|
337 individuals
 PGP000128 |
Sinnott-Armstrong N et al. Nat Genet (2021)
 Reported Trait: Glucose [mmol/L] — — R²: 0.05599
Spearman's ρ: 0.227		 Age, sex, PCs(1-40) —
PPM001552 PSS000698|
European Ancestry|
2,208 individuals
 PGP000128 |
Sinnott-Armstrong N et al. Nat Genet (2021)
 Reported Trait: Glucose [mmol/L] — — R²: 0.06966
Spearman's ρ: 0.214		 Age, sex, PCs(1-40) —
PPM001583 PSS000813|
European Ancestry|
2,129 individuals
 PGP000128 |
Sinnott-Armstrong N et al. Nat Genet (2021)
 Reported Trait: Glucose [mmol/L] — — Spearman's ρ: 0.132 Age, sex —
PPM001584 PSS000814|
European Ancestry|
2,002 individuals
 PGP000128 |
Sinnott-Armstrong N et al. Nat Genet (2021)
 Reported Trait: Glucose [mmol/L] — — Spearman's ρ: 0.135 Age, sex —
PPM001412 PSS000694|
African Ancestry|
760 individuals
 PGP000128 |
Sinnott-Armstrong N et al. Nat Genet (2021)
 Reported Trait: Glucose [mmol/L] — — R²: 0.05168
Spearman's ρ: 0.059		 Age, sex, PCs(1-40) —
PPM007345 PSS007151|
African Ancestry|
5,651 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
|Ext.		 Reported Trait: Glucose — — R²: 0.02744 [0.01961, 0.03527]
Incremental R2 (full-covars): 0.00103
PGS R2 (no covariates): 0.00255 [0.0001, 0.005]		 age, sex, UKB array type, Genotype PCs —
PPM007346 PSS007152|
East Asian Ancestry|
1,474 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
|Ext.		 Reported Trait: Glucose — — R²: 0.04784 [0.02811, 0.06758]
Incremental R2 (full-covars): 0.00354
PGS R2 (no covariates): 0.00962 [0.00041, 0.01883]		 age, sex, UKB array type, Genotype PCs —
PPM007347 PSS007153|
European Ancestry|
21,725 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
|Ext.		 Reported Trait: Glucose — — R²: 0.01933 [0.01594, 0.02271]
Incremental R2 (full-covars): 0.00451
PGS R2 (no covariates): 0.01332 [0.01049, 0.01615]		 age, sex, UKB array type, Genotype PCs —
PPM007348 PSS007154|
South Asian Ancestry|
6,787 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
|Ext.		 Reported Trait: Glucose — — R²: 0.02105 [0.01476, 0.02734]
Incremental R2 (full-covars): 0.00223
PGS R2 (no covariates): 0.01136 [0.0067, 0.01603]		 age, sex, UKB array type, Genotype PCs —
PPM007349 PSS007155|
European Ancestry|
59,031 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
|Ext.		 Reported Trait: Glucose — — R²: 0.01813 [0.01614, 0.02013]
Incremental R2 (full-covars): 0.00467
PGS R2 (no covariates): 0.01444 [0.01265, 0.01622]		 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
PSS000813 — — 2,129 individuals — European Participants self-identifying as white MESA —
PSS000814 — — 2,002 individuals — European Participants self-identifying as white MESA —
PSS000694 — — 760 individuals — African unspecified — UKB —
PSS000695 — — 60 individuals — East Asian — UKB —
PSS000696 — — 986 individuals — European Non-British White UKB —
PSS000697 — — 337 individuals — South Asian — UKB —
PSS000698 — — 2,208 individuals — European
(British)		 — UKB —
PSS007151 — — 5,651 individuals — African unspecified — UKB —
PSS007152 — — 1,474 individuals — East Asian — UKB —
PSS007153 — — 21,725 individuals — European non-white British ancestry UKB —
PSS007154 — — 6,787 individuals — South Asian — UKB —
PSS007155 — — 59,031 individuals — European white British ancestry UKB Testing cohort (heldout set)