Polygenic Score (PGS) ID: PGS000685

Predicted Trait
Reported Trait HbA1c [mmol/mol]
Mapped Trait(s) HbA1c measurement (EFO_0004541)
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.Glycated_haemoglobin_HbA1c
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 14,658
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
PPM001413 PSS000704|
African Ancestry|
4,847 individuals
 PGP000128 |
Sinnott-Armstrong N et al. Nat Genet (2021)
 Reported Trait: HbA1c [mmol/mol] — — R²: 0.07974
Spearman's ρ: 0.132		 Age, sex, PCs(1-40) —
PPM001448 PSS000705|
East Asian Ancestry|
1,032 individuals
 PGP000128 |
Sinnott-Armstrong N et al. Nat Genet (2021)
 Reported Trait: HbA1c [mmol/mol] — — R²: 0.16979
Spearman's ρ: 0.285		 Age, sex, PCs(1-40) —
PPM001483 PSS000706|
European Ancestry|
22,518 individuals
 PGP000128 |
Sinnott-Armstrong N et al. Nat Genet (2021)
 Reported Trait: HbA1c [mmol/mol] — — R²: 0.17335
Spearman's ρ: 0.367		 Age, sex, PCs(1-40) —
PPM001518 PSS000707|
South Asian Ancestry|
6,895 individuals
 PGP000128 |
Sinnott-Armstrong N et al. Nat Genet (2021)
 Reported Trait: HbA1c [mmol/mol] — — R²: 0.12743
Spearman's ρ: 0.268		 Age, sex, PCs(1-40) —
PPM001553 PSS000708|
European Ancestry|
60,920 individuals
 PGP000128 |
Sinnott-Armstrong N et al. Nat Genet (2021)
 Reported Trait: HbA1c [mmol/mol] — — R²: 0.16381
Spearman's ρ: 0.375		 Age, sex, PCs(1-40) —
PPM001585 PSS000817|
European Ancestry|
1,995 individuals
 PGP000128 |
Sinnott-Armstrong N et al. Nat Genet (2021)
 Reported Trait: HbA1c [mmol/mol] — — Spearman's ρ: 0.217 Age, sex —
PPM007350 PSS007156|
African Ancestry|
5,219 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
|Ext.		 Reported Trait: Glycated haemoglobin (HbA1c) — — R²: 0.05396 [0.04328, 0.06464]
Incremental R2 (full-covars): 0.00054
PGS R2 (no covariates): 0.00619 [0.00239, 0.00998]		 age, sex, UKB array type, Genotype PCs —
PPM007351 PSS007157|
East Asian Ancestry|
1,622 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
|Ext.		 Reported Trait: Glycated haemoglobin (HbA1c) — — R²: 0.1264 [0.09696, 0.15583]
Incremental R2 (full-covars): 0.00207
PGS R2 (no covariates): 0.04145 [0.02295, 0.05994]		 age, sex, UKB array type, Genotype PCs —
PPM007352 PSS007158|
European Ancestry|
23,762 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
|Ext.		 Reported Trait: Glycated haemoglobin (HbA1c) — — R²: 0.06205 [0.05625, 0.06785]
Incremental R2 (full-covars): 0.00348
PGS R2 (no covariates): 0.06567 [0.05972, 0.07162]		 age, sex, UKB array type, Genotype PCs —
PPM007353 PSS007159|
South Asian Ancestry|
7,345 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
|Ext.		 Reported Trait: Glycated haemoglobin (HbA1c) — — R²: 0.05344 [0.04375, 0.06313]
Incremental R2 (full-covars): 0.00135
PGS R2 (no covariates): 0.03576 [0.02769, 0.04383]		 age, sex, UKB array type, Genotype PCs —
PPM007354 PSS007160|
European Ancestry|
64,432 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
|Ext.		 Reported Trait: Glycated haemoglobin (HbA1c) — — R²: 0.05264 [0.04936, 0.05592]
Incremental R2 (full-covars): 0.00369
PGS R2 (no covariates): 0.06933 [0.06563, 0.07303]		 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
PSS007158 — — 23,762 individuals — European non-white British ancestry UKB —
PSS007159 — — 7,345 individuals — South Asian — UKB —
PSS000817 — — 1,995 individuals — European Participants self-identifying as white MESA —
PSS007160 — — 64,432 individuals — European white British ancestry UKB Testing cohort (heldout set)
PSS007157 — — 1,622 individuals — East Asian — UKB —
PSS007156 — — 5,219 individuals — African unspecified — UKB —
PSS000704 — — 4,847 individuals — African unspecified — UKB —
PSS000705 — — 1,032 individuals — East Asian — UKB —
PSS000706 — — 22,518 individuals — European Non-British White UKB —
PSS000707 — — 6,895 individuals — South Asian — UKB —
PSS000708 — — 60,920 individuals — European
(British)		 — UKB —