Polygenic Score (PGS) ID: PGS004057

Predicted Trait
Reported Trait HbA1c
Mapped Trait(s) HbA1c measurement (EFO_0004541)
Released in PGS Catalog: Dec. 19, 2023
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Terms and Licenses
PGS obtained from the Catalog should be cited appropriately, and used in accordance with any licensing restrictions set by the authors. See EBI Terms of Use (https://www.ebi.ac.uk/about/terms-of-use/) for additional details.

Score Details

Score Construction
PGS Name megaprs.auto.GCST007954.HbA1c
Development Method
Name megaprs.auto
Parameters Model:Model205,Type:bayesr,Her_Scaling:1,Lasso_lambda:NA,Lasso_s:NA,Bolt_p:NA,Bolt_f2:NA,BayesR_p1:0.78,BayesR_p2:0.2,BayesR_p3:0.01,BayesR_p4:0.01
Variants
Original Genome Build GRCh38
Number of Variants 514,367
Effect Weight Type beta
PGS Source
PGS Catalog Publication (PGP) ID PGP000517
Citation (link to publication) Monti M R et al. medRxiv (2023) Preprint
Ancestry Distribution
Source of Variant
Associations (GWAS)
European: 100%
88,355 individuals (100%)
Score Development/Training
European: 100%
344,209 individuals (100%)
PGS Evaluation
European: 50%
South Asian: 50%
4 Sample Sets

Development Samples

Source of Variant Associations (GWAS)
Study Identifiers Sample Numbers Sample Ancestry Cohort(s)
GWAS Catalog: GCST007954
Europe PMC: 28898252
 88,355 individuals European NR
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
— 344,209 individuals European UKB data field 30750 — — — —

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
PPM019673 PSS011242|
South Asian Ancestry|
12,948 individuals
 PGP000517 |
Monti M R et al. medRxiv (2023)
|Pre		 Reported Trait: Haemoglobin A1C β: 0.02167 — — 0 beta = sd_trait/sd_pgs = pearson correlation
PPM019674 PSS011258|
European Ancestry|
34,192 individuals
 PGP000517 |
Monti M R et al. medRxiv (2023)
|Pre		 Reported Trait: Haemoglobin A1C β: 0.16342 — — 0 beta = sd_trait/sd_pgs = pearson correlation
PPM019675 PSS011286|
South Asian Ancestry|
8,748 individuals
 PGP000517 |
Monti M R et al. medRxiv (2023)
|Pre		 Reported Trait: Haemoglobin A1C β: 0.16331 — — 0 beta = sd_trait/sd_pgs = pearson correlation
PPM019676 PSS011272|
European Ancestry|
86,050 individuals
 PGP000517 |
Monti M R et al. medRxiv (2023)
|Pre		 Reported Trait: Haemoglobin A1C β: 0.18961 — — 0 beta = sd_trait/sd_pgs = pearson correlation

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
PSS011258 — — 34,192 individuals — European — HUNT —
PSS011272 — — 86,050 individuals — European — UKB —
PSS011242 — — 12,948 individuals — South Asian — G&H —
PSS011286 — — 8,748 individuals — South Asian — UKB —