Polygenic Score (PGS) ID: PGS002648

Predicted Trait
Reported Trait HbA1c
Mapped Trait(s) HbA1c measurement (EFO_0004541)
Released in PGS Catalog: June 9, 2022
Download Score FTP directory
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 biochemistry_HbA1c.PolyFun-pred
Development Method
Name PolyFun-pred
Parameters NR
Variants
Original Genome Build GRCh37
Number of Variants 394,312
Effect Weight Type beta
PGS Source
PGS Catalog Publication (PGP) ID PGP000332
Citation (link to publication) Weissbrod O et al. Nat Genet (2022)
Ancestry Distribution
Source of Variant
Associations (GWAS)
European: 100%
318,400 individuals (100%)
PGS Evaluation
African: 25%
East Asian: 25%
European: 25%
South Asian: 25%
4 Sample Sets

Development Samples

Source of Variant Associations (GWAS)
Study Identifiers Sample Numbers Sample Ancestry Cohort(s)
— 318,400 individuals European UKB

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
PPM014364 PSS009767|
African Ancestry|
4,803 individuals
 PGP000332 |
Weissbrod O et al. Nat Genet (2022)
 Reported Trait: HbA1c — — Incremental R2 (full model when combined with BOLT-LMM vs. covariates alone): 0.0239 age, sex, age*sex, assessment center, genotyping array, 10 PCs See biochemistry_HbA1c.mixweights file at http://data.broadinstitute.org/alkesgroup/polypred_results for combination weights
PPM014413 PSS009768|
East Asian Ancestry|
841 individuals
 PGP000332 |
Weissbrod O et al. Nat Genet (2022)
 Reported Trait: HbA1c — — Incremental R2 (full model when combined with BOLT-LMM vs. covariates alone): 0.0785 age, sex, age*sex, assessment center, genotyping array, 10 PCs See biochemistry_HbA1c.mixweights file at http://data.broadinstitute.org/alkesgroup/polypred_results for combination weights
PPM014511 PSS009770|
South Asian Ancestry|
6,861 individuals
 PGP000332 |
Weissbrod O et al. Nat Genet (2022)
 Reported Trait: HbA1c — — Incremental R2 (full model when combined with BOLT-LMM vs. covariates alone): 0.064 age, sex, age*sex, assessment center, genotyping array, 10 PCs See biochemistry_HbA1c.mixweights file at http://data.broadinstitute.org/alkesgroup/polypred_results for combination weights
PPM014462 PSS009769|
European Ancestry|
38,991 individuals
 PGP000332 |
Weissbrod O et al. Nat Genet (2022)
 Reported Trait: HbA1c — — Incremental R2 (full model when combined with BOLT-LMM vs. covariates alone): 0.1252 age, sex, age*sex, assessment center, genotyping array, 10 PCs See biochemistry_HbA1c.mixweights file at http://data.broadinstitute.org/alkesgroup/polypred_results for combination weights

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
PSS009767 — — 4,803 individuals — African unspecified — UKB —
PSS009768 — — 841 individuals — East Asian — UKB —
PSS009769 — — 38,991 individuals — European Non-British European UKB —
PSS009770 — — 6,861 individuals — South Asian — UKB —