Polygenic Score (PGS) ID: PGS001352

Predicted Trait
Reported Trait Glycated haemoglobin levels (HbA1c)
Mapped Trait(s) HbA1c measurement (EFO_0004541)
Released in PGS Catalog: Nov. 4, 2021
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 MAGICTA_EUR_PGS_HbA1c
Development Method
Name PRS-CS
Parameters auto
Variants
Original Genome Build GRCh37
Number of Variants 1,018,836
Effect Weight Type NR
PGS Source
PGS Catalog Publication (PGP) ID PGP000246
Citation (link to publication) Chen J et al. Nat Genet (2021)
Ancestry Distribution
Source of Variant
Associations (GWAS)
European: 100%
146,806 individuals (100%)
Score Development/Training
European: 100%
65,704 individuals (100%)
PGS Evaluation
African: 50%
East Asian: 25%
European: 25%
4 Sample Sets

Development Samples

Source of Variant Associations (GWAS)
Study Identifiers Sample Numbers Sample Ancestry Cohort(s)
GWAS Catalog: GCST90002244
Europe PMC: 34059833
 146,806 individuals European 40 cohorts
  • AGES
  • ,ALSPAC
  • ,ARIC
  • ,BioMe
  • ,COPSAC
  • ,DGI
  • ,DIAGEN
  • ,DPS
  • ,EPIC
  • ,EPIC-Norfolk
  • ,Ely
  • ,FHS
  • ,FIN-D2D
  • ,Fenland
  • ,GOYA
  • ,GoDARTS
  • ,Health2006
  • ,Inter99
  • ,KORA
  • ,LOLIPOP
  • ,LURIC
  • ,Leipzig
  • ,Leipzig_Adults
  • ,LifeLines
  • ,MESA
  • ,METSIM
  • ,NEO
  • ,NSHD
  • ,NTR
  • ,ORCADES
  • ,PROCARDIS
  • ,SardiNIA
  • ,TRAILS
  • ,Tromso
  • ,TwinGene
  • ,UKHLS
  • ,ULSAM
  • ,VIKING
  • ,WGHS
  • ,Whitehall
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
— 65,704 individuals European 20 cohorts
  • AGES
  • ,ALSPAC
  • ,ARIC
  • ,BioMe
  • ,COPSAC
  • ,DGI
  • ,FHS
  • ,Fenland
  • ,GOYA
  • ,KORA
  • ,LOLIPOP
  • ,LURIC
  • ,MESA
  • ,NEO
  • ,NTR
  • ,ORCADES
  • ,PROCARDIS
  • ,SardiNIA
  • ,TRAILS
  • ,TwinGene
 — — — — Additional participants were obtained from French Adult Control, Fenland-OMICS

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
PPM005139 PSS003594|
European Ancestry|
61,820 individuals
 PGP000246 |
Chen J et al. Nat Genet (2021)
 Reported Trait: Glycated haemoglobin levels (HbA1c) — — R²: 0.178 — —
PPM005142 PSS003591|
African Ancestry|
6,647 individuals
 PGP000246 |
Chen J et al. Nat Genet (2021)
 Reported Trait: Glycated haemoglobin levels (HbA1c) — — R²: 0.012 — —
PPM005145 PSS003593|
East Asian Ancestry|
31,236 individuals
 PGP000246 |
Chen J et al. Nat Genet (2021)
 Reported Trait: Glycated haemoglobin levels (HbA1c) — — R²: 0.026 — —
PPM005146 PSS003592|
African Ancestry|
4,441 individuals
 PGP000246 |
Chen J et al. Nat Genet (2021)
 Reported Trait: Glycated haemoglobin levels (HbA1c) — — R²: 0.006 — —

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
PSS003594 — — 61,820 individuals — European — EPIC, InterAct, LifeLines, METSIM, WGHS —
PSS003591 — — 6,647 individuals — African American or Afro-Caribbean — ARIC, BioMe, HANDLS, JHS, MESA —
PSS003592 — — 4,441 individuals — Sub-Saharan African
(Ugandan)		 — NR —
PSS003593 — — 31,236 individuals — East Asian
(Japanese, Chinese, Malay, Han Chinese)		 — 15 cohorts
  • AASC
  • ,BES
  • ,CAGE
  • ,CHNS
  • ,CRC
  • ,KARE
  • ,Living-Biobank
  • ,MESA
  • ,NHAPC
  • ,Nagahama_Study
  • ,SBCS
  • ,SCES
  • ,SIMES
  • ,SP2
  • ,TWSC
 —