Polygenic Score (PGS) ID: PGS001350

Predicted Trait
Reported Trait Fasting glucose
Mapped Trait(s) fasting blood glucose measurement (EFO_0004465)
Released in PGS Catalog: Nov. 4, 2021
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Score Details

Score Construction
PGS Name MAGICTA_EUR_PGS_FG
Development Method
Name PRS-CS
Parameters auto
Variants
Original Genome Build GRCh37
Number of Variants 1,023,373
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%
200,622 individuals (100%)
Score Development/Training
European: 100%
120,477 individuals (100%)
PGS Evaluation
African: 33.3%
East Asian: 33.3%
European: 33.3%
3 Sample Sets

Development Samples

Source of Variant Associations (GWAS)
Study Identifiers Sample Numbers Sample Ancestry Cohort(s)
GWAS Catalog: GCST90002232
Europe PMC: 34059833
 200,622 individuals European 69 cohorts
  • AGES
  • ,ALSPAC
  • ,AMISH
  • ,ARIC
  • ,ASCOT
  • ,B58C
  • ,BioMe
  • ,CHS
  • ,CROATIA-KORCULA
  • ,CROATIA-SPLIT
  • ,CROATIA-VIS
  • ,CoLaus
  • ,DGI
  • ,DIAGEN
  • ,DPS
  • ,DRS_EXTRA
  • ,EGCUT
  • ,ERF
  • ,Ely
  • ,EpiHealth
  • ,FHS
  • ,FIN-D2D
  • ,FUSION
  • ,FamHS
  • ,Fenland
  • ,GENOA
  • ,GOYA
  • ,GS:SFHS
  • ,GeneSTAR
  • ,GoDARTS
  • ,HELIC
  • ,Health2006
  • ,IMPROVE
  • ,InCHIANTI
  • ,Inter99
  • ,KORA
  • ,LLS
  • ,LOLIPOP
  • ,LURIC
  • ,Leipzig
  • ,Leipzig_Adults
  • ,LifeLines
  • ,MEGA
  • ,MESA
  • ,METSIM
  • ,MICROS
  • ,NEO
  • ,NFBC
  • ,NSHD
  • ,NTR
  • ,OBB
  • ,ORCADES
  • ,PIVUS
  • ,PREVEND
  • ,PROCARDIS
  • ,PROSPER
  • ,RISC
  • ,RS
  • ,SCARFSHEEP
  • ,SORBS
  • ,SardiNIA
  • ,TRAILS
  • ,Tromso
  • ,TwinGene
  • ,TwinsUK
  • ,UKHLS
  • ,ULSAM
  • ,VIKING
  • ,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
— 120,477 individuals European 48 cohorts
  • AGES
  • ,ALSPAC
  • ,AMISH
  • ,ARIC
  • ,ASCOT
  • ,B58C
  • ,BioMe
  • ,CHS
  • ,CROATIA-KORCULA
  • ,CROATIA-SPLIT
  • ,CROATIA-VIS
  • ,CoLaus
  • ,DGI
  • ,EGCUT
  • ,ERF
  • ,EpiHealth
  • ,FHS
  • ,FUSION
  • ,FamHS
  • ,Fenland
  • ,GENOA
  • ,GOYA
  • ,GS:SFHS
  • ,GeneSTAR
  • ,HELIC
  • ,InCHIANTI
  • ,KORA
  • ,LLS
  • ,LOLIPOP
  • ,LURIC
  • ,LifeLines
  • ,MEGA
  • ,MESA
  • ,MICROS
  • ,NEO
  • ,NFBC
  • ,NTR
  • ,ORCADES
  • ,PREVEND
  • ,PROCARDIS
  • ,PROSPER
  • ,RISC
  • ,RS
  • ,SORBS
  • ,SardiNIA
  • ,TRAILS
  • ,TwinsUK
  • ,ULSAM
 — — — — Additional participants were obtained from Amsterdam Born Children and their Development (ABCD), French Adult Control, French Adult Obese, French Young Control, French Young Obese, Raine Study, HELICMANOLIS, BC1936

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
PPM005137 PSS003587|
European Ancestry|
45,038 individuals
 PGP000246 |
Chen J et al. Nat Genet (2021)
 Reported Trait: Fasting glucose — — R²: 0.229 — —
PPM005140 PSS003585|
African Ancestry|
16,579 individuals
 PGP000246 |
Chen J et al. Nat Genet (2021)
 Reported Trait: Fasting glucose — — R²: 0.032 — —
PPM005143 PSS003586|
East Asian Ancestry|
31,669 individuals
 PGP000246 |
Chen J et al. Nat Genet (2021)
 Reported Trait: Fasting glucose — — R²: 0.027 — —

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
PSS003586 — — 31,669 individuals — East Asian
(Japanese, Chinese, Malay, Filipino, Han Chinese)		 — 13 cohorts
  • AASC
  • ,CAGE
  • ,CHNS
  • ,CLHNS
  • ,CRC
  • ,KARE
  • ,Living-Biobank
  • ,MESA
  • ,NHAPC
  • ,Nagahama_Study
  • ,SBCS
  • ,SMHS
  • ,SP2
 —
PSS003587 — — 45,038 individuals — European — ARIC, LifeLines, METSIM, TwinGene Additional cases and controls were obtained from Fenland-OMICS.
PSS003585 — — 16,579 individuals — African American or Afro-Caribbean — 10 cohorts
  • ARIC
  • ,BioMe
  • ,CHS
  • ,FamHS
  • ,GENOA
  • ,GeneSTAR
  • ,HANDLS
  • ,JHS
  • ,MESA
  • ,WHI
 —