Polygenic Score (PGS) ID: PGS001351

Predicted Trait
Reported Trait Fasting insulin
Mapped Trait(s) fasting blood insulin measurement (EFO_0004466)
Released in PGS Catalog: Nov. 4, 2021
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Score Details

Score Construction
PGS Name MAGICTA_EUR_PGS_FI
Development Method
Name PRS-CS
Parameters auto
Variants
Original Genome Build GRCh37
Number of Variants 1,025,098
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%
151,013 individuals (100%)
Score Development/Training
European: 100%
95,002 individuals (100%)
PGS Evaluation
African: 40%
European: 40%
East Asian: 20%
5 Sample Sets

Development Samples

Source of Variant Associations (GWAS)
Study Identifiers Sample Numbers Sample Ancestry Cohort(s)
GWAS Catalog: GCST90002238
Europe PMC: 34059833
 151,013 individuals European 55 cohorts
  • AGES
  • ,ALSPAC
  • ,AMISH
  • ,ARIC
  • ,B58C
  • ,CHS
  • ,CROATIA-KORCULA
  • ,CROATIA-VIS
  • ,CoLaus
  • ,DGI
  • ,DIAGEN
  • ,DPS
  • ,DRS_EXTRA
  • ,EGCUT
  • ,ERF
  • ,Ely
  • ,FHS
  • ,FIN-D2D
  • ,FUSION
  • ,FamHS
  • ,Fenland
  • ,GENOA
  • ,GOYA
  • ,GeneSTAR
  • ,GoDARTS
  • ,HELIC
  • ,Health2006
  • ,IMPROVE
  • ,InCHIANTI
  • ,Inter99
  • ,KORA
  • ,LLS
  • ,LOLIPOP
  • ,LURIC
  • ,Leipzig
  • ,Leipzig_Adults
  • ,MESA
  • ,METSIM
  • ,NEO
  • ,NFBC
  • ,NTR
  • ,OBB
  • ,ORCADES
  • ,PIVUS
  • ,PREVEND
  • ,PROSPER
  • ,RISC
  • ,RS
  • ,SCARFSHEEP
  • ,SardiNIA
  • ,TRAILS
  • ,TwinsUK
  • ,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
— 95,002 individuals European 38 cohorts
  • AGES
  • ,ALSPAC
  • ,AMISH
  • ,CFS
  • ,CHS
  • ,CROATIA-KORCULA
  • ,CROATIA-VIS
  • ,CoLaus
  • ,DGI
  • ,EGCUT
  • ,ERF
  • ,FHS
  • ,FUSION
  • ,FamHS
  • ,Fenland
  • ,GENOA
  • ,GOYA
  • ,GeneSTAR
  • ,HELIC
  • ,InCHIANTI
  • ,KORA
  • ,LLS
  • ,LOLIPOP
  • ,LURIC
  • ,MESA
  • ,NEO
  • ,NFBC
  • ,ORCADES
  • ,PIVUS
  • ,PREVEND
  • ,PROSPER
  • ,RISC
  • ,RS
  • ,SORBS
  • ,SardiNIA
  • ,TRAILS
  • ,TwinsUK
  • ,ULSAM
 — — — — Additional participants were obtained from French Adult Control, French Adult Obese, French Young Obese, Raine Study, BC1936, Fendland-OMICS, HELICMANOLIS

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
PPM005138 PSS003590|
European Ancestry|
29,123 individuals
 PGP000246 |
Chen J et al. Nat Genet (2021)
 Reported Trait: Fasting insulin — — R²: 0.095 — —
PPM005141 PSS003588|
African Ancestry|
8,101 individuals
 PGP000246 |
Chen J et al. Nat Genet (2021)
 Reported Trait: Fasting insulin — — R²: 0.028 — —
PPM005144 PSS003589|
East Asian Ancestry|
26,691 individuals
 PGP000246 |
Chen J et al. Nat Genet (2021)
 Reported Trait: Fasting insulin — — R²: 0.014 — —
PPM020887 PSS011442|
European Ancestry|
564 individuals
 PGP000599 |
Guarischi-Sousa R et al. Circ Genom Precis Med (2023)
|Ext.		 Reported Trait: Raised coronary lesion OR: 1.1 [0.91, 1.34] — — — —
PPM020892 PSS011441|
African Ancestry|
504 individuals
 PGP000599 |
Guarischi-Sousa R et al. Circ Genom Precis Med (2023)
|Ext.		 Reported Trait: Raised coronary lesion OR: 1.15 [0.92, 1.42] — — — —

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
PSS011441 — —
[
  • 165 cases
  • , 339 controls
]
,
82.0 % Male samples
 Mean = 27.5 years African unspecified — PDAY —
PSS011442 — —
[
  • 181 cases
  • , 383 controls
]
,
77.0 % Male samples
 Mean = 26.7 years European — PDAY —
PSS003588 — — 8,101 individuals — African American or Afro-Caribbean — 9 cohorts
  • ARIC
  • ,CHS
  • ,FamHS
  • ,GENOA
  • ,GeneSTAR
  • ,HANDLS
  • ,JHS
  • ,MESA
  • ,WHI
 —
PSS003589 — — 26,691 individuals — East Asian
(Japanese, Filipino, Chinese, Han Chinese)		 — 10 cohorts
  • AASC
  • ,CAGE
  • ,CHNS
  • ,CRC
  • ,KARE
  • ,MESA
  • ,NHAPC
  • ,Nagahama_Study
  • ,SMHS
  • ,SP2
 —
PSS003590 — — 29,123 individuals — European — ARIC, METSIM, NTR, PROCARDIS —