Polygenic Score (PGS) ID: PGS000854

Predicted Trait
Reported Trait Type 2 diabetes (based on SNPs associated with beta cell function)
Mapped Trait(s) type 2 diabetes mellitus (MONDO_0005148)
Released in PGS Catalog: Nov. 4, 2021
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Score Details

Score Construction
PGS Name T2D_BetaCell
Development Method
Name Genome-wide significant variants
Parameters NR
Variants
Original Genome Build GRCh37
Number of Variants 27
Effect Weight Type NR
PGS Source
PGS Catalog Publication (PGP) ID PGP000211
Citation (link to publication) Aly DM et al. Nat Genet (2021)
Ancestry Distribution
Source of Variant
Associations (GWAS)
Multi-ancestry (including European): 100%
  • African
  • East Asian
  • European
  • Hispanic or Latin American
  • South Asian
  • Not Reported
17,365 individuals (100%)
PGS Evaluation
European: 62.5%
South Asian: 37.5%
8 Sample Sets

Development Samples

Source of Variant Associations (GWAS)
Study Identifiers Sample Numbers Sample Ancestry Cohort(s)
Europe PMC: 30240442
 17,365 individuals African American or Afro-Caribbean, East Asian, European, Hispanic or Latin American, South Asian, NR METSIM, PHB, 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
PPM002353 PSS001086|
European Ancestry|
3,194 individuals
 PGP000211 |
Aly DM et al. Nat Genet (2021)
 Reported Trait: Severe Autoimmune Diabetes OR: 1.0 [0.91, 1.11] — — PC1-10 —
PPM002354 PSS001087|
European Ancestry|
3,930 individuals
 PGP000211 |
Aly DM et al. Nat Genet (2021)
 Reported Trait: Severe Insulin-Deficient Diabetes OR: 1.32 [1.23, 1.42] — — PC1-10 —
PPM002355 PSS001088|
European Ancestry|
3,869 individuals
 PGP000211 |
Aly DM et al. Nat Genet (2021)
 Reported Trait: Severe Insulin-Resistant Diabetes OR: 1.01 [0.94, 1.08] — — PC1-10 —
PPM002357 PSS001084|
European Ancestry|
5,597 individuals
 PGP000211 |
Aly DM et al. Nat Genet (2021)
 Reported Trait: Moderate Age-Related Diabetes OR: 1.27 [1.2, 1.34] — — PC1-10 —
PPM002356 PSS001085|
European Ancestry|
4,116 individuals
 PGP000211 |
Aly DM et al. Nat Genet (2021)
 Reported Trait: Moderate Obesity-related Diabetes OR: 1.21 [1.13, 1.3] — — PC1-10 —
PPM020168 PSS011301|
South Asian Ancestry|
1,282 individuals
 PGP000525 |
Yajnik CS et al. Lancet Reg Health Southeast Asia (2023)
|Ext.		 Reported Trait: Type 2 diabetes OR: 0.89 [0.79, 1.0] — — sex —
PPM020188 PSS011302|
South Asian Ancestry|
830 individuals
 PGP000525 |
Yajnik CS et al. Lancet Reg Health Southeast Asia (2023)
|Ext.		 Reported Trait: Severe insulin deficiency diabetes OR: 0.87 [0.75, 1.0] — — sex —
PPM020209 PSS011305|
South Asian Ancestry|
624 individuals
 PGP000525 |
Yajnik CS et al. Lancet Reg Health Southeast Asia (2023)
|Ext.		 Reported Trait: Mild age-related diabetes OR: 0.81 [0.67, 0.97] — — sex —

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
PSS011305 — —
[
  • 163 cases
  • , 461 controls
]
 — South Asian
(Indian)		 — WellGen —
PSS011301 — —
[
  • 821 cases
  • , 461 controls
]
 — South Asian
(Indian)		 — WellGen —
PSS011302 — —
[
  • 369 cases
  • , 461 controls
]
 — South Asian
(Indian)		 — WellGen —
PSS001084 Moderate Age-Related Diabetes (MARD) vs. controls —
[
  • 2,853 cases
  • , 2,744 controls
]
 — European Swedish ANDIS —
PSS001085 Moderate Obesity-related Diabetes (MOD) vs. controls —
[
  • 1,372 cases
  • , 2,744 controls
]
 — European Swedish ANDIS —
PSS001086 Severe Autoimmune Diabetes (SAID) vs. controls —
[
  • 450 cases
  • , 2,744 controls
]
 — European Swedish ANDIS —
PSS001087 Severe Insulin-Deficient Diabetes (SIDD) vs. controls —
[
  • 1,186 cases
  • , 2,744 controls
]
 — European Swedish ANDIS —
PSS001088 Severe Insulin-Resistant Diabetes (SIRD) vs. controls —
[
  • 1,125 cases
  • , 2,744 controls
]
 — European Swedish ANDIS —