Polygenic Score (PGS) ID: PGS004620

Predicted Trait
Reported Trait Type 2 diabetes (T2D)
Mapped Trait(s) type 2 diabetes mellitus (MONDO_0005148)
Released in PGS Catalog: July 31, 2024
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Score Details

Score Construction
PGS Name PGS_weights_BBJ2nd_LowBMI_of_2groups
Development Method
Name PRS-CSx
Parameters phi='auto', --meta=TRUE
Variants
Original Genome Build GRCh37
Number of Variants 728,824
Effect Weight Type beta
PGS Source
PGS Catalog Publication (PGP) ID PGP000593
Citation (link to publication) Ojima T et al. Nat Genet (2024)
Ancestry Distribution
Source of Variant
Associations (GWAS)
East Asian: 100%
97,884 individuals (100%)
PGS Evaluation
Greater Middle Eastern: 66.7%
East Asian: 33.3%
3 Sample Sets

Development Samples

Source of Variant Associations (GWAS)
Study Identifiers Sample Numbers Sample Ancestry Cohort(s)
—
[
  • 27,642 cases
  • , 70,242 controls
]
,
65.0 % Male samples
 East Asian
(Japanese)		 BBJ, 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
PPM020804 PSS011416|
East Asian Ancestry|
33,096 individuals
 PGP000593 |
Ojima T et al. Nat Genet (2024)
 Reported Trait: Type 2 diabetes — AUROC: 0.636 liability R2 (nested model): 0.081 age, age2, sex, sex × age, sex × age2 and the top 20 principal components —
PPM020805 PSS011416|
East Asian Ancestry|
33,096 individuals
 PGP000593 |
Ojima T et al. Nat Genet (2024)
 Reported Trait: Type 2 diabetes — AUROC: 0.682 liability R2 (nested model): 0.143 age, age2, sex, sex × age, sex × age2 and the top 20 principal components —
PPM022870 PSS012080|
Greater Middle Eastern Ancestry|
4,534 individuals
 PGP000753 |
Aliyu U et al. Diabetes Obes Metab (2025)
|Ext.		 Reported Trait: Prediabetes OR: 1.135 [1.066, 1.208] AUROC: 0.644 [0.628, 0.66] R²: 0.08 sex, baseline age, BMI, PCs1-10 —
PPM022973 PSS012081|
Greater Middle Eastern Ancestry|
2,143 individuals
 PGP000753 |
Aliyu U et al. Diabetes Obes Metab (2025)
|Ext.		 Reported Trait: Incident T2D in prediabetics HR: 1.328 [1.144, 1.542] AUROC: 0.751 [0.718, 0.784] — sex, baseline age, BMI, PCs1-10 —

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
PSS012081 — Median = 6.0 years
[
  • 199 cases
  • , 1,944 controls
]
,
54.22 % Male samples
 — Greater Middle Eastern (Middle Eastern, North African or Persian)
(Qatari)		 — QBB —
PSS012080 age-matched cohort —
[
  • 2,267 cases
  • , 2,267 controls
]
 — Greater Middle Eastern (Middle Eastern, North African or Persian)
(Qatari)		 — QBB —
PSS011416 — —
[
  • 11,236 cases
  • , 21,860 controls
]
,
65.0 % Male samples
 — East Asian
(Japanese)		 — BBJ —