Polygenic Score (PGS) ID: PGS004313

Predicted Trait
Reported Trait Type 2 diabetes (T2D)
Mapped Trait(s) type 2 diabetes mellitus (MONDO_0005148)
Released in PGS Catalog: June 12, 2024
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Score Details

Score Construction
PGS Name GenoBoost_type_2_diabetes_3
Development Method
Name GenoBoost
Parameters lr=0.05, #snv=8000, model=Additive GenoBoost
Variants
Original Genome Build hg19
Number of Variants 8,000
Effect Weight Type beta
PGS Source
PGS Catalog Publication (PGP) ID PGP000546
Citation (link to publication) Ohta R et al. Nat Commun (2024)
Ancestry Distribution
Score Development/Training
European: 100%
269,710 individuals (100%)
PGS Evaluation
Greater Middle Eastern: 66.7%
European: 33.3%
3 Sample Sets

Development Samples

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
—
[
  • 20,500 cases
  • , 249,210 controls
]
,
46.4 % Male samples
 European
(White British)		 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
PPM020381 PSS011343|
European Ancestry|
67,428 individuals
 PGP000546 |
Ohta R et al. Nat Commun (2024)
 Reported Trait: Type 2 diabetes — AUROC: 0.70228 Covariate-adjusted pseudo-R2: 0.03838
AUPRC: 0.70228		 age, sex, PC1-10 —
PPM022861 PSS012080|
Greater Middle Eastern Ancestry|
4,534 individuals
 PGP000753 |
Aliyu U et al. Diabetes Obes Metab (2025)
|Ext.		 Reported Trait: Prediabetes OR: 1.209 [1.134, 1.289] AUROC: 0.65 [0.634, 0.666] R²: 0.085 sex, baseline age, BMI, PCs1-10 —
PPM022901 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: 1.525 [1.314, 1.77] AUROC: 0.763 [0.73, 0.796] — 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
PSS011343 — —
[
  • 5,089 cases
  • , 62,339 controls
]
,
46.0 % Male samples
 — European
(White British)		 — UKB —
PSS012080 age-matched cohort —
[
  • 2,267 cases
  • , 2,267 controls
]
 — Greater Middle Eastern (Middle Eastern, North African or Persian)
(Qatari)		 — QBB —
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 —