Polygenic Score (PGS) ID: PGS003751

Predicted Trait
Reported Trait Type 2 diabetes (T2D)
Mapped Trait(s) type 2 diabetes mellitus (MONDO_0005148)
Released in PGS Catalog: June 22, 2023
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Score Details

Score Construction
PGS Name ModelT2D_over45
Development Method
Name Genome-wide significant SNPs
Parameters r2<=0.1
Variants
Original Genome Build GRCh37
Number of Variants 354
Effect Weight Type beta
PGS Source
PGS Catalog Publication (PGP) ID PGP000472
Citation (link to publication) Shoaib M et al. Genet Epidemiol (2023)
Ancestry Distribution
Source of Variant
Associations (GWAS)
European: 100%
159,208 individuals (100%)
Score Development/Training
European: 100%
183,216 individuals (100%)
PGS Evaluation
European: 100%
2 Sample Sets

Development Samples

Source of Variant Associations (GWAS)
Study Identifiers Sample Numbers Sample Ancestry Cohort(s)
GWAS Catalog: GCST004774
Europe PMC: 28566273
 159,208 individuals European NR
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
—
[
  • 4,601 cases
  • , 178,615 controls
]
 European 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
PPM018510 PSS011003|
European Ancestry|
122,144 individuals
 PGP000472 |
Shoaib M et al. Genet Epidemiol (2023)
 Reported Trait: Type 2 diabetes with age of diagnosis over 45 — AUROC: 0.596 Nagelkerke R2: 0.016 — —
PPM018513 PSS011000|
European Ancestry|
7,067 individuals
 PGP000472 |
Shoaib M et al. Genet Epidemiol (2023)
 Reported Trait: Discrimination of Type 1 diabetes from Type 2 diabetes — AUROC: 0.527 — — —

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
PSS011003 — —
[
  • 3,069 cases
  • , 119,075 controls
]
 — European — UKB —
PSS011000 — —
[
  • 953 cases
  • , 6,114 controls
]
 — European — UKB —