Polygenic Score (PGS) ID: PGS005023

Predicted Trait
Reported Trait Type 2 diabetes (T2D) (PheCode 250.2)
Mapped Trait(s) type 2 diabetes mellitus (MONDO_0005148)
Released in PGS Catalog: Oct. 8, 2024
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Terms and Licenses
PGS obtained from the Catalog should be cited appropriately, and used in accordance with any licensing restrictions set by the authors. See EBI Terms of Use (https://www.ebi.ac.uk/about/terms-of-use/) for additional details.

Score Details

Score Construction
PGS Name Phe_250_2_ldpred_HISss_amrld
Development Method
Name ldpred
Parameters NR
Variants
Original Genome Build GRCh37
Number of Variants 1,286,612
Effect Weight Type beta
PGS Source
PGS Catalog Publication (PGP) ID PGP000679
Citation (link to publication) Gunn S et al. HGG Adv (2024)
Ancestry Distribution
Source of Variant
Associations (GWAS)
Not Reported: 50.3%
European: 36.1%
African: 9.5%
Hispanic or Latin American: 4%
1,216,910 individuals (100%)
PGS Evaluation
African: 33.3%
Hispanic or Latin American: 33.3%
European: 33.3%
3 Sample Sets

Development Samples

Source of Variant Associations (GWAS)
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Study Identifiers
Sample Numbers
Sample Ancestry
Cohort(s)
—
[
  • 51,469 cases
  • , 64,357 controls
]
African American or Afro-CaribbeanMVP
—
[
  • 156,343 cases
  • , 283,166 controls
]
EuropeanMVP
—
[
  • 19,574 cases
  • , 29,653 controls
]
Hispanic or Latin AmericanMVP
—
[
  • 229,933 cases
  • , 382,415 controls
]
Not reportedMVP
Showing 1 to 4 of 4 rows

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.

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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
PPM021885PSS011807|
Hispanic or Latin American Ancestry|
8,102 individuals
PGP000679 |
Gunn S et al. HGG Adv (2024)
Reported Trait: Type 2 diabetesOR: 1.656 [1.52, 1.8]C-index: 0.78141—age, sex, 20 PCs—
PPM021891PSS011817|
European Ancestry|
30,374 individuals
PGP000679 |
Gunn S et al. HGG Adv (2024)
Reported Trait: Type 2 diabetesOR: 1.342 [1.3, 1.38]C-index: 0.69576—age, sex, 20 PCs—
PPM021897PSS011797|
African Ancestry|
10,808 individuals
PGP000679 |
Gunn S et al. HGG Adv (2024)
Reported Trait: Type 2 diabetesOR: 1.22 [1.16, 1.28]C-index: 0.71211—age, sex, 20 PCs—
Showing 1 to 3 of 3 rows

Evaluated Samples

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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
PSS011797——
[
  • 3,016 cases
  • , 7,792 controls
]
—African American or Afro-Caribbean—AllofUs—
PSS011807——
[
  • 2,144 cases
  • , 5,958 controls
]
—Hispanic or Latin American—AllofUs—
PSS011817——
[
  • 5,958 cases
  • , 24,416 controls
]
—European—AllofUs—
Showing 1 to 3 of 3 rows