Polygenic Score (PGS) ID: PGS003735

Predicted Trait
Reported Trait Type 2 diabetes (T2D)
Mapped Trait(s) type 2 diabetes mellitus (MONDO_0005148)
Released in PGS Catalog: June 1, 2023
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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 PS_T2D_276-AFR-DIAMANTE
Development Method
Name Pruning and Thresholding (P+T)
Parameters NR
Variants
Original Genome Build GRCh37
Number of Variants 276
Effect Weight Type log(OR)
PGS Source
PGS Catalog Publication (PGP) ID PGP000469
Citation (link to publication) Wedekind LE et al. Diabetologia (2023)
Ancestry Distribution
Source of Variant
Associations (GWAS)
African: 100%
32,593 individuals (100%)
PGS Evaluation
Additional Diverse Ancestries: 100%
3 Sample Sets

Development Samples

Source of Variant Associations (GWAS)
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Study Identifiers
Sample Numbers
Sample Ancestry
Cohort(s)
GWAS Catalog: GCST90132188
Europe PMC: 35551307
30,167 individualsAfrican American or Afro-CaribbeanDIAMANTE
GWAS Catalog: GCST90132188
Europe PMC: 35551307
2,426 individualsSub-Saharan AfricanDIAMANTE
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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
PPM018470PSS010982|
Additional Diverse Ancestries|
2,333 individuals
PGP000469 |
Wedekind LE et al. Diabetologia (2023)
Reported Trait: Incident type 2 diabetes (adult cohort at 10 year follow-up)HR: 1.13 [1.04, 1.22]—∆AUC: 0.003 [0.0, 0.007]
Net reclassification improvement: 0.181 [0.047, 0.316]		age, sex, parental diabetes, BMI, fasting plasma glucose and HbA1c.—
PPM018478PSS010984|
Additional Diverse Ancestries|
2,229 individuals
PGP000469 |
Wedekind LE et al. Diabetologia (2023)
Reported Trait: Incident type 2 diabetes (youth cohort at 10 year follow-up)HR: 1.21 [1.06, 1.38]—Net reclassification improvement: 0.185 [-0.017, 0.388]
∆AUC: 0.005 [-0.001, 0.01]		age, sex, parental diabetes, modified BMI z score, fasting plasma glucose—
PPM018486PSS010983|
Additional Diverse Ancestries|
2,894 individuals
PGP000469 |
Wedekind LE et al. Diabetologia (2023)
Reported Trait: Incident type 2 diabetes (birth cohort at 30 year follow-up)HR: 1.28 [1.16, 1.41]—Net reclassification improvement: 0.231 [0.091, 0.376]
∆AUC: 0.042 [0.019, 0.065]		sex, parental diabetes, and birth weight—
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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
PSS010982—Mean = 7.15 years
[
  • 640 cases
  • , 1,693 controls
]
Mean = 31.04 years
Sd = 10.43 years		Native American—NR—
PSS010983—Mean = 21.28 years
[
  • 438 cases
  • , 2,456 controls
]
—Native American—NR—
PSS010984—Mean = 7.99 years
[
  • 228 cases
  • , 2,001 controls
]
Mean = 12.05 years
Sd = 3.73 years		Native American—NR—
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