Polygenic Score (PGS) ID: PGS003730

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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Score Details

Score Construction
PGS Name PS_T2D_287-DIAMANTE
Development Method
Name Pruning and Thresholding (P+T)
Parameters NR
Variants
Original Genome Build GRCh37
Number of Variants 287
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)
European: 51.1%
East Asian: 28.4%
South Asian: 8.3%
African: 6.6%
Hispanic or Latin American: 5.6%
492,192 individuals (100%)
PGS Evaluation
Additional Diverse Ancestries: 100%
3 Sample Sets

Development Samples

Source of Variant Associations (GWAS)
Study Identifiers Sample Numbers Sample Ancestry Cohort(s)
GWAS Catalog: GCST90132183
Europe PMC: 35551307
 251,740 individuals European DIAMANTE
GWAS Catalog: GCST90132183
Europe PMC: 35551307
 139,705 individuals East Asian DIAMANTE
GWAS Catalog: GCST90132183
Europe PMC: 35551307
 40,737 individuals South Asian DIAMANTE
GWAS Catalog: GCST90132183
Europe PMC: 35551307
 27,417 individuals Hispanic or Latin American DIAMANTE
GWAS Catalog: GCST90132183
Europe PMC: 35551307
 30,167 individuals African American or Afro-Caribbean DIAMANTE
GWAS Catalog: GCST90132183
Europe PMC: 35551307
 2,426 individuals Sub-Saharan African DIAMANTE

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
PPM018471 PSS010982|
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: 1.2 [1.1, 1.3] — Net reclassification improvement: 0.216 [0.094, 0.338]
∆AUC: 0.004 [-0.001, 0.009]		 age, sex, parental diabetes, BMI, fasting plasma glucose and HbA1c. —
PPM018479 PSS010984|
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: 1.34 [1.17, 1.54] — Net reclassification improvement: 0.314 [0.116, 0.512]
∆AUC: 0.004 [-0.001, 0.009]		 age, sex, parental diabetes, modified BMI z score, fasting plasma glucose —
PPM018487 PSS010983|
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: 1.45 [1.32, 1.6] — Net reclassification improvement: 0.259 [0.115, 0.403]
∆AUC: 0.073		 sex, parental diabetes, and birth weight —

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
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 —
PSS010982 — Mean = 7.15 years
[
  • 640 cases
  • , 1,693 controls
]
 Mean = 31.04 years
Sd = 10.43 years		 Native American — NR —