Polygenic Score (PGS) ID: PGS003728

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_183-AGEN
Development Method
Name Pruning and Thresholding (P+T)
Parameters NR
Variants
Original Genome Build GRCh37
Number of Variants 183
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)
East Asian: 100%
433,540 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: GCST010118
Europe PMC: 32499647
 433,540 individuals East Asian AGEN

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
PPM018476 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: 1.28 [1.12, 1.46] — Net reclassification improvement: 0.331 [0.141, 0.521]
∆AUC: 0.005 [-0.003, 0.012]		 age, sex, parental diabetes, modified BMI z score, fasting plasma glucose —
PPM018484 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: 1.27 [1.15, 1.39] — Net reclassification improvement: 0.164 [0.025, 0.303]
∆AUC: 0.037 [0.013, 0.06]		 sex, parental diabetes, and birth weight —
PPM018468 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: 1.14 [1.06, 1.24] — Net reclassification improvement: 0.115 [-0.014, 0.244]
∆AUC: 0.001 [-0.003, 0.005]		 age, sex, parental diabetes, BMI, fasting plasma glucose and HbA1c. —

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 —