Polygenic Score (PGS) ID: PGS002308

Predicted Trait
Reported Trait Type 2 diabetes (T2D)
Mapped Trait(s) type 2 diabetes mellitus (MONDO_0005148)
Released in PGS Catalog: July 5, 2022
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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 PRScsx_T2D
Development Method
Name PRS-CSx
Parameters PRS-CSx with --auto and --meta options
Variants
Original Genome Build hg19
Number of Variants 1,259,754
Effect Weight Type beta
PGS Source
PGS Catalog Publication (PGP) ID PGP000331
Citation (link to publication) Ge T et al. Genome Med (2022)
Ancestry Distribution
Source of Variant
Associations (GWAS)
European: 81.7%
East Asian: 16.1%
African: 2.2%
1,099,372 individuals (100%)
PGS Evaluation
African: 50%
East Asian: 30%
Hispanic or Latin American: 10%
European: 10%
10 Sample Sets

Development Samples

Source of Variant Associations (GWAS)
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Study Identifiers
Sample Numbers
Sample Ancestry
Cohort(s)
GWAS Catalog: GCST002560
Europe PMC: 25102180
[
  • 8,284 cases
  • , 15,543 controls
]
African American or Afro-Caribbean
(African)		NR
GWAS Catalog: GCST009379
Europe PMC: 30297969
[
  • 74,124 cases
  • , 824,006 controls
]
European
(European)		NR
GWAS Catalog: GCST90018706
Europe PMC: 34594039
[
  • 45,383 cases
  • , 132,032 controls
]
East Asian
(Japanese)		NR
Showing 1 to 3 of 3 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
PPM013064PSS009677|
European Ancestry|
54,793 individuals
PGP000331 |
Ge T et al. Genome Med (2022)
Reported Trait: Type 2 diabetesOR: 1.96 [1.91, 2.02]AUROC: 0.793R²: 0.092age, sex, top 10 PCs, study site—
PPM013065PSS009676|
African Ancestry|
12,472 individuals
PGP000331 |
Ge T et al. Genome Med (2022)
Reported Trait: Type 2 diabetesOR: 1.54 [1.46, 1.64]AUROC: 0.848R²: 0.028age, sex, top 10 PCs, study site—
PPM013066PSS009678|
Hispanic or Latin American Ancestry|
2,374 individuals
PGP000331 |
Ge T et al. Genome Med (2022)
Reported Trait: Type 2 diabetesOR: 2.08 [1.84, 2.35]AUROC: 0.851R²: 0.08age, sex, top 10 PCs, study site—
PPM013067PSS009671|
African Ancestry|
6,745 individuals
PGP000331 |
Ge T et al. Genome Med (2022)
Reported Trait: Type 2 diabetesOR: 1.7 [1.58, 1.84]AUROC: 0.631R²: 0.046age, sex, top 10 PCs—
PPM013068PSS009669|
African Ancestry|
5,498 individuals
PGP000331 |
Ge T et al. Genome Med (2022)
Reported Trait: Type 2 diabetesOR: 1.85 [1.7, 2.01]AUROC: 0.633R²: 0.036age, sex, top 10 PCs—
PPM013069PSS009670|
African Ancestry|
1,896 individuals
PGP000331 |
Ge T et al. Genome Med (2022)
Reported Trait: Type 2 diabetesOR: 1.75 [1.52, 2.02]AUROC: 0.757R²: 0.062age, sex, top 10 PCs—
PPM013070PSS009675|
African Ancestry|
655 individuals
PGP000331 |
Ge T et al. Genome Med (2022)
Reported Trait: Type 2 diabetesOR: 1.37 [1.13, 1.65]AUROC: 0.631R²: 0.015age, sex, top 10 PCs—
PPM013071PSS009672|
East Asian Ancestry|
25,110 individuals
PGP000331 |
Ge T et al. Genome Med (2022)
Reported Trait: Type 2 diabetesOR: 2.19 [2.05, 2.33]AUROC: 0.81R²: 0.151age, sex, top 10 PCs—
PPM013072PSS009673|
East Asian Ancestry|
54,078 individuals
PGP000331 |
Ge T et al. Genome Med (2022)
Reported Trait: Type 2 diabetesOR: 2.01 [1.93, 2.1]AUROC: 0.781R²: 0.129age, sex, top 10 PCs—
PPM013073PSS009674|
East Asian Ancestry|
10,378 individuals
PGP000331 |
Ge T et al. Genome Med (2022)
Reported Trait: Type 2 diabetesOR: 2.16 [1.96, 2.38]AUROC: 0.802R²: 0.153age, sex, top 10 PCs—
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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
PSS009669T2D cases were defined with T2D ICD codes, a single measurement of glucose (fasting glucose ≥126 mg/... dL [7 mmol/L] or random glucose ≥ 200 mg/dL [11.1 mmol/L]) or use of any glucose-lowering medications.Show more—
[
  • 2,776 cases
  • , 2,722 controls
]
—African American or Afro-Caribbean
(African)		—GenHAT—
PSS009670T2D cases were defined with T2D ICD codes, a single measurement of glucose (fasting glucose ≥126 mg/... dL [7 mmol/L] or random glucose ≥ 200 mg/dL [11.1 mmol/L]) or use of any glucose-lowering medications.Show more—
[
  • 402 cases
  • , 1,494 controls
]
—African American or Afro-Caribbean
(African)		—HYPERGEN—
PSS009671T2D cases were defined with T2D ICD codes, a single measurement of glucose (fasting glucose ≥126 mg/... dL [7 mmol/L] or random glucose ≥ 200 mg/dL [11.1 mmol/L]) or use of any glucose-lowering medications.Show more—
[
  • 1,659 cases
  • , 5,086 controls
]
—African American or Afro-Caribbean
(African)		—REGARDS—
PSS009672Self-reported T2D—
[
  • 1,248 cases
  • , 23,862 controls
]
—East Asian
(Taiwanese)		—TWB—
PSS009673Self-reported T2D—
[
  • 2,806 cases
  • , 51,272 controls
]
—East Asian
(Taiwanese)		—TWB—
PSS009674Self-reported T2D—
[
  • 516 cases
  • , 9,862 controls
]
—East Asian
(Taiwanese)		—TWB—
PSS009675T2D cases were defined with T2D ICD codes, a single measurement of glucose (fasting glucose ≥126 mg/... dL [7 mmol/L] or random glucose ≥ 200 mg/dL [11.1 mmol/L]) or use of any glucose-lowering medications.Show more—
[
  • 300 cases
  • , 355 controls
]
—African American or Afro-Caribbean
(African)		—WPC—
PSS009676An EHR-based phenotyping algorithm of T2D implemented across eMERGE sites—
[
  • 2,688 cases
  • , 9,784 controls
]
—African American or Afro-Caribbean
(African)		—eMERGE—
PSS009677An EHR-based phenotyping algorithm of T2D implemented across eMERGE sites—
[
  • 8,389 cases
  • , 46,404 controls
]
—European
(European)		—eMERGE—
PSS009678An EHR-based phenotyping algorithm of T2D implemented across eMERGE sites—
[
  • 868 cases
  • , 1,506 controls
]
—Hispanic or Latin American
(Hispanic/Latino)		—eMERGE—
Showing 1 to 10 of 10 rows