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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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)
Study Identifiers Sample Numbers Sample Ancestry Cohort(s)
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
GWAS Catalog: GCST002560
Europe PMC: 25102180
[
  • 8,284 cases
  • , 15,543 controls
]
 African American or Afro-Caribbean
(African)		 NR

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
PPM013067 PSS009671|
African Ancestry|
6,745 individuals
 PGP000331 |
Ge T et al. Genome Med (2022)
 Reported Trait: Type 2 diabetes OR: 1.7 [1.58, 1.84] AUROC: 0.631 R²: 0.046 age, sex, top 10 PCs —
PPM013064 PSS009677|
European Ancestry|
54,793 individuals
 PGP000331 |
Ge T et al. Genome Med (2022)
 Reported Trait: Type 2 diabetes OR: 1.96 [1.91, 2.02] AUROC: 0.793 R²: 0.092 age, sex, top 10 PCs, study site —
PPM013065 PSS009676|
African Ancestry|
12,472 individuals
 PGP000331 |
Ge T et al. Genome Med (2022)
 Reported Trait: Type 2 diabetes OR: 1.54 [1.46, 1.64] AUROC: 0.848 R²: 0.028 age, sex, top 10 PCs, study site —
PPM013066 PSS009678|
Hispanic or Latin American Ancestry|
2,374 individuals
 PGP000331 |
Ge T et al. Genome Med (2022)
 Reported Trait: Type 2 diabetes OR: 2.08 [1.84, 2.35] AUROC: 0.851 R²: 0.08 age, sex, top 10 PCs, study site —
PPM013068 PSS009669|
African Ancestry|
5,498 individuals
 PGP000331 |
Ge T et al. Genome Med (2022)
 Reported Trait: Type 2 diabetes OR: 1.85 [1.7, 2.01] AUROC: 0.633 R²: 0.036 age, sex, top 10 PCs —
PPM013069 PSS009670|
African Ancestry|
1,896 individuals
 PGP000331 |
Ge T et al. Genome Med (2022)
 Reported Trait: Type 2 diabetes OR: 1.75 [1.52, 2.02] AUROC: 0.757 R²: 0.062 age, sex, top 10 PCs —
PPM013070 PSS009675|
African Ancestry|
655 individuals
 PGP000331 |
Ge T et al. Genome Med (2022)
 Reported Trait: Type 2 diabetes OR: 1.37 [1.13, 1.65] AUROC: 0.631 R²: 0.015 age, sex, top 10 PCs —
PPM013071 PSS009672|
East Asian Ancestry|
25,110 individuals
 PGP000331 |
Ge T et al. Genome Med (2022)
 Reported Trait: Type 2 diabetes OR: 2.19 [2.05, 2.33] AUROC: 0.81 R²: 0.151 age, sex, top 10 PCs —
PPM013072 PSS009673|
East Asian Ancestry|
54,078 individuals
 PGP000331 |
Ge T et al. Genome Med (2022)
 Reported Trait: Type 2 diabetes OR: 2.01 [1.93, 2.1] AUROC: 0.781 R²: 0.129 age, sex, top 10 PCs —
PPM013073 PSS009674|
East Asian Ancestry|
10,378 individuals
 PGP000331 |
Ge T et al. Genome Med (2022)
 Reported Trait: Type 2 diabetes OR: 2.16 [1.96, 2.38] AUROC: 0.802 R²: 0.153 age, sex, top 10 PCs —

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
PSS009669 T2D 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. —
[
  • 2,776 cases
  • , 2,722 controls
]
 — African American or Afro-Caribbean
(African)		 — GenHAT —
PSS009670 T2D 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. —
[
  • 402 cases
  • , 1,494 controls
]
 — African American or Afro-Caribbean
(African)		 — HYPERGEN —
PSS009671 T2D 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. —
[
  • 1,659 cases
  • , 5,086 controls
]
 — African American or Afro-Caribbean
(African)		 — REGARDS —
PSS009672 Self-reported T2D —
[
  • 1,248 cases
  • , 23,862 controls
]
 — East Asian
(Taiwanese)		 — TWB —
PSS009673 Self-reported T2D —
[
  • 2,806 cases
  • , 51,272 controls
]
 — East Asian
(Taiwanese)		 — TWB —
PSS009674 Self-reported T2D —
[
  • 516 cases
  • , 9,862 controls
]
 — East Asian
(Taiwanese)		 — TWB —
PSS009675 T2D 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. —
[
  • 300 cases
  • , 355 controls
]
 — African American or Afro-Caribbean
(African)		 — WPC —
PSS009676 An EHR-based phenotyping algorithm of T2D implemented across eMERGE sites —
[
  • 2,688 cases
  • , 9,784 controls
]
 — African American or Afro-Caribbean
(African)		 — eMERGE —
PSS009677 An EHR-based phenotyping algorithm of T2D implemented across eMERGE sites —
[
  • 8,389 cases
  • , 46,404 controls
]
 — European
(European)		 — eMERGE —
PSS009678 An EHR-based phenotyping algorithm of T2D implemented across eMERGE sites —
[
  • 868 cases
  • , 1,506 controls
]
 — Hispanic or Latin American
(Hispanic/Latino)		 — eMERGE —