PGS Publication: PGP000331

Publication Information (EuropePMC)
Title Development and validation of a trans-ancestry polygenic risk score for type 2 diabetes in diverse populations.
PubMed ID 35765100(Europe PMC)
doi 10.1186/s13073-022-01074-2
Publication Date June 29, 2022
Journal Genome Med
Author(s) Ge T, Irvin MR, Patki A, Srinivasasainagendra V, Lin YF, Tiwari HK, Armstrong ND, Benoit B, Chen CY, Choi KW, Cimino JJ, Davis BH, Dikilitas O, Etheridge B, Feng YA, Gainer V, Huang H, Jarvik GP, Kachulis C, Kenny EE, Khan A, Kiryluk K, Kottyan L, Kullo IJ, Lange C, Lennon N, Leong A, Malolepsza E, Miles AD, Murphy S, Namjou B, Narayan R, O'Connor MJ, Pacheco JA, Perez E, Rasmussen-Torvik LJ, Rosenthal EA, Schaid D, Stamou M, Udler MS, Wei WQ, Weiss ST, Ng MCY, Smoller JW, Lebo MS, Meigs JB, Limdi NA, Karlson EW.
Released in PGS Catalog: July 5, 2022

Associated Polygenic Score(s)

Filter PGS by Participant Ancestry
Individuals included in:
G - Source of Variant Associations (GWAS)
D - Score Development/Training
E - PGS Evaluation
List of ancestries includes:
Display options:
Ancestry legend
Multi-ancestry (including European)
Multi-ancestry (excluding European)
African
East Asian
South Asian
Additional Asian Ancestries
European
Greater Middle Eastern
Hispanic or Latin American
Additional Diverse Ancestries
Not Reported

PGS Developed By This Publication

Polygenic Score ID & Name PGS Publication ID (PGP) Reported Trait Mapped Trait(s) (Ontology) Number of Variants Ancestry distribution
GWAS
Dev
Eval
 Scoring File (FTP Link)
PGS002308
(PRScsx_T2D)
 PGP000331 |
Ge T et al. Genome Med (2022)
 Type 2 diabetes (T2D) type 2 diabetes mellitus 1,259,754
-
 https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS002308/ScoringFiles/PGS002308.txt.gz

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) 		Evaluated Score 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 PGS002308
(PRScsx_T2D)
 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 PGS002308
(PRScsx_T2D)
 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 PGS002308
(PRScsx_T2D)
 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 PGS002308
(PRScsx_T2D)
 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 PGS002308
(PRScsx_T2D)
 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 PGS002308
(PRScsx_T2D)
 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 PGS002308
(PRScsx_T2D)
 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 PGS002308
(PRScsx_T2D)
 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 PGS002308
(PRScsx_T2D)
 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 PGS002308
(PRScsx_T2D)
 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 —