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.Show more
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

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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 mellitus1,259,754
G
-
E
 https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS002308/ScoringFiles/PGS002308.txt.gz
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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)
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
PPM013064PGS002308
(PRScsx_T2D)
PSS009677|
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—
PPM013065PGS002308
(PRScsx_T2D)
PSS009676|
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—
PPM013066PGS002308
(PRScsx_T2D)
PSS009678|
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—
PPM013067PGS002308
(PRScsx_T2D)
PSS009671|
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—
PPM013068PGS002308
(PRScsx_T2D)
PSS009669|
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—
PPM013069PGS002308
(PRScsx_T2D)
PSS009670|
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—
PPM013070PGS002308
(PRScsx_T2D)
PSS009675|
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—
PPM013071PGS002308
(PRScsx_T2D)
PSS009672|
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—
PPM013072PGS002308
(PRScsx_T2D)
PSS009673|
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—
PPM013073PGS002308
(PRScsx_T2D)
PSS009674|
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—
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