Polygenic Score (PGS) ID: PGS004859

Predicted Trait
Reported Trait Type 2 diabetes (T2D)
Mapped Trait(s) type 2 diabetes mellitus (MONDO_0005148)
Released in PGS Catalog: March 28, 2024
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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 T2D_PRS_CS
Development Method
Name PRS-CS
Parameters a=1, b=0.5, phi=auto, MCMC iterations = 1000, burnin iterations = 500, LD reference panel = UK Biobank (EUR)
Variants
Original Genome Build hg19
Number of Variants 1,108,235
Effect Weight Type beta
PGS Source
PGS Catalog Publication (PGP) ID PGP000605
Citation (link to publication) Deutsch AJ et al. Diabetes Care (2023)
Ancestry Distribution
Source of Variant
Associations (GWAS)
European: 81.9%
Multi-ancestry (excluding European): 13.4%
  • East Asian
  • South Asian
African: 3.5%
Hispanic or Latin American: 1.3%
1,619,633 individuals (100%)
PGS Evaluation
Multi-ancestry (including European): 28.6%
  • African
  • Hispanic or Latin American
  • East Asian
  • European
  • South Asian
  • Additional Asian Ancestries
  • Not Reported
African: 14.3%
Hispanic or Latin American: 14.3%
East Asian: 14.3%
European: 14.3%
South Asian: 14.3%
7 Sample Sets

Development Samples

Source of Variant Associations (GWAS)
Study Identifiers Sample Numbers Sample Ancestry Cohort(s)
GWAS Catalog: GCST010555
Europe PMC: 32541925
 1,114,458 individuals European DIAMANTE, MVP
GWAS Catalog: GCST010556
Europe PMC: 32541925
 56,092 individuals African American or Afro-Caribbean DIAMANTE, MVP
GWAS Catalog: GCST010554
Europe PMC: 32541925
 20,445 individuals Hispanic or Latin American DIAMANTE, MVP
GWAS Catalog: GCST010553
Europe PMC: 32541925
 216,287 individuals East Asian, South Asian DIAMANTE, MVP
Europe PMC: 36653562
[
  • 29,166 cases
  • , 183,185 controls
]
 European
(Finnish)		 FinnGen

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
PPM021085 PSS011514|
African Ancestry|
7,010 individuals
 PGP000606 |
Szczerbinski L et al. medRxiv (2023)
|Ext.|Pre		 Reported Trait: Type 2 diabetes OR: 1.43 [1.35, 1.52] AUROC: 0.76 [0.74, 0.77] — age, sex, 10 principal components —
PPM021086 PSS011516|
Hispanic or Latin American Ancestry|
5,382 individuals
 PGP000606 |
Szczerbinski L et al. medRxiv (2023)
|Ext.|Pre		 Reported Trait: Type 2 diabetes OR: 2.09 [1.92, 2.27] AUROC: 0.84 [0.82, 0.86] — age, sex, 10 principal components —
PPM021087 PSS011517|
East Asian Ancestry|
663 individuals
 PGP000606 |
Szczerbinski L et al. medRxiv (2023)
|Ext.|Pre		 Reported Trait: Type 2 diabetes OR: 1.8 [1.4, 2.32] AUROC: 0.84 [0.79, 0.9] — age, sex, 10 principal components —
PPM021088 PSS011518|
European Ancestry|
22,306 individuals
 PGP000606 |
Szczerbinski L et al. medRxiv (2023)
|Ext.|Pre		 Reported Trait: Type 2 diabetes OR: 2.33 [2.23, 2.43] AUROC: 0.77 [0.76, 0.78] — age, sex, 10 principal components —
PPM021089 PSS011519|
South Asian Ancestry|
323 individuals
 PGP000606 |
Szczerbinski L et al. medRxiv (2023)
|Ext.|Pre		 Reported Trait: Type 2 diabetes OR: 2.28 [1.64, 3.16] AUROC: 0.88 [0.81, 0.95] — age, sex, 10 principal components —
PPM021090 PSS011515|
Multi-ancestry (including European)|
35,684 individuals
 PGP000606 |
Szczerbinski L et al. medRxiv (2023)
|Ext.|Pre		 Reported Trait: Type 2 diabetes OR: 1.93 [1.87, 1.99] AUROC: 0.75 [0.74, 0.75] — age, sex, 10 principal components —
PPM021084 PSS011513|
Multi-ancestry (including European)|
546 individuals
 PGP000605 |
Deutsch AJ et al. Diabetes Care (2023)
 Reported Trait: Glucocorticoid-induced hyperglycemia OR: 1.44 [1.02, 2.04] AUROC: 0.68 — eGFR, glucocorticoid dose —

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
PSS011513 Manual curation of electronic medical records. Cases had no ICD code for diabetes, received a glucocorticoid dose equivalent to >= 10 mg of prednisone, and had random blood glucose >= 200 mg/dL or fasting blood glucose >= 126 mg/dL (drawn between 4:00 AM and 6:59 AM) —
[
  • 2 cases
  • , 4 controls
]
 — Asian unspecified — MGBB —
PSS011513 Manual curation of electronic medical records. Cases had no ICD code for diabetes, received a glucocorticoid dose equivalent to >= 10 mg of prednisone, and had random blood glucose >= 200 mg/dL or fasting blood glucose >= 126 mg/dL (drawn between 4:00 AM and 6:59 AM) —
[
  • 13 cases
  • , 16 controls
]
 — African American or Afro-Caribbean — MGBB —
PSS011513 Manual curation of electronic medical records. Cases had no ICD code for diabetes, received a glucocorticoid dose equivalent to >= 10 mg of prednisone, and had random blood glucose >= 200 mg/dL or fasting blood glucose >= 126 mg/dL (drawn between 4:00 AM and 6:59 AM) —
[
  • 182 cases
  • , 296 controls
]
 — European — MGBB —
PSS011513 Manual curation of electronic medical records. Cases had no ICD code for diabetes, received a glucocorticoid dose equivalent to >= 10 mg of prednisone, and had random blood glucose >= 200 mg/dL or fasting blood glucose >= 126 mg/dL (drawn between 4:00 AM and 6:59 AM) —
[
  • 13 cases
  • , 20 controls
]
 — Not reported — MGBB —
PSS011514 — —
[
  • 2,004 cases
  • , 5,006 controls
]
 — African American or Afro-Caribbean — AllofUs —
PSS011515 — —
[
  • 2,004 cases
  • , 5,006 controls
]
 — African American or Afro-Caribbean — AllofUs —
PSS011515 — —
[
  • 1,325 cases
  • , 4,057 controls
]
 — Hispanic or Latin American — AllofUs —
PSS011515 — —
[
  • 100 cases
  • , 563 controls
]
 — East Asian — AllofUs —
PSS011515 — —
[
  • 3,646 cases
  • , 18,660 controls
]
 — European — AllofUs —
PSS011515 — —
[
  • 88 cases
  • , 235 controls
]
 — South Asian — AllofUs —
PSS011516 — —
[
  • 1,325 cases
  • , 4,057 controls
]
 — Hispanic or Latin American — AllofUs —
PSS011517 — —
[
  • 100 cases
  • , 563 controls
]
 — East Asian — AllofUs —
PSS011518 — —
[
  • 3,646 cases
  • , 18,660 controls
]
 — European — AllofUs —
PSS011519 — —
[
  • 88 cases
  • , 235 controls
]
 — South Asian — AllofUs —