PGS Preprint: PGP000606

Publication Information (EuropePMC)
Title Algorithms for the identification of prevalent diabetes in the All of Us Research Program validated using polygenic scores - a new resource for diabetes precision medicine
doi 10.1101/2023.09.05.23295061
Publication Date Sept. 5, 2023
Journal medRxiv Preprint
Author(s) Szczerbinski L, Mandla R, Schroeder P, Porneala BC, Li JH, Florez JC, Mercader JM, Manning AK, Udler MS.
Released in PGS Catalog: March 28, 2024

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

External PGS Evaluated 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)
PGS004859
(T2D_PRS_CS)
 PGP000605 |
Deutsch AJ et al. Diabetes Care (2023)
 Type 2 diabetes (T2D) type 2 diabetes mellitus 1,108,235
-
 https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS004859/ScoringFiles/PGS004859.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
PPM021085 PGS004859
(T2D_PRS_CS)
 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 PGS004859
(T2D_PRS_CS)
 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 PGS004859
(T2D_PRS_CS)
 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 PGS004859
(T2D_PRS_CS)
 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 PGS004859
(T2D_PRS_CS)
 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 PGS004859
(T2D_PRS_CS)
 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 —

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
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 —