PGS Publication: PGP000472

Publication Information (EuropePMC)
Title Evaluation of polygenic risk scores to differentiate between type 1 and type 2 diabetes.
PubMed ID 36821788(Europe PMC)
doi 10.1002/gepi.22521
Publication Date Feb. 23, 2023
Journal Genet Epidemiol
Author(s) Shoaib M, Ye Q, IglayReger H, Tan MH, Boehnke M, Burant CF, Soleimanpour SA, Gagliano Taliun SA.
Released in PGS Catalog: June 22, 2023

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)
PGS003752
(ModelT2D)
 PGP000472 |
Shoaib M et al. Genet Epidemiol (2023)
 Type 2 diabetes (T2D) type 2 diabetes mellitus 333
https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS003752/ScoringFiles/PGS003752.txt.gz
PGS003749
(ModelT1D_under25)
 PGP000472 |
Shoaib M et al. Genet Epidemiol (2023)
 Type 1 diabetes (T1D) type 1 diabetes mellitus 6,612
https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS003749/ScoringFiles/PGS003749.txt.gz
PGS003750
(ModelT1D)
 PGP000472 |
Shoaib M et al. Genet Epidemiol (2023)
 Type 1 diabetes (T1D) type 1 diabetes mellitus 7,835
https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS003750/ScoringFiles/PGS003750.txt.gz
PGS003751
(ModelT2D_over45)
 PGP000472 |
Shoaib M et al. Genet Epidemiol (2023)
 Type 2 diabetes (T2D) type 2 diabetes mellitus 354
https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS003751/ScoringFiles/PGS003751.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
PPM018508 PGS003749
(ModelT1D_under25)
 PSS011001|
European Ancestry|
119,273 individuals
 PGP000472 |
Shoaib M et al. Genet Epidemiol (2023)
 Reported Trait: Type 1 diabetes with age of diagnosis under 25 — AUROC: 0.797 Nagelkerke R2: 0.099 — —
PPM018509 PGS003750
(ModelT1D)
 PSS010999|
European Ancestry|
120,028 individuals
 PGP000472 |
Shoaib M et al. Genet Epidemiol (2023)
 Reported Trait: Type 1 diabetes — AUROC: 0.64 Nagelkerke R2: 0.014 — —
PPM018510 PGS003751
(ModelT2D_over45)
 PSS011003|
European Ancestry|
122,144 individuals
 PGP000472 |
Shoaib M et al. Genet Epidemiol (2023)
 Reported Trait: Type 2 diabetes with age of diagnosis over 45 — AUROC: 0.596 Nagelkerke R2: 0.016 — —
PPM018511 PGS003752
(ModelT2D)
 PSS011002|
European Ancestry|
125,189 individuals
 PGP000472 |
Shoaib M et al. Genet Epidemiol (2023)
 Reported Trait: Type 2 diabetes — AUROC: 0.578 Nagelkerke R2: 0.014 — —
PPM018512 PGS003749
(ModelT1D_under25)
 PSS011000|
European Ancestry|
7,067 individuals
 PGP000472 |
Shoaib M et al. Genet Epidemiol (2023)
 Reported Trait: Discrimination of Type 1 diabetes from Type 2 diabetes — AUROC: 0.792 — — —
PPM018513 PGS003751
(ModelT2D_over45)
 PSS011000|
European Ancestry|
7,067 individuals
 PGP000472 |
Shoaib M et al. Genet Epidemiol (2023)
 Reported Trait: Discrimination of Type 1 diabetes from Type 2 diabetes — AUROC: 0.527 — — —
PPM018514 PGS003749
(ModelT1D_under25)
 PSS010998|
European Ancestry|
2,494 individuals
 PGP000472 |
Shoaib M et al. Genet Epidemiol (2023)
 Reported Trait: Discrimination of Type 1 diabetes from Type 2 diabetes — AUROC: 0.686 — — —

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
PSS010998 — —
[
  • 1,070 cases
  • , 1,424 controls
]
 — European — MGI —
PSS010999 — —
[
  • 953 cases
  • , 119,075 controls
]
 — European — UKB —
PSS011000 — —
[
  • 953 cases
  • , 6,114 controls
]
 — European — UKB —
PSS011001 — —
[
  • 198 cases
  • , 119,075 controls
]
 — European — UKB —
PSS011002 — —
[
  • 6,114 cases
  • , 119,075 controls
]
 — European — UKB —
PSS011003 — —
[
  • 3,069 cases
  • , 119,075 controls
]
 — European — UKB —