PGS Publication: PGP000013

Publication Information (EuropePMC)
Title Type 1 Diabetes Risk in African-Ancestry Participants and Utility of an Ancestry-Specific Genetic Risk Score.
PubMed ID 30659077(Europe PMC)
doi 10.2337/dc18-1727
Publication Date Jan. 18, 2019
Journal Diabetes Care
Author(s) Onengut-Gumuscu S, Chen WM, Robertson CC, Bonnie JK, Farber E, Zhu Z, Oksenberg JR, Brant SR, Bridges SL, Edberg JC, Kimberly RP, Gregersen PK, Rewers MJ, Steck AK, Black MH, Dabelea D, Pihoker C, Atkinson MA, Wagenknecht LE, Divers J, Bell RA, SEARCH for Diabetes in Youth, Type 1 Diabetes Genetics Consortium, Erlich HA, Concannon P, Rich SS.
Released in PGS Catalog: Oct. 14, 2019

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)
PGS000023
(AA_GRS)
 PGP000013 |
Onengut-Gumuscu S et al. Diabetes Care (2019)
 Type 1 diabetes (T1D) type 1 diabetes mellitus 7
-
 https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS000023/ScoringFiles/PGS000023.txt.gz

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)
PGS000021
(GRS1)
 PGP000011 |
Oram RA et al. Diabetes Care (2015)
 Type 1 diabetes (T1D) type 1 diabetes mellitus 33
https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS000021/ScoringFiles/PGS000021.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
PPM000045 PGS000023
(AA_GRS)
 PSS000030|
African Ancestry|
3,949 individuals
 PGP000013 |
Onengut-Gumuscu S et al. Diabetes Care (2019)
 Reported Trait: Type 1 diabetes — AUROC: 0.87 — — NOTE: Evaluated using cross-validation on training samples (20% heldout, 1000 iterations)
PPM000046 PGS000021
(GRS1)
 PSS000030|
African Ancestry|
3,949 individuals
 PGP000013 |
Onengut-Gumuscu S et al. Diabetes Care (2019)
|Ext.		 Reported Trait: Type 1 diabetes — AUROC: 0.798 — — —
PPM000047 PGS000023
(AA_GRS)
 PSS000031|
African Ancestry|
145 individuals
 PGP000013 |
Onengut-Gumuscu S et al. Diabetes Care (2019)
 Reported Trait: Type 1 diabetes — AUROC: 0.779 — — —

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
PSS000031 Cases are diagnosed with type 1 diabetes. —
[
  • 61 cases
  • , 54 controls
]
 — African unspecified — UOF —
PSS000030 — —
[
  • 1,021 cases
  • , 2,928 controls
]
 — African unspecified — 7 cohorts
  • BDC
  • ,CLEAR
  • ,GoKinD
  • ,NYCP
  • ,SEARCH
  • ,T1DGC
  • ,UAB
 —