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: Oct. 14, 2019

Associated Polygenic Score(s)

PGS Developed By This Publication

Polygenic Score (PGS) ID PGS Name PGS Publication (PGP) ID Reported Trait Mapped Trait(s) (Ontology) Number of Variants PGS Scoring File (FTP Link)
PGS000023 AA_GRS PGP000013
Onengut-Gumuscu S et al. Diabetes Care (2019)
Type 1 diabetes type I diabetes mellitus 7 http://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS000023/ScoringFiles/PGS000023.txt.gz

External PGS Evaluated By This Publication

Polygenic Score (PGS) ID PGS Name PGS Publication (PGP) ID Reported Trait Mapped Trait(s) (Ontology) Number of Variants PGS Scoring File (FTP Link)
PGS000021 GRS1 PGP000011
Oram RA et al. Diabetes Care (2015)
Type 1 diabetes type I diabetes mellitus 30 http://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS000021/ScoringFiles/PGS000021.txt.gz

PGS 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 ID)
Evaluated Score PGS Sample Set ID
(PSS ID)
Performance Source Trait PGS Effect Sizes
(per SD change)
PGS Classification Metrics Other Metrics Covariates Included in the Model PGS Performance: Other Relevant Information
PPM000046 PGS000021 (GRS1) PSS000030 PGP000013
Onengut-Gumuscu S et al. (2019)
Ext.
Reported Trait: Type 1 diabetes AUROC: 0.798
PPM000047 PGS000023 (AA_GRS) PSS000031 PGP000013
Onengut-Gumuscu S et al. (2019)
Reported Trait: Type 1 diabetes AUROC: 0.779
PPM000045 PGS000023 (AA_GRS) PSS000030 PGP000013
Onengut-Gumuscu S et al. (2019)
Reported Trait: Type 1 diabetes AUROC: 0.87 NOTE: Evaluated using cross-validation on training samples (20% heldout, 1000 iterations)

Evaluated Samples

PGS Sample Set ID
(PSS ID)
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