Polygenic Score (PGS) ID: PGS000023

Predicted Trait
Reported Trait Type 1 diabetes
Mapped Trait(s) type 1 diabetes mellitus (MONDO_0005147)
Released in PGS Catalog: Oct. 14, 2019
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Terms and Licenses
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Score Details

Score Construction
PGS Name AA_GRS
Development Method
Name Genome-wide significant variants
Parameters NR
Variants
Original Genome Build NR
Number of Variants 7
Effect Weight Type NR
PGS Source
PGS Catalog Publication (PGP) ID PGP000013
Citation (link to publication) Onengut-Gumuscu S et al. Diabetes Care (2019)
Ancestry Distribution
Source of Variant
Associations (GWAS)
African: 100%
3,949 individuals (100%)
PGS Evaluation
African: 100%
2 Sample Sets

Development Samples

Source of Variant Associations (GWAS)
Study Identifiers Sample Numbers Sample Ancestry Cohort(s)
Europe PMC: 30659077
[
  • 59 cases
  • , 42 controls
]
,
40.59 % Male samples
 African unspecified BDC
Europe PMC: 30659077
[
  • 0 cases
  • , 368 controls
]
,
28.5 % Male samples
 African unspecified CLEAR
Europe PMC: 30659077
[
  • 41 cases
  • , 0 controls
]
,
41.5 % Male samples
 African unspecified GoKinD
Europe PMC: 30659077
[
  • 0 cases
  • , 801 controls
]
,
21.6 % Male samples
 African unspecified NYCP
Europe PMC: 30659077
[
  • 255 cases
  • , 0 controls
]
,
43.9 % Male samples
 African unspecified SEARCH
Europe PMC: 30659077
[
  • 666 cases
  • , 596 controls
]
,
35.66 % Male samples
 African unspecified T1DGC
Europe PMC: 30659077
[
  • 0 cases
  • , 659 controls
]
,
26.7 % Male samples
 African unspecified UAB
Europe PMC: 30659077
[
  • 0 cases
  • , 462 controls
]
,
34.6 % Male samples
 African unspecified UCSF

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
PPM000045 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)
PPM000047 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
 —