Polygenic Score (PGS) ID: PGS000023

Predicted Trait
Reported Trait Type 1 diabetes (T1D)
Mapped Trait(s) type 1 diabetes mellitus (MONDO_0005147)
Released in PGS Catalog: Oct. 14, 2019
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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: 25%
European: 25%
Multi-ancestry (including European): 25%
  • European
  • African
  • Hispanic or Latin American
Multi-ancestry (excluding European): 25%
  • Additional Diverse Ancestries
  • Additional Asian Ancestries
  • East Asian
  • South Asian
  • African
  • Hispanic or Latin American
8 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 — — —
PPM018536 PSS011012|
Multi-ancestry (including European)|
39,820 individuals
 PGP000477 |
Deutsch AJ et al. Diabetes Care (2023)
|Ext.		 Reported Trait: Type 1 diabetes — AUROC: 0.781 — — —
PPM018537 PSS011009|
Multi-ancestry (including European)|
57,643 individuals
 PGP000477 |
Deutsch AJ et al. Diabetes Care (2023)
|Ext.		 Reported Trait: Type 1 diabetes — AUROC: 0.817 — — —
PPM018539 PSS011011|
European Ancestry|
16,663 individuals
 PGP000477 |
Deutsch AJ et al. Diabetes Care (2023)
|Ext.		 Reported Trait: Type 1 diabetes — — PPV (+PRS): 97.0 %
PPV (reference): 86.0 %		 eMERGE type 1 diabetes algorithm —
PPM018541 PSS011010|
Multi-ancestry (excluding European)|
40,980 individuals
 PGP000477 |
Deutsch AJ et al. Diabetes Care (2023)
|Ext.		 Reported Trait: Type 1 diabetes — — PPV (+PRS): 86.0 %
PPV (reference): 71.0 %		 eMERGE type 1 diabetes algorithm —
PPM018543 PSS011013|
Multi-ancestry (excluding European)|
4,881 individuals
 PGP000477 |
Deutsch AJ et al. Diabetes Care (2023)
|Ext.		 Reported Trait: Type 1 diabetes — — PPV (+PRS): 83.0 %
PPV (reference): 53.0 %		 eMERGE type 1 diabetes algorithm —
PPM021725 PSS011762|
European Ancestry|
8,417 individuals
 PGP000665 |
Moreno-Grau S et al. Human Genomics (2024)
|Ext.		 Reported Trait: Type 1 diabetes mellitus OR: 2.31 [2.0, 2.68] AUROC: 0.77 — — —

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
PSS011012 — — 1,511 individuals,
36.0 % Male samples
 Mean = 46.9 years
Sd = 16.3 years		 Native American, Asian unspecified, Oceanian, Other — MGBB —
PSS011013 At each site, a trained medical reviewer performed manual record review for all individuals identified as having type 1 diabetes by the eMERGE algorithm. To confirm a diagnosis of type 1 diabetes, participants had to meet all of the following criteria, modified from (13): Diagnosis confirmed by an endocrinologist or primary care physician Current use of basal-bolus insulin or pump No secondary cause of diabetes listed in the medical record: gestational diabetes, checkpoint inhibitor use, glucocorticoid-induced diabetes, cystic fibrosis diagnosis, hemochromatosis, pancreatogenic diabetes, posttransplantation diabetes, maturity-onset diabetes of the young, or diagnosis of type 1.5 diabetes — 2,101 individuals,
37.0 % Male samples
 Mean = 52.1 years
Sd = 16.3 years		 African American or Afro-Caribbean Self-identified race = Black MGBB —
PSS011013 At each site, a trained medical reviewer performed manual record review for all individuals identified as having type 1 diabetes by the eMERGE algorithm. To confirm a diagnosis of type 1 diabetes, participants had to meet all of the following criteria, modified from (13): Diagnosis confirmed by an endocrinologist or primary care physician Current use of basal-bolus insulin or pump No secondary cause of diabetes listed in the medical record: gestational diabetes, checkpoint inhibitor use, glucocorticoid-induced diabetes, cystic fibrosis diagnosis, hemochromatosis, pancreatogenic diabetes, posttransplantation diabetes, maturity-onset diabetes of the young, or diagnosis of type 1.5 diabetes — 1,269 individuals,
34.0 % Male samples
 Mean = 46.4 years
Sd = 16.1 years		 Hispanic or Latin American Self-identified race = Hispanic MGBB —
PSS011013 At each site, a trained medical reviewer performed manual record review for all individuals identified as having type 1 diabetes by the eMERGE algorithm. To confirm a diagnosis of type 1 diabetes, participants had to meet all of the following criteria, modified from (13): Diagnosis confirmed by an endocrinologist or primary care physician Current use of basal-bolus insulin or pump No secondary cause of diabetes listed in the medical record: gestational diabetes, checkpoint inhibitor use, glucocorticoid-induced diabetes, cystic fibrosis diagnosis, hemochromatosis, pancreatogenic diabetes, posttransplantation diabetes, maturity-onset diabetes of the young, or diagnosis of type 1.5 diabetes — 1,511 individuals,
36.0 % Male samples
 Mean = 46.9 years
Sd = 16.3 years		 Native American, Asian unspecified, Oceanian, Other Self-identified race = Other MGBB —
PSS000030 — —
[
  • 1,021 cases
  • , 2,928 controls
]
 — African unspecified — 7 cohorts
  • BDC
  • ,CLEAR
  • ,GoKinD
  • ,NYCP
  • ,SEARCH
  • ,T1DGC
  • ,UAB
 —
PSS000031 Cases are diagnosed with type 1 diabetes. —
[
  • 61 cases
  • , 54 controls
]
 — African unspecified — UOF —
PSS011762 — — 8,417 individuals — European — BBofA —
PSS011009 At each site, a trained medical reviewer performed manual record review for all individuals identified as having type 1 diabetes by the eMERGE algorithm. To confirm a diagnosis of type 1 diabetes, participants had to meet all of the following criteria, modified from (13): Diagnosis confirmed by an endocrinologist or primary care physician Current use of basal-bolus insulin or pump No secondary cause of diabetes listed in the medical record: gestational diabetes, checkpoint inhibitor use, glucocorticoid-induced diabetes, cystic fibrosis diagnosis, hemochromatosis, pancreatogenic diabetes, posttransplantation diabetes, maturity-onset diabetes of the young, or diagnosis of type 1.5 diabetes — 16,663 individuals,
48.0 % Male samples
 Mean = 51.9 years
Sd = 14.8 years		 European Self-identified race = White BioMe —
PSS011009 At each site, a trained medical reviewer performed manual record review for all individuals identified as having type 1 diabetes by the eMERGE algorithm. To confirm a diagnosis of type 1 diabetes, participants had to meet all of the following criteria, modified from (13): Diagnosis confirmed by an endocrinologist or primary care physician Current use of basal-bolus insulin or pump No secondary cause of diabetes listed in the medical record: gestational diabetes, checkpoint inhibitor use, glucocorticoid-induced diabetes, cystic fibrosis diagnosis, hemochromatosis, pancreatogenic diabetes, posttransplantation diabetes, maturity-onset diabetes of the young, or diagnosis of type 1.5 diabetes — 11,443 individuals,
39.0 % Male samples
 Mean = 48.4 years
Sd = 14.1 years		 African American or Afro-Caribbean Self-identified race = Black BioMe —
PSS011009 At each site, a trained medical reviewer performed manual record review for all individuals identified as having type 1 diabetes by the eMERGE algorithm. To confirm a diagnosis of type 1 diabetes, participants had to meet all of the following criteria, modified from (13): Diagnosis confirmed by an endocrinologist or primary care physician Current use of basal-bolus insulin or pump No secondary cause of diabetes listed in the medical record: gestational diabetes, checkpoint inhibitor use, glucocorticoid-induced diabetes, cystic fibrosis diagnosis, hemochromatosis, pancreatogenic diabetes, posttransplantation diabetes, maturity-onset diabetes of the young, or diagnosis of type 1.5 diabetes — 19,524 individuals,
37.0 % Male samples
 Mean = 50.3 years
Sd = 15.3 years		 Hispanic or Latin American Self-identified race = Hispanic BioMe —
PSS011009 At each site, a trained medical reviewer performed manual record review for all individuals identified as having type 1 diabetes by the eMERGE algorithm. To confirm a diagnosis of type 1 diabetes, participants had to meet all of the following criteria, modified from (13): Diagnosis confirmed by an endocrinologist or primary care physician Current use of basal-bolus insulin or pump No secondary cause of diabetes listed in the medical record: gestational diabetes, checkpoint inhibitor use, glucocorticoid-induced diabetes, cystic fibrosis diagnosis, hemochromatosis, pancreatogenic diabetes, posttransplantation diabetes, maturity-onset diabetes of the young, or diagnosis of type 1.5 diabetes — 10,013 individuals,
46.0 % Male samples
 Mean = 55.9 years
Sd = 13.9 years		 East Asian, South East Asian, Native American, South Asian, Other Self-identified race = Other BioMe —
PSS011010 At each site, a trained medical reviewer performed manual record review for all individuals identified as having type 1 diabetes by the eMERGE algorithm. To confirm a diagnosis of type 1 diabetes, participants had to meet all of the following criteria, modified from (13): Diagnosis confirmed by an endocrinologist or primary care physician Current use of basal-bolus insulin or pump No secondary cause of diabetes listed in the medical record: gestational diabetes, checkpoint inhibitor use, glucocorticoid-induced diabetes, cystic fibrosis diagnosis, hemochromatosis, pancreatogenic diabetes, posttransplantation diabetes, maturity-onset diabetes of the young, or diagnosis of type 1.5 diabetes — 11,443 individuals,
39.0 % Male samples
 Mean = 48.4 years
Sd = 14.1 years		 African American or Afro-Caribbean Self-identified race = Black BioMe —
PSS011010 At each site, a trained medical reviewer performed manual record review for all individuals identified as having type 1 diabetes by the eMERGE algorithm. To confirm a diagnosis of type 1 diabetes, participants had to meet all of the following criteria, modified from (13): Diagnosis confirmed by an endocrinologist or primary care physician Current use of basal-bolus insulin or pump No secondary cause of diabetes listed in the medical record: gestational diabetes, checkpoint inhibitor use, glucocorticoid-induced diabetes, cystic fibrosis diagnosis, hemochromatosis, pancreatogenic diabetes, posttransplantation diabetes, maturity-onset diabetes of the young, or diagnosis of type 1.5 diabetes — 19,524 individuals,
37.0 % Male samples
 Mean = 50.3 years
Sd = 15.3 years		 Hispanic or Latin American Self-identified race = Hispanic BioMe —
PSS011010 At each site, a trained medical reviewer performed manual record review for all individuals identified as having type 1 diabetes by the eMERGE algorithm. To confirm a diagnosis of type 1 diabetes, participants had to meet all of the following criteria, modified from (13): Diagnosis confirmed by an endocrinologist or primary care physician Current use of basal-bolus insulin or pump No secondary cause of diabetes listed in the medical record: gestational diabetes, checkpoint inhibitor use, glucocorticoid-induced diabetes, cystic fibrosis diagnosis, hemochromatosis, pancreatogenic diabetes, posttransplantation diabetes, maturity-onset diabetes of the young, or diagnosis of type 1.5 diabetes — 10,013 individuals,
46.0 % Male samples
 Mean = 55.9 years
Sd = 13.9 years		 East Asian, South East Asian, Native American, South Asian, Other Self-identified race = Other BioMe —
PSS011011 At each site, a trained medical reviewer performed manual record review for all individuals identified as having type 1 diabetes by the eMERGE algorithm. To confirm a diagnosis of type 1 diabetes, participants had to meet all of the following criteria, modified from (13): Diagnosis confirmed by an endocrinologist or primary care physician Current use of basal-bolus insulin or pump No secondary cause of diabetes listed in the medical record: gestational diabetes, checkpoint inhibitor use, glucocorticoid-induced diabetes, cystic fibrosis diagnosis, hemochromatosis, pancreatogenic diabetes, posttransplantation diabetes, maturity-onset diabetes of the young, or diagnosis of type 1.5 diabetes — 16,663 individuals,
48.0 % Male samples
 Mean = 51.9 years
Sd = 14.8 years		 European Self-identified race = White BioMe —
PSS011012 — — 34,939 individuals,
47.0 % Male samples
 Mean = 59.1 years
Sd = 16.9 years		 European Self-identified race = white MGBB —
PSS011012 — — 2,101 individuals,
37.0 % Male samples
 Mean = 52.1 years
Sd = 16.3 years		 African American or Afro-Caribbean
(Black)		 — MGBB —
PSS011012 — — 1,269 individuals,
34.0 % Male samples
 Mean = 46.4 years
Sd = 16.1 years		 Hispanic or Latin American
(Hispanic)		 — MGBB —