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
Download Score FTP directory
Terms and Licenses
PGS obtained from the Catalog should be cited appropriately, and used in accordance with any licensing restrictions set by the authors. See EBI Terms of Use (https://www.ebi.ac.uk/about/terms-of-use/) for additional details.

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: 28.6%
Multi-ancestry (including European): 28.6%
  • European
  • African
  • Hispanic or Latin American
Multi-ancestry (excluding European): 28.6%
  • Additional Diverse Ancestries
  • Additional Asian Ancestries
  • East Asian
  • South Asian
  • African
  • Hispanic or Latin American
European: 14.3%
7 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

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
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