PGS Publication: PGP000477

Publication Information (EuropePMC)
Title Polygenic Scores Help Reduce Racial Disparities in Predictive Accuracy of Automated Type 1 Diabetes Classification Algorithms.
PubMed ID 36745605(Europe PMC)
doi 10.2337/dc22-1833
Publication Date April 1, 2023
Journal Diabetes Care
Author(s) Deutsch AJ, Stalbow L, Majarian TD, Mercader JM, Manning AK, Florez JC, Loos RJF, Udler MS.
Released in PGS Catalog: June 22, 2023

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

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)
PGS000024
(GRS2)
PGP000014 |
Sharp SA et al. Diabetes Care (2019)
Type 1 diabetes (T1D) type 1 diabetes mellitus 67
-
https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS000024/ScoringFiles/PGS000024.txt.gz
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

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
PPM018536 PGS000023
(AA_GRS)
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
PPM018532 PGS000024
(GRS2)
PSS011012|
Multi-ancestry (including European)|
39,820 individuals
PGP000477 |
Deutsch AJ et al. Diabetes Care (2023)
|Ext.
Reported Trait: Type 1 diabetes AUROC: 0.875
PPM018533 PGS000024
(GRS2)
PSS011009|
Multi-ancestry (including European)|
57,643 individuals
PGP000477 |
Deutsch AJ et al. Diabetes Care (2023)
|Ext.
Reported Trait: Type 1 diabetes AUROC: 0.822
PPM018534 PGS000024
(GRS2)
PSS011014|
European Ancestry|
34,939 individuals
PGP000477 |
Deutsch AJ et al. Diabetes Care (2023)
|Ext.
Reported Trait: Type 1 diabetes AUROC: 0.888
PPM018535 PGS000024
(GRS2)
PSS011014|
European Ancestry|
34,939 individuals
PGP000477 |
Deutsch AJ et al. Diabetes Care (2023)
|Ext.
Reported Trait: Type 1 diabetes AUROC: 0.858
PPM018537 PGS000023
(AA_GRS)
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
PPM018538 PGS000024
(GRS2)
PSS011011|
European Ancestry|
16,663 individuals
PGP000477 |
Deutsch AJ et al. Diabetes Care (2023)
|Ext.
Reported Trait: Type 1 diabetes PPV (+PRS): 100.0 %
PPV (reference): 86.0 %
eMERGE type 1 diabetes algorithm
PPM018539 PGS000023
(AA_GRS)
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
PPM018540 PGS000024
(GRS2)
PSS011010|
Multi-ancestry (excluding European)|
40,980 individuals
PGP000477 |
Deutsch AJ et al. Diabetes Care (2023)
|Ext.
Reported Trait: Type 1 diabetes PPV (+PRS): 93.0 %
PPV (reference): 71.0 %
eMERGE type 1 diabetes algorithm
PPM018541 PGS000023
(AA_GRS)
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
PPM018542 PGS000024
(GRS2)
PSS011014|
European Ancestry|
34,939 individuals
PGP000477 |
Deutsch AJ et al. Diabetes Care (2023)
|Ext.
Reported Trait: Type 1 diabetes PPV (+PRS): 97.0 %
PPV (reference): 71.0 %
eMERGE type 1 diabetes algorithm
PPM018543 PGS000023
(AA_GRS)
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
PSS011014 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 34,939 individuals,
47.0 % Male samples
Mean = 59.1 years
Sd = 16.9 years
European Self-identified race = White MGBB
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