Polygenic Score (PGS) ID: PGS000024

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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Terms and Licenses
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Score Details

Score Construction
PGS Name GRS2
Development Method
Name Genome-wide significant associations and interaction modelling
Parameters Significance threshold for interactions: p < 10^-4
Variants
Original Genome Build NR
Number of Variants 85
Number of Variant Interaction Terms 18
Effect Weight Type log(OR)
PGS Source
PGS Catalog Publication (PGP) ID PGP000014
Citation (link to publication) Sharp SA et al. Diabetes Care (2019)
Ancestry Distribution
Source of Variant
Associations (GWAS)
European: 100%
16,086 individuals (100%)
PGS Evaluation
European: 57.9%
Not Reported: 15.8%
Multi-ancestry (including European): 10.5%
  • European
  • African
  • Hispanic or Latin American
African: 5.3%
Hispanic or Latin American: 5.3%
Multi-ancestry (excluding European): 5.3%
  • Additional Diverse Ancestries
  • Additional Asian Ancestries
  • East Asian
  • South Asian
  • African
  • Hispanic or Latin American
19 Sample Sets

Development Samples

Source of Variant Associations (GWAS)
Study Identifiers Sample Numbers Sample Ancestry Cohort(s)
GWAS Catalog: GCST000392
Europe PMC: 19956093
[
  • 6,670 cases
  • , 9,416 controls
]
 European T1DGC

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
PPM000048 PSS000032|
European Ancestry|
374,000 individuals
 PGP000014 |
Sharp SA et al. Diabetes Care (2019)
 Reported Trait: Type 1 diabetes — AUROC: 0.921 Youden index: 0.698 — —
PPM000753 PSS000368|
Ancestry Not Reported|
7,798 individuals
 PGP000091 |
Ferrat LA et al. Nat Med (2020)
|Ext.		 Reported Trait: Type 1 diabetes (5 years horizon time; landmark age 2 years) — AUROC: 0.93 — autoantibodies, family history —
PPM000754 PSS000368|
Ancestry Not Reported|
7,798 individuals
 PGP000091 |
Ferrat LA et al. Nat Med (2020)
|Ext.		 Reported Trait: Type 1 diabetes (8 years horizon time; landmark age 2 years) — AUROC: 0.87 — autoantibodies, family history —
PPM000755 PSS000368|
Ancestry Not Reported|
7,798 individuals
 PGP000091 |
Ferrat LA et al. Nat Med (2020)
|Ext.		 Reported Trait: Type 1 diabetes (5 years horizon time; landmark age 4 years) — AUROC: 0.96 — autoantibodies, family history —
PPM000751 PSS000368|
Ancestry Not Reported|
7,798 individuals
 PGP000091 |
Ferrat LA et al. Nat Med (2020)
|Ext.		 Reported Trait: Type 1 diabetes (1 year horizon time; landmark age 2 years) — AUROC: 0.96 — autoantibodies, family history —
PPM000752 PSS000368|
Ancestry Not Reported|
7,798 individuals
 PGP000091 |
Ferrat LA et al. Nat Med (2020)
|Ext.		 Reported Trait: Type 1 diabetes (3 years horizon time; landmark age 2 years) — AUROC: 0.94 — autoantibodies, family history —
PPM000750 PSS000368|
Ancestry Not Reported|
7,798 individuals
 PGP000091 |
Ferrat LA et al. Nat Med (2020)
|Ext.		 Reported Trait: Type 1 diabetes (by age 8; landmark age 2 years) — AUROC: 0.73 [0.7, 0.77] — — —
PPM002249 PSS001087|
European Ancestry|
3,930 individuals
 PGP000211 |
Aly DM et al. Nat Genet (2021)
|Ext.		 Reported Trait: Severe Insulin-Deficient Diabetes OR: 1.0 [0.93, 1.07] — — PC1-10 8 proxy variants were used to evaluate this score
PPM002250 PSS001088|
European Ancestry|
3,869 individuals
 PGP000211 |
Aly DM et al. Nat Genet (2021)
|Ext.		 Reported Trait: Severe Insulin-Resistant Diabetes OR: 1.0 [0.93, 1.07] — — PC1-10 8 proxy variants were used to evaluate this score
PPM002251 PSS001085|
European Ancestry|
4,116 individuals
 PGP000211 |
Aly DM et al. Nat Genet (2021)
|Ext.		 Reported Trait: Moderate Obesity-related Diabetes OR: 1.01 [0.95, 1.08] — — PC1-10 8 proxy variants were used to evaluate this score
PPM002252 PSS001084|
European Ancestry|
5,597 individuals
 PGP000211 |
Aly DM et al. Nat Genet (2021)
|Ext.		 Reported Trait: Moderate Age-Related Diabetes OR: 0.99 [0.94, 1.04] — — PC1-10 8 proxy variants were used to evaluate this score
PPM002248 PSS001086|
European Ancestry|
3,194 individuals
 PGP000211 |
Aly DM et al. Nat Genet (2021)
|Ext.		 Reported Trait: Severe Autoimmune Diabetes OR: 2.55 [2.28, 2.86] — — PC1-10 8 proxy variants were used to evaluate this score
PPM014801 PSS009895|
European Ancestry|
1,168 individuals
 PGP000338 |
Oram RA et al. Diabetes Care (2022)
|Ext.		 Reported Trait: Diabetes autoantibody positive insulin sensitive — AUROC: 0.864 [0.823, 0.905] — — —
PPM014803 PSS009893|
African Ancestry|
366 individuals
 PGP000338 |
Oram RA et al. Diabetes Care (2022)
|Ext.		 Reported Trait: Diabetes autoantibody positive insulin sensitive — AUROC: 0.851 [0.805, 0.897] — — —
PPM014805 PSS009894|
Hispanic or Latin American Ancestry|
412 individuals
 PGP000338 |
Oram RA et al. Diabetes Care (2022)
|Ext.		 Reported Trait: Diabetes autoantibody positive insulin sensitive — AUROC: 0.935 [0.906, 0.964] — — —
PPM014807 PSS009896|
Ancestry Not Reported|
99 individuals
 PGP000338 |
Oram RA et al. Diabetes Care (2022)
|Ext.		 Reported Trait: Diabetes autoantibody positive insulin sensitive — AUROC: 0.79 [0.679, 0.902] — — —
PPM018532 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 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 PSS011014|
European Ancestry|
34,939 individuals
 PGP000477 |
Deutsch AJ et al. Diabetes Care (2023)
|Ext.		 Reported Trait: Type 1 diabetes — AUROC: 0.888 — — —
PPM018535 PSS011014|
European Ancestry|
34,939 individuals
 PGP000477 |
Deutsch AJ et al. Diabetes Care (2023)
|Ext.		 Reported Trait: Type 1 diabetes — AUROC: 0.858 — — —
PPM018538 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 —
PPM018540 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 —
PPM018542 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 —
PPM020098 PSS011295|
Ancestry Not Reported|
1,798 individuals
 PGP000519 |
Thomas NJ et al. Diabetes Care (2023)
|Ext.		 Reported Trait: Type 1 diabetes vs autoantibody negative T2D — — p-value (inferior to): 0.0001 — —
PPM021124 PSS011531|
European Ancestry|
9,465 individuals
 PGP000614 |
Qu HQ et al. Diabetes Obes Metab (2021)
|Ext.		 Reported Trait: Type 1 diabetes β: -0.22 AUROC: 0.87 — — —
PPM021125 PSS011532|
European Ancestry|
9,450 individuals
 PGP000614 |
Qu HQ et al. Diabetes Obes Metab (2021)
|Ext.		 Reported Trait: Type 1 diabetes β: -0.234 AUROC: 0.862 — — —

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
PSS000368 TEDDY children were followed prospectively from 3–4 months of age, with visits every 3 months until 4 years of age. Each evaluation tested the three islet antibodies (GADA, IA2A and IAA), changes in family history, as well as other measurements specified by the TEDDY protocol. After 4 years of age, children with any islet autoantibodies remained on quarterly visits, while antibody-negative children were evaluated every 6 months. Children were followed prospectively until 15 years of age or until T1D onset, as defined using the American Diabetes Association’s criteria for diagnosis (doi: 10.1196/annals.1447.062) Median = 9.3 years
Range = [0.0833, 14.0] years
[
  • 305 cases
  • , 7,493 controls
]
,
50.86 % Male samples
 Range = [3.0, 4.0] years NR — TEDDY From 2004–2010, 424,788 newborns were screened at six US and European centers for high-risk HLA genotypes. TEDDY then enrolled 8,676 eligible infants with the intent to follow them until 15 years of age. The three major eligible HLA DR–DQ haplotypes are DR3–DQA1*0501–DQB1*0201, DR4–DQA1*0301–DQB1*0302 and DR8–DQA1*0401–DQB1*0402.
PSS011531 Cases were individuals with T1D —
[
  • 3,299 cases
  • , 6,166 controls
]
,
53.51 % Male samples
 — European — NR —
PSS011532 Cases were individuals with T1D —
[
  • 3,293 cases
  • , 6,157 controls
]
,
53.79 % Male samples
 — European — NR —
PSS011295 — — 1,798 individuals — Not reported — NR StartRight
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 —
PSS001084 Moderate Age-Related Diabetes (MARD) vs. controls —
[
  • 2,853 cases
  • , 2,744 controls
]
 — European Swedish ANDIS —
PSS001085 Moderate Obesity-related Diabetes (MOD) vs. controls —
[
  • 1,372 cases
  • , 2,744 controls
]
 — European Swedish ANDIS —
PSS001086 Severe Autoimmune Diabetes (SAID) vs. controls —
[
  • 450 cases
  • , 2,744 controls
]
 — European Swedish ANDIS —
PSS001087 Severe Insulin-Deficient Diabetes (SIDD) vs. controls —
[
  • 1,186 cases
  • , 2,744 controls
]
 — European Swedish ANDIS —
PSS001088 Severe Insulin-Resistant Diabetes (SIRD) vs. controls —
[
  • 1,125 cases
  • , 2,744 controls
]
 — European Swedish ANDIS —
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 — — 1,511 individuals,
36.0 % Male samples
 Mean = 46.9 years
Sd = 16.3 years		 Native American, Asian unspecified, Oceanian, Other — MGBB —
PSS011012 — — 1,269 individuals,
34.0 % Male samples
 Mean = 46.4 years
Sd = 16.1 years		 Hispanic or Latin American
(Hispanic)		 — MGBB —
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 —
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 —
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 —
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 —
PSS009893 — — 366 individuals — African American or Afro-Caribbean — SEARCH —
PSS009894 — — 412 individuals — Hispanic or Latin American — SEARCH —
PSS009895 — — 1,168 individuals — European — SEARCH —
PSS009896 — — 99 individuals — Not reported — SEARCH —
PSS000032 Type 1 Diabetes Case Definition = Clinical diagnosis of diabetes at less than or equal to 20 years of age; On insulin within 1 year from the time of diagnosis; Still on insulin at the time of recruit- ment; Not using oral antihyperglycemic agents; Did not ever self-report as having type 2 diabetes (T2D) —
[
  • 387 cases
  • , 373,613 controls
]
 — European — UKB —