Polygenic Score (PGS) ID: PGS000805

Predicted Trait
Reported Trait Type 2 diabetes (T2D)
Mapped Trait(s) type 2 diabetes mellitus (MONDO_0005148)
Released in PGS Catalog: June 11, 2021
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Terms and Licenses
Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)

Score Details

Score Construction
PGS Name GRS582_T2Deur
Development Method
Name Genome-wide significant variants
Parameters NR
Variants
Original Genome Build NR
Number of Variants 582
Effect Weight Type beta
PGS Source
PGS Catalog Publication (PGP) ID PGP000193
Citation (link to publication) Polfus LM et al. HGG Adv (2021)
Ancestry Distribution
Source of Variant
Associations (GWAS)
European: 100%
1,114,458 individuals (100%)
PGS Evaluation
African: 20%
East Asian: 20%
European: 20%
South Asian: 20%
Hispanic or Latin American: 6.7%
Additional Asian Ancestries: 6.7%
Additional Diverse Ancestries: 6.7%
15 Sample Sets

Development Samples

Source of Variant Associations (GWAS)
Study Identifiers Sample Numbers Sample Ancestry Cohort(s)
GWAS Catalog: GCST010555
Europe PMC: 32541925
 1,114,458 individuals European 32 cohorts
  • BioMe
  • ,DGDG
  • ,DGI
  • ,EGCUT
  • ,FHS
  • ,FUSION
  • ,GCKD
  • ,GENOA
  • ,GERA
  • ,GOMAP
  • ,GoDARTS
  • ,HPFS
  • ,InterAct
  • ,KORA
  • ,MDC
  • ,MESA
  • ,METSIM
  • ,MGI
  • ,MVP
  • ,MedSTAR
  • ,NHS
  • ,Nugene
  • ,PIVUS
  • ,PMB
  • ,PROSPER
  • ,PennCATH
  • ,RS
  • ,UKB
  • ,ULSAM
  • ,UPCH
  • ,WTCCC
  • ,deCODE

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
PPM002120 PSS001046|
European Ancestry|
423,729 individuals
 PGP000193 |
Polfus LM et al. HGG Adv (2021)
 Reported Trait: Type 2 diabetes — AUROC: 0.8253 [0.8224, 0.8281] Odds Ratio (OR, top 10% vs middle 20%): 2.95 [2.81, 3.1] Age, sex, body mass index, PCs(1-10) Only 579 SNPs from the 582 SNP GRS, were utilised with imputation INFO scores > 0.45. 3 SNPs were not included as they were not present in the cohorts.
PPM002122 PSS001046|
European Ancestry|
423,729 individuals
 PGP000193 |
Polfus LM et al. HGG Adv (2021)
 Reported Trait: Type 2 diabetes — AUROC: 0.6593 [0.6555, 0.6632] — — Only 579 SNPs from the 582 SNP GRS, were utilised with imputation INFO scores > 0.45. 3 SNPs were not included as they were not present in the cohorts.
PPM002134 PSS001048|
Additional Diverse Ancestries|
3,551 individuals
 PGP000193 |
Polfus LM et al. HGG Adv (2021)
 Reported Trait: Type 2 diabetes — AUROC: 0.6213 [0.6029, 0.6397] — — Only 579 SNPs from the 582 SNP GRS, were utilised with imputation INFO scores > 0.45. 3 SNPs were not included as they were not present in the cohorts. Population-specific weights were not available for indiviuals of an Oceanian ancestry (Native Hawaiian). Therefore, GRS582_T2Deur was utilised to predict type 2 diabetes in individuals of an Oceanian ancestry.
PPM002132 PSS001048|
Additional Diverse Ancestries|
3,551 individuals
 PGP000193 |
Polfus LM et al. HGG Adv (2021)
 Reported Trait: Type 2 diabetes — AUROC: 0.7985 [0.7842, 0.8129] Odds Ratio (OR, top 10% vs middle 20%): 2.13 [1.63, 2.79] Age, sex, body mass index, PCs(1-10) Only 579 SNPs from the 582 SNP GRS, were utilised with imputation INFO scores > 0.45. 3 SNPs were not included as they were not present in the cohorts. Population-specific weights were not available for indiviuals of an Oceanian ancestry (Native Hawaiian). Therefore, GRS582_T2Deur was utilised to predict type 2 diabetes in individuals of an Oceanian ancestry.
PPM021422 PSS011737|
European Ancestry|
109,021 individuals
 PGP000656 |
Ritchie SC et al. medRxiv (2024)
|Ext.|Pre		 Reported Trait: Type 2 diabetes OR: 1.59 [1.56, 1.63] AUROC: 0.707 [0.702, 0.712] — Age at baseline, sex (PGS adjusted for 20 PCs prior to model fitting) —
PPM021457 PSS011738|
European Ancestry|
38,941 individuals
 PGP000656 |
Ritchie SC et al. medRxiv (2024)
|Ext.|Pre		 Reported Trait: Incident type 2 diabetes HR: 1.59 [1.48, 1.71] C-index: 0.736 [0.718, 0.753] — Age at baseline, sex (PGS adjusted for 20 PCs prior to model fitting) —
PPM021477 PSS011735|
African Ancestry|
44,346 individuals
 PGP000656 |
Ritchie SC et al. medRxiv (2024)
|Ext.|Pre		 Reported Trait: Type 2 diabetes OR: 1.23 [1.2, 1.27] AUROC: 0.718 [0.711, 0.724] — Age at baseline, sex (PGS adjusted for 20 PCs prior to model fitting) —
PPM021497 PSS011736|
Hispanic or Latin American Ancestry|
33,652 individuals
 PGP000656 |
Ritchie SC et al. medRxiv (2024)
|Ext.|Pre		 Reported Trait: Type 2 diabetes OR: 1.49 [1.44, 1.55] AUROC: 0.764 [0.758, 0.771] — Age at baseline, sex (PGS adjusted for 20 PCs prior to model fitting) —
PPM021518 PSS011740|
East Asian Ancestry|
1,149 individuals
 PGP000656 |
Ritchie SC et al. medRxiv (2024)
|Ext.|Pre		 Reported Trait: Incident type 2 diabetes OR: 1.3 [1.11, 1.52] AUROC: 0.613 [0.572, 0.654] — Age at baseline, sex (PGS adjusted for 20 PCs prior to model fitting) —
PPM021561 PSS011739|
Additional Asian Ancestries|
870 individuals
 PGP000656 |
Ritchie SC et al. medRxiv (2024)
|Ext.|Pre		 Reported Trait: Incident type 2 diabetes OR: 1.58 [1.33, 1.88] AUROC: 0.701 [0.659, 0.743] — Age at baseline, sex (PGS adjusted for 20 PCs prior to model fitting) —
PPM021590 PSS011743|
African Ancestry|
6,871 individuals
 PGP000656 |
Ritchie SC et al. medRxiv (2024)
|Ext.|Pre		 Reported Trait: Type 2 diabetes OR: 1.27 [1.18, 1.38] AUROC: 0.714 [0.694, 0.733] — Age at baseline, sex assessment centre (PGS adjusted for 20 PCs prior to model fitting) —
PPM021603 PSS011745|
East Asian Ancestry|
1,432 individuals
 PGP000656 |
Ritchie SC et al. medRxiv (2024)
|Ext.|Pre		 Reported Trait: Type 2 diabetes OR: 1.7 [1.35, 2.16] AUROC: 0.734 [0.679, 0.788] — Age at baseline, sex assessment centre (PGS adjusted for 20 PCs prior to model fitting) —
PPM021629 PSS011749|
South Asian Ancestry|
6,992 individuals
 PGP000656 |
Ritchie SC et al. medRxiv (2024)
|Ext.|Pre		 Reported Trait: Type 2 diabetes OR: 1.61 [1.51, 1.73] AUROC: 0.721 [0.706, 0.736] — Age at baseline, sex assessment centre (PGS adjusted for 20 PCs prior to model fitting) —
PPM021640 PSS011742|
African Ancestry|
6,019 individuals
 PGP000656 |
Ritchie SC et al. medRxiv (2024)
|Ext.|Pre		 Reported Trait: Incident type 2 diabetes HR: 1.19 [1.08, 1.31] C-index: 0.646 [0.619, 0.673] — Age at baseline, sex assessment centre (PGS adjusted for 20 PCs prior to model fitting) —
PPM021673 PSS011744|
East Asian Ancestry|
1,350 individuals
 PGP000656 |
Ritchie SC et al. medRxiv (2024)
|Ext.|Pre		 Reported Trait: Incident type 2 diabetes HR: 1.28 [0.93, 1.76] C-index: 0.679 [0.606, 0.753] — Age at baseline, sex assessment centre (PGS adjusted for 20 PCs prior to model fitting) —
PPM021688 PSS011748|
South Asian Ancestry|
5,685 individuals
 PGP000656 |
Ritchie SC et al. medRxiv (2024)
|Ext.|Pre		 Reported Trait: Incident type 2 diabetes HR: 1.26 [1.16, 1.38] C-index: 0.617 [0.594, 0.64] — Age at baseline, sex assessment centre (PGS adjusted for 20 PCs prior to model fitting) —
PPM021537 PSS011741|
South Asian Ancestry|
852 individuals
 PGP000656 |
Ritchie SC et al. medRxiv (2024)
|Ext.|Pre		 Reported Trait: Incident type 2 diabetes OR: 1.45 [1.23, 1.72] AUROC: 0.674 [0.633, 0.716] — Age at baseline, sex (PGS adjusted for 20 PCs prior to model fitting) —

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
PSS001046 Cases are individuals with type 2 diabetes (T2D). T2D cases were defined as individuals with (1) a T2D diagnosis by a physician/medical professional and use of medication for treatment of diabetes,and/or (2)a fasting(R8h)blood glucose measurement R126 mg/dL indicated in examination records. For the UKB cohort, T2D cases were defined by an ICD-10 code of E11.X or a self-reported diagnosis in an interview with a trained nurse. —
[
  • 19,786 cases
  • , 403,943 controls
]
 — European — UKB Possible significant sample overlap with this dataset and the datasets used to source/develop GRS582_T2Dmulti and GRS582_T2Deur
PSS001048 Cases are individuals with type 2 diabetes (T2D). T2D cases were defined as individualswith (1) a T2D diagnosis by a physician/medical professional and use of medication for treat-mentofdiabetes,and/or (2)a fasting(R8h)blood glucose measurement R126 mg/dL indicated in examination records. For the MEC cohort, T2D cases were defined using the following criteria: (a) a self-report of diabetes on the baseline questionnaire, 2nd questionnaire or 3rd questionnaire; and (b) self-report of taking medication for T2D at the time of blood draw; and (c) no diagnosis of T1D in the absence of a T2D diagnosis from the California Office of Statewide Health Planning and Development (OSHPD) for California Residents. In addition, cases included individuals who were linked to the diabetes registries of Hawaii Medical Service Association (HMSA) or Kaiser Permanente Hawaii (KPH) health plans, or who were designated as diabetic in the Chronic Conditions Data Warehouse (CCW) of Medicare. —
[
  • 1,534 cases
  • , 2,017 controls
]
 — Oceanian
(Native Hawaiian)		 — MEC —
PSS011735 T2D cases were ascertained based on a combination of hospital diagnosis codes, prescription medication, and lab results from blood tests occurring prior to baseline assessment. Participants were considered controls if they had no history of any diabetes diagnoses, T2D medication, or abnormal glucose or HbA1c lab results. Participants with T1D or uncertain diabetes status were excluded from analysis —
[
  • 5,663 cases
  • , 38,683 controls
]
 — African unspecified Ancestry label assigned based on genetic similarity with 1000 Genomes reference panel superpopulations AllofUs —
PSS011736 T2D cases were ascertained based on a combination of hospital diagnosis codes, prescription medication, and lab results from blood tests occurring prior to baseline assessment. Participants were considered controls if they had no history of any diabetes diagnoses, T2D medication, or abnormal glucose or HbA1c lab results. Participants with T1D or uncertain diabetes status were excluded from analysis —
[
  • 4,033 cases
  • , 29,619 controls
]
 — Hispanic or Latin American Ancestry label assigned based on genetic similarity with 1000 Genomes reference panel superpopulations AllofUs —
PSS011737 T2D cases were ascertained based on a combination of hospital diagnosis codes, prescription medication, and lab results from blood tests occurring prior to baseline assessment. Participants were considered controls if they had no history of any diabetes diagnoses, T2D medication, or abnormal glucose or HbA1c lab results. Participants with T1D or uncertain diabetes status were excluded from analysis —
[
  • 10,069 cases
  • , 98,952 controls
]
 — European Ancestry label assigned based on genetic similarity with 1000 Genomes reference panel superpopulations AllofUs —
PSS011738 T2D was defined using ICD-10 codes E10-E14, G59.0, G63.2, H28.0, H36.0, M14.2, N08.3, or O24.0-O24.3. Participants with any diabetes history were excluded from analysis. Incident diabetes events were treated as incident T2D —
[
  • 726 cases
  • , 38,215 controls
]
 — European Ancestry label assigned based on genetic similarity with 1000 Genomes reference panel superpopulations INTERVAL —
PSS011739 Incident T2D was ascertained through a combination of linkage to national healthcare records, self-reported medical history at follow-up assessment (either diagnosis from a primary care physician or current diabetes medication usage), or with blood biomarker concentrations indicative of diabetes following the American Diabetes Association criteria (fasting glucose ≥ 7 mmol/L or HbA1c ≥ 6.5% or random blood glucose ≥11 mmol/L) —
[
  • 187 cases
  • , 683 controls
]
 — South East Asian
(Malay Singaporean)		 Ancestry label assigned based on Malay being the majority reported ethnicity within the genetic cluster SingaporeMEC —
PSS011740 Incident T2D was ascertained through a combination of linkage to national healthcare records, self-reported medical history at follow-up assessment (either diagnosis from a primary care physician or current diabetes medication usage), or with blood biomarker concentrations indicative of diabetes following the American Diabetes Association criteria (fasting glucose ≥ 7 mmol/L or HbA1c ≥ 6.5% or random blood glucose ≥11 mmol/L) —
[
  • 205 cases
  • , 944 controls
]
 — East Asian
(Chinese Singaporean)		 Ancestry label assigned based on genetic similarity with 1000 Genomes reference panel superpopulations SingaporeMEC —
PSS011741 Incident T2D was ascertained through a combination of linkage to national healthcare records, self-reported medical history at follow-up assessment (either diagnosis from a primary care physician or current diabetes medication usage), or with blood biomarker concentrations indicative of diabetes following the American Diabetes Association criteria (fasting glucose ≥ 7 mmol/L or HbA1c ≥ 6.5% or random blood glucose ≥11 mmol/L) —
[
  • 194 cases
  • , 658 controls
]
 — South Asian
(Indian Singaporean)		 Ancestry label assigned based on genetic similarity with 1000 Genomes reference panel superpopulations SingaporeMEC —
PSS011742 Prevalent T2D status at baseline was adjudicated from a combination of retrospective hospital episode records, self-reported history of diabetes, and baseline medication using the Eastwood et al. algorithms. Incident T2D cases were ascertained following the Eastwood et al. algorithms on the basis of ICD-10 diagnosis coding E11 in either the hospital inpatient or death registry data —
[
  • 395 cases
  • , 5,624 controls
]
 — African unspecified Ancestry label assigned based on genetic similarity with 1000 Genomes reference panel superpopulations UKB —
PSS011743 Prevalent T2D status at baseline was adjudicated from a combination of retrospective hospital episode records, self-reported history of diabetes, and baseline medication using the Eastwood et al. algorithms. Incident T2D cases were ascertained following the Eastwood et al. algorithms on the basis of ICD-10 diagnosis coding E11 in either the hospital inpatient or death registry data —
[
  • 766 cases
  • , 6,105 controls
]
 — African unspecified Ancestry label assigned based on genetic similarity with 1000 Genomes reference panel superpopulations UKB —
PSS011744 Prevalent T2D status at baseline was adjudicated from a combination of retrospective hospital episode records, self-reported history of diabetes, and baseline medication using the Eastwood et al. algorithms. Incident T2D cases were ascertained following the Eastwood et al. algorithms on the basis of ICD-10 diagnosis coding E11 in either the hospital inpatient or death registry data —
[
  • 37 cases
  • , 1,313 controls
]
 — East Asian Ancestry label assigned based on genetic similarity with 1000 Genomes reference panel superpopulations UKB —
PSS011745 Prevalent T2D status at baseline was adjudicated from a combination of retrospective hospital episode records, self-reported history of diabetes, and baseline medication using the Eastwood et al. algorithms. Incident T2D cases were ascertained following the Eastwood et al. algorithms on the basis of ICD-10 diagnosis coding E11 in either the hospital inpatient or death registry data —
[
  • 76 cases
  • , 1,356 controls
]
 — East Asian Ancestry label assigned based on genetic similarity with 1000 Genomes reference panel superpopulations UKB —
PSS011748 Prevalent T2D status at baseline was adjudicated from a combination of retrospective hospital episode records, self-reported history of diabetes, and baseline medication using the Eastwood et al. algorithms. Incident T2D cases were ascertained following the Eastwood et al. algorithms on the basis of ICD-10 diagnosis coding E11 in either the hospital inpatient or death registry data —
[
  • 513 cases
  • , 5,172 controls
]
 — South Asian Ancestry label assigned based on genetic similarity with 1000 Genomes reference panel superpopulations UKB —
PSS011749 Prevalent T2D status at baseline was adjudicated from a combination of retrospective hospital episode records, self-reported history of diabetes, and baseline medication using the Eastwood et al. algorithms. Incident T2D cases were ascertained following the Eastwood et al. algorithms on the basis of ICD-10 diagnosis coding E11 in either the hospital inpatient or death registry data —
[
  • 1,253 cases
  • , 5,739 controls
]
 — South Asian Ancestry label assigned based on genetic similarity with 1000 Genomes reference panel superpopulations UKB —