Polygenic Score (PGS) ID: PGS000014

Predicted Trait
Reported Trait Type 2 diabetes (T2D)
Mapped Trait(s) type 2 diabetes mellitus (MONDO_0005148)
Released in PGS Catalog: Oct. 14, 2019
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Terms and Licenses
Freely available to the academic community for research use. Parties interested in using the scores for commercial purposes should contact the Broad Office of Strategic Alliances and Partnering (partnering@broadinstitute.org).

Score Details

Score Construction
PGS Name GPS_T2D
Development Method
Name LDpred
Parameters ρ = 0.01; LD panel = 503 1000G Europeans
Variants
Original Genome Build hg19
Number of Variants 6,917,436
Effect Weight Type NR
PGS Source
PGS Catalog Publication (PGP) ID PGP000006
Citation (link to publication) Khera AV et al. Nat Genet (2018)
Ancestry Distribution
Source of Variant
Associations (GWAS)
European: 100%
318,416 individuals (100%)
Score Development/Training
European: 100%
120,280 individuals (100%)
PGS Evaluation
European: 31.6%
African: 15.8%
East Asian: 15.8%
South Asian: 15.8%
Not Reported: 5.3%
Hispanic or Latin American: 5.3%
Additional Asian Ancestries: 5.3%
Multi-ancestry (including European): 5.3%
  • African
  • Additional Asian Ancestries
  • Additional Diverse Ancestries
  • European
19 Sample Sets

Development Samples

Source of Variant Associations (GWAS)
Study Identifiers Sample Numbers Sample Ancestry Cohort(s)
GWAS Catalog: GCST004773
Europe PMC: 28566273
 159,208 individuals European DIAGRAM, EPIC, GERA
GWAS Catalog: GCST004774
Europe PMC: 28566273
 159,208 individuals European DIAGRAM, EPIC, GERA
Score Development/Training
Study Identifiers Sample Numbers Sample Ancestry Cohort(s) Phenotype Definitions & Methods Age of Study Participants Participant Follow-up Time Additional Ancestry Description Additional Sample/Cohort Information
—
[
  • 2,785 cases
  • , 117,495 controls
]
 European UKB Type 2 diabetes ascertainment was based on self-report in an interview with a trained nurse or an ICD-10 code of E11.X in hospitalization records. — — — UKB Phase 1

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
PPM000023 PSS000017|
European Ancestry|
288,978 individuals
 PGP000006 |
Khera AV et al. Nat Genet (2018)
 Reported Trait: Type 2 diabetes — AUROC: 0.73 [0.72, 0.73] Nagelkerke’s R2 (estimate of variance explained by the PGS after covariate adjustment): 0.029 age; sex; Ancestry PC 1-4; genotyping chip —
PPM002477 PSS001117|
European Ancestry|
68,229 individuals
 PGP000218 |
He Y et al. Diabetes Care (2021)
|Ext.		 Reported Trait: Incident type II diabetes — C-index: 0.709 [0.696, 0.722] Hazard ratio (HR, top 10% vs. remaining 90%): 2.0 [1.73, 2.31] Sex, age, principal components, assessment center —
PPM002478 PSS001117|
European Ancestry|
68,229 individuals
 PGP000218 |
He Y et al. Diabetes Care (2021)
|Ext.		 Reported Trait: Incident type II diabetes in males — C-index: 0.68 [0.663, 0.697] — Age, principal components and assessment center —
PPM002479 PSS001117|
European Ancestry|
68,229 individuals
 PGP000218 |
He Y et al. Diabetes Care (2021)
|Ext.		 Reported Trait: Incident type II diabetes in females — C-index: 0.705 [0.682, 0.728] — Age, principal components and assessment center —
PPM002480 PSS001117|
European Ancestry|
68,229 individuals
 PGP000218 |
He Y et al. Diabetes Care (2021)
|Ext.		 Reported Trait: Incident type II diabetes — C-index: 0.776 [0.764, 0.788] — Sex, age, principal components, assessment center, polyexposure score —
PPM002481 PSS001117|
European Ancestry|
68,229 individuals
 PGP000218 |
He Y et al. Diabetes Care (2021)
|Ext.		 Reported Trait: Incident type II diabetes — C-index: 0.844 [0.834, 0.854] — Sex, age, principal components, assessment center, clinical risk score —
PPM002482 PSS001117|
European Ancestry|
68,229 individuals
 PGP000218 |
He Y et al. Diabetes Care (2021)
|Ext.		 Reported Trait: Incident type II diabetes — C-index: 0.855 [0.845, 0.865] — Sex, age, principal components, assessment center, polyexposure socre, clinical risk score —
PPM002483 PSS001117|
European Ancestry|
68,229 individuals
 PGP000218 |
He Y et al. Diabetes Care (2021)
|Ext.		 Reported Trait: Incident type II diabetes in females — C-index: 0.786 [0.765, 0.807] — Age, principal components, assessment center, polyexposure score —
PPM002485 PSS001117|
European Ancestry|
68,229 individuals
 PGP000218 |
He Y et al. Diabetes Care (2021)
|Ext.		 Reported Trait: Incident type II diabetes in females — C-index: 0.859 [0.842, 0.876] — Sex, age, principal components, assessment center, clinical risk score —
PPM002486 PSS001117|
European Ancestry|
68,229 individuals
 PGP000218 |
He Y et al. Diabetes Care (2021)
|Ext.		 Reported Trait: Incident type II diabetes in males — C-index: 0.749 [0.734, 0.764] — Age, principal components, assessment center, polyexposure score —
PPM002487 PSS001117|
European Ancestry|
68,229 individuals
 PGP000218 |
He Y et al. Diabetes Care (2021)
|Ext.		 Reported Trait: Incident type II diabetes in males — C-index: 0.821 [0.808, 0.834] — Age, principal components, assessment center, polyexposure socre, clinical risk score —
PPM002488 PSS001117|
European Ancestry|
68,229 individuals
 PGP000218 |
He Y et al. Diabetes Care (2021)
|Ext.		 Reported Trait: Incident type II diabetes in males — C-index: 0.834 [0.821, 0.847] — Sex, age, principal components, assessment center, clinical risk score —
PPM002484 PSS001117|
European Ancestry|
68,229 individuals
 PGP000218 |
He Y et al. Diabetes Care (2021)
|Ext.		 Reported Trait: Incident type II diabetes in females — C-index: 0.869 [0.853, 0.885] — Age, principal components, assessment center, polyexposure socre, clinical risk score —
PPM015522 PSS009971|
Multi-ancestry (including European)|
36,422 individuals
 PGP000381 |
Hao L et al. Nat Med (2022)
|Ext.		 Reported Trait: Type 2 diabetes mellitus OR: 1.75 [1.57, 1.95] — — 4 genetic PCs —
PPM019100 PSS011181|
Ancestry Not Reported|
3,071 individuals
 PGP000504 |
Duschek E et al. Sci Rep (2023)
|Ext.		 Reported Trait: Incident type 2 diabetes — AUROC: 0.613 [0.565, 0.657] — — —
PPM019098 PSS011181|
Ancestry Not Reported|
3,071 individuals
 PGP000504 |
Duschek E et al. Sci Rep (2023)
|Ext.		 Reported Trait: Incident type 2 diabetes OR: 1.67 [1.37, 2.03] — — Age, Sex, BMI, Physical activity, FamRS —
PPM019099 PSS011181|
Ancestry Not Reported|
3,071 individuals
 PGP000504 |
Duschek E et al. Sci Rep (2023)
|Ext.		 Reported Trait: Prevelant type 2 diabetes — AUROC: 0.869 [0.842, 0.896] — — —
PPM019097 PSS011181|
Ancestry Not Reported|
3,071 individuals
 PGP000504 |
Duschek E et al. Sci Rep (2023)
|Ext.		 Reported Trait: Prevelant type 2 diabetes OR: 6.21 [5.06, 7.74] — — Age, Sex, BMI, Physical activity, FamRS —
PPM021428 PSS011737|
European Ancestry|
109,021 individuals
 PGP000656 |
Ritchie SC et al. medRxiv (2024)
|Ext.|Pre		 Reported Trait: Type 2 diabetes OR: 1.51 [1.48, 1.55] AUROC: 0.7 [0.695, 0.705] — Age at baseline, sex (PGS adjusted for 20 PCs prior to model fitting) —
PPM021437 PSS011747|
European Ancestry|
245,177 individuals
 PGP000656 |
Ritchie SC et al. medRxiv (2024)
|Ext.|Pre		 Reported Trait: Type 2 diabetes OR: 1.71 [1.67, 1.74] AUROC: 0.731 [0.726, 0.736] — Age at baseline, sex assessment centre (PGS adjusted for 20 PCs prior to model fitting) —
PPM021458 PSS011738|
European Ancestry|
38,941 individuals
 PGP000656 |
Ritchie SC et al. medRxiv (2024)
|Ext.|Pre		 Reported Trait: Incident type 2 diabetes HR: 1.58 [1.47, 1.7] C-index: 0.737 [0.719, 0.754] — Age at baseline, sex (PGS adjusted for 20 PCs prior to model fitting) —
PPM021465 PSS011746|
European Ancestry|
232,808 individuals
 PGP000656 |
Ritchie SC et al. medRxiv (2024)
|Ext.|Pre		 Reported Trait: Incident type 2 diabetes HR: 1.45 [1.42, 1.49] C-index: 0.686 [0.679, 0.692] — Age at baseline, sex assessment centre (PGS adjusted for 20 PCs prior to model fitting) —
PPM021484 PSS011735|
African Ancestry|
44,346 individuals
 PGP000656 |
Ritchie SC et al. medRxiv (2024)
|Ext.|Pre		 Reported Trait: Type 2 diabetes OR: 1.21 [1.17, 1.24] AUROC: 0.717 [0.71, 0.723] — Age at baseline, sex (PGS adjusted for 20 PCs prior to model fitting) —
PPM021506 PSS011736|
Hispanic or Latin American Ancestry|
33,652 individuals
 PGP000656 |
Ritchie SC et al. medRxiv (2024)
|Ext.|Pre		 Reported Trait: Type 2 diabetes OR: 1.39 [1.34, 1.44] AUROC: 0.757 [0.75, 0.764] — Age at baseline, sex (PGS adjusted for 20 PCs prior to model fitting) —
PPM021531 PSS011740|
East Asian Ancestry|
1,149 individuals
 PGP000656 |
Ritchie SC et al. medRxiv (2024)
|Ext.|Pre		 Reported Trait: Incident type 2 diabetes OR: 0.99 [0.85, 1.16] AUROC: 0.585 [0.541, 0.629] — Age at baseline, sex (PGS adjusted for 20 PCs prior to model fitting) —
PPM021553 PSS011741|
South Asian Ancestry|
852 individuals
 PGP000656 |
Ritchie SC et al. medRxiv (2024)
|Ext.|Pre		 Reported Trait: Incident type 2 diabetes OR: 1.03 [0.87, 1.21] AUROC: 0.639 [0.596, 0.683] — Age at baseline, sex (PGS adjusted for 20 PCs prior to model fitting) —
PPM021571 PSS011739|
Additional Asian Ancestries|
870 individuals
 PGP000656 |
Ritchie SC et al. medRxiv (2024)
|Ext.|Pre		 Reported Trait: Incident type 2 diabetes OR: 0.82 [0.69, 0.97] AUROC: 0.662 [0.618, 0.706] — Age at baseline, sex (PGS adjusted for 20 PCs prior to model fitting) —
PPM021589 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 [0.695, 0.733] — Age at baseline, sex assessment centre (PGS adjusted for 20 PCs prior to model fitting) —
PPM021615 PSS011745|
East Asian Ancestry|
1,432 individuals
 PGP000656 |
Ritchie SC et al. medRxiv (2024)
|Ext.|Pre		 Reported Trait: Type 2 diabetes OR: 1.28 [1.01, 1.61] AUROC: 0.705 [0.648, 0.763] — Age at baseline, sex assessment centre (PGS adjusted for 20 PCs prior to model fitting) —
PPM021635 PSS011749|
South Asian Ancestry|
6,992 individuals
 PGP000656 |
Ritchie SC et al. medRxiv (2024)
|Ext.|Pre		 Reported Trait: Type 2 diabetes OR: 1.48 [1.39, 1.58] AUROC: 0.711 [0.696, 0.726] — Age at baseline, sex assessment centre (PGS adjusted for 20 PCs prior to model fitting) —
PPM021653 PSS011742|
African Ancestry|
6,019 individuals
 PGP000656 |
Ritchie SC et al. medRxiv (2024)
|Ext.|Pre		 Reported Trait: Incident type 2 diabetes HR: 1.12 [1.01, 1.23] C-index: 0.641 [0.614, 0.669] — Age at baseline, sex assessment centre (PGS adjusted for 20 PCs prior to model fitting) —
PPM021677 PSS011744|
East Asian Ancestry|
1,350 individuals
 PGP000656 |
Ritchie SC et al. medRxiv (2024)
|Ext.|Pre		 Reported Trait: Incident type 2 diabetes HR: 1.24 [0.9, 1.7] C-index: 0.684 [0.609, 0.758] — Age at baseline, sex assessment centre (PGS adjusted for 20 PCs prior to model fitting) —
PPM021699 PSS011748|
South Asian Ancestry|
5,685 individuals
 PGP000656 |
Ritchie SC et al. medRxiv (2024)
|Ext.|Pre		 Reported Trait: Incident type 2 diabetes HR: 1.14 [1.05, 1.24] C-index: 0.605 [0.582, 0.628] — Age at baseline, sex assessment centre (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
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 —
PSS011746 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 —
[
  • 6,016 cases
  • , 226,792 controls
]
 — European Ancestry label assigned based on genetic similarity with 1000 Genomes reference panel superpopulations UKB —
PSS011747 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 —
[
  • 11,080 cases
  • , 234,097 controls
]
 — European 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 —
PSS011181 — — 3,071 individuals,
48.8 % Male samples
 Mean = 57.4 years
Sd = 12.88 years		 Not reported — KORA —
PSS009971 — — 30,716 individuals — European — MGBB —
PSS009971 — — 1,807 individuals — African unspecified
(Black)		 — MGBB —
PSS009971 — — 786 individuals — Asian unspecified — MGBB —
PSS009971 — — 3,113 individuals — Other — MGBB —
PSS000017 Type 2 diabetes ascertainment was based on self-report in an interview with a trained nurse or an ICD-10 code of E11.X in hospitalization records. —
[
  • 5,853 cases
  • , 283,125 controls
]
 — European — UKB UKB Phase 2
PSS001117 T2D cases were defined as having an ICD-10 code of E11.X or having self-reported T2D in the in- terview. Only cases in which the individuals did not have T2D during the first assessment visit period (2006–2010) but were subsequently fol- lowed up for incident T2D events were considered. Median = 3.58 years
[
  • 1,281 cases
  • , 66,948 controls
]
,
47.81 % Male samples
 — European — UKB —