Polygenic Score (PGS) ID: PGS002243

Predicted Trait
Reported Trait Type 2 diabetes (T2D)
Mapped Trait(s) type 2 diabetes mellitus (MONDO_0005148)
Released in PGS Catalog: April 13, 2022
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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 ldpred_t2d
Development Method
Name LDpred
Parameters p = 0.003, LD radius = 2000, LD reference panel: European ancestry in 1000 Genomes
Variants
Original Genome Build GRCh37
Number of Variants 6,431,973
Effect Weight Type beta
PGS Source
PGS Catalog Publication (PGP) ID PGP000271
Citation (link to publication) Mars N et al. Cell Genom (2022)
Ancestry Distribution
Source of Variant
Associations (GWAS)
European: 100%
159,208 individuals (100%)
Score Development/Training
European: 100%
175,364 individuals (100%)
PGS Evaluation
European: 37.5%
African: 20.8%
East Asian: 16.7%
South Asian: 16.7%
Hispanic or Latin American: 4.2%
Additional Asian Ancestries: 4.2%
24 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 NR
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
—
[
  • 24,226 cases
  • , 151,138 controls
]
 European
(Finnish)		 FinnGen — — — — —

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
PPM012733 PSS009522|
European Ancestry|
258,402 individuals
 PGP000271 |
Mars N et al. Cell Genom (2022)
 Reported Trait: Type 2 diabetes OR: 1.58 [1.56, 1.6] — — age, sex, 10 PCs (+/- dataset-specific technical covariates) —
PPM012737 PSS009518|
European Ancestry|
110,597 individuals
 PGP000271 |
Mars N et al. Cell Genom (2022)
 Reported Trait: Type 2 diabetes OR: 1.55 [1.51, 1.59] — — age, sex, 10 PCs (+/- dataset-specific technical covariates) —
PPM012741 PSS009514|
East Asian Ancestry|
178,726 individuals
 PGP000271 |
Mars N et al. Cell Genom (2022)
 Reported Trait: Type 2 diabetes OR: 1.37 [1.36, 1.39] — — age, sex, 10 PCs (+/- dataset-specific technical covariates) —
PPM012745 PSS009526|
European Ancestry|
69,422 individuals
 PGP000271 |
Mars N et al. Cell Genom (2022)
 Reported Trait: Type 2 diabetes OR: 1.64 [1.6, 1.69] — — birth year, sex, 10 PCs (+/- dataset-specific technical covariates) —
PPM012749 PSS009534|
European Ancestry|
25,696 individuals
 PGP000271 |
Mars N et al. Cell Genom (2022)
 Reported Trait: Type 2 diabetes OR: 1.46 [1.41, 1.51] — — age, sex, 10 PCs (+/- dataset-specific technical covariates) —
PPM012753 PSS009530|
African Ancestry|
1,535 individuals
 PGP000271 |
Mars N et al. Cell Genom (2022)
 Reported Trait: Type 2 diabetes OR: 1.24 [1.09, 1.42] — — age, sex, 10 PCs (+/- dataset-specific technical covariates) —
PPM012757 PSS009542|
European Ancestry|
343,676 individuals
 PGP000271 |
Mars N et al. Cell Genom (2022)
 Reported Trait: Type 2 diabetes OR: 1.78 [1.75, 1.81] — — age, sex, 10 PCs (+/- dataset-specific technical covariates) —
PPM012762 PSS009538|
African Ancestry|
7,618 individuals
 PGP000271 |
Mars N et al. Cell Genom (2022)
 Reported Trait: Type 2 diabetes OR: 1.46 [1.32, 1.62] — — age, sex, 10 PCs (+/- dataset-specific technical covariates) —
PPM012767 PSS009546|
South Asian Ancestry|
7,628 individuals
 PGP000271 |
Mars N et al. Cell Genom (2022)
 Reported Trait: Type 2 diabetes OR: 1.66 [1.55, 1.79] — — age, sex, 10 PCs (+/- dataset-specific technical covariates) —
PPM021425 PSS011737|
European Ancestry|
109,021 individuals
 PGP000656 |
Ritchie SC et al. medRxiv (2024)
|Ext.|Pre		 Reported Trait: Type 2 diabetes OR: 1.55 [1.52, 1.59] AUROC: 0.703 [0.698, 0.708] — Age at baseline, sex (PGS adjusted for 20 PCs prior to model fitting) —
PPM021434 PSS011747|
European Ancestry|
245,177 individuals
 PGP000656 |
Ritchie SC et al. medRxiv (2024)
|Ext.|Pre		 Reported Trait: Type 2 diabetes OR: 1.78 [1.75, 1.82] AUROC: 0.737 [0.733, 0.742] — Age at baseline, sex assessment centre (PGS adjusted for 20 PCs prior to model fitting) —
PPM021453 PSS011738|
European Ancestry|
38,941 individuals
 PGP000656 |
Ritchie SC et al. medRxiv (2024)
|Ext.|Pre		 Reported Trait: Incident type 2 diabetes HR: 1.64 [1.53, 1.77] C-index: 0.741 [0.723, 0.758] — Age at baseline, sex (PGS adjusted for 20 PCs prior to model fitting) —
PPM021462 PSS011746|
European Ancestry|
232,808 individuals
 PGP000656 |
Ritchie SC et al. medRxiv (2024)
|Ext.|Pre		 Reported Trait: Incident type 2 diabetes HR: 1.49 [1.45, 1.52] C-index: 0.689 [0.683, 0.695] — Age at baseline, sex assessment centre (PGS adjusted for 20 PCs prior to model fitting) —
PPM021476 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 [0.712, 0.725] — Age at baseline, sex (PGS adjusted for 20 PCs prior to model fitting) —
PPM021503 PSS011736|
Hispanic or Latin American Ancestry|
33,652 individuals
 PGP000656 |
Ritchie SC et al. medRxiv (2024)
|Ext.|Pre		 Reported Trait: Type 2 diabetes OR: 1.43 [1.38, 1.48] AUROC: 0.76 [0.753, 0.767] — Age at baseline, sex (PGS adjusted for 20 PCs prior to model fitting) —
PPM021528 PSS011740|
East Asian Ancestry|
1,149 individuals
 PGP000656 |
Ritchie SC et al. medRxiv (2024)
|Ext.|Pre		 Reported Trait: Incident type 2 diabetes OR: 1.08 [0.93, 1.26] AUROC: 0.592 [0.548, 0.635] — Age at baseline, sex (PGS adjusted for 20 PCs prior to model fitting) —
PPM021548 PSS011741|
South Asian Ancestry|
852 individuals
 PGP000656 |
Ritchie SC et al. medRxiv (2024)
|Ext.|Pre		 Reported Trait: Incident type 2 diabetes OR: 1.12 [0.95, 1.32] AUROC: 0.643 [0.6, 0.685] — Age at baseline, sex (PGS adjusted for 20 PCs prior to model fitting) —
PPM021569 PSS011739|
Additional Asian Ancestries|
870 individuals
 PGP000656 |
Ritchie SC et al. medRxiv (2024)
|Ext.|Pre		 Reported Trait: Incident type 2 diabetes OR: 1.32 [1.11, 1.57] AUROC: 0.669 [0.625, 0.712] — Age at baseline, sex (PGS adjusted for 20 PCs prior to model fitting) —
PPM021585 PSS011743|
African Ancestry|
6,871 individuals
 PGP000656 |
Ritchie SC et al. medRxiv (2024)
|Ext.|Pre		 Reported Trait: Type 2 diabetes OR: 1.31 [1.21, 1.42] AUROC: 0.716 [0.696, 0.735] — Age at baseline, sex assessment centre (PGS adjusted for 20 PCs prior to model fitting) —
PPM021614 PSS011745|
East Asian Ancestry|
1,432 individuals
 PGP000656 |
Ritchie SC et al. medRxiv (2024)
|Ext.|Pre		 Reported Trait: Type 2 diabetes OR: 1.36 [1.08, 1.73] AUROC: 0.708 [0.65, 0.766] — Age at baseline, sex assessment centre (PGS adjusted for 20 PCs prior to model fitting) —
PPM021631 PSS011749|
South Asian Ancestry|
6,992 individuals
 PGP000656 |
Ritchie SC et al. medRxiv (2024)
|Ext.|Pre		 Reported Trait: Type 2 diabetes OR: 1.57 [1.47, 1.67] AUROC: 0.718 [0.703, 0.733] — Age at baseline, sex assessment centre (PGS adjusted for 20 PCs prior to model fitting) —
PPM021657 PSS011742|
African Ancestry|
6,019 individuals
 PGP000656 |
Ritchie SC et al. medRxiv (2024)
|Ext.|Pre		 Reported Trait: Incident type 2 diabetes HR: 1.1 [1.0, 1.22] C-index: 0.641 [0.614, 0.668] — Age at baseline, sex assessment centre (PGS adjusted for 20 PCs prior to model fitting) —
PPM021679 PSS011744|
East Asian Ancestry|
1,350 individuals
 PGP000656 |
Ritchie SC et al. medRxiv (2024)
|Ext.|Pre		 Reported Trait: Incident type 2 diabetes HR: 1.15 [0.83, 1.58] C-index: 0.679 [0.606, 0.752] — Age at baseline, sex assessment centre (PGS adjusted for 20 PCs prior to model fitting) —
PPM021695 PSS011748|
South Asian Ancestry|
5,685 individuals
 PGP000656 |
Ritchie SC et al. medRxiv (2024)
|Ext.|Pre		 Reported Trait: Incident type 2 diabetes HR: 1.17 [1.08, 1.28] C-index: 0.609 [0.586, 0.632] — 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
PSS009514 — —
[
  • 40,121 cases
  • , 138,605 controls
]
 — East Asian
(Japanese)		 — BBJ —
PSS009518 — —
[
  • 7,066 cases
  • , 103,531 controls
]
 — European
(Estonian)		 — EB —
PSS009522 — —
[
  • 37,001 cases
  • , 221,401 controls
]
 — European
(Finnish)		 — FinnGen —
PSS009526 — —
[
  • 5,228 cases
  • , 64,194 controls
]
 — European Norwegian HUNT —
PSS009530 — —
[
  • 660 cases
  • , 875 controls
]
 — African American or Afro-Caribbean — MGBB —
PSS009534 — —
[
  • 5,182 cases
  • , 20,514 controls
]
 — European — MGBB —
PSS009538 — —
[
  • 691 cases
  • , 6,927 controls
]
 — African unspecified — UKB —
PSS009542 — —
[
  • 13,616 cases
  • , 330,060 controls
]
 — European British UKB —
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 —
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 —
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 —
PSS009546 — —
[
  • 1,120 cases
  • , 6,508 controls
]
 — South Asian — UKB —
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 —
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 —
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 —
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 —
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 —
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 —
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 —
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 —