Polygenic Score (PGS) ID: PGS004923

Predicted Trait
Reported Trait Type 2 diabetes (T2D)
Mapped Trait(s) type 2 diabetes mellitus (MONDO_0005148)
Released in PGS Catalog: Aug. 29, 2024
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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 T2D_metaGRS
Development Method
Name MetaGRS of 44 component PGS
Parameters LDpred2 on 44 underlying GWAS + elasticnet logistic regression on 44 resulting PGS (alpha = 1, lambda = 7.558722e-05)
Variants
Original Genome Build GRCh37
Number of Variants 1,349,896
Effect Weight Type beta
PGS Source
PGS Catalog Publication (PGP) ID PGP000656
Citation (link to publication) Ritchie SC et al. medRxiv (2024) Preprint
Ancestry Distribution
Source of Variant
Associations (GWAS)
European: 80.8%
East Asian: 14.3%
Multi-ancestry (excluding European): 3.6%
  • South Asian
  • East Asian
  • African
  • Hispanic or Latin American
Hispanic or Latin American: 0.5%
African: 0.4%
South Asian: 0.3%
Additional Diverse Ancestries: 0.05%
Greater Middle Eastern: 0.03%
Not Reported: 0.01%
8,527,717 individuals (100%)
Score Development/Training
European: 100%
130,816 individuals (100%)
PGS Evaluation
European: 26.7%
African: 20%
East Asian: 20%
South Asian: 20%
Hispanic or Latin American: 6.7%
Additional Asian Ancestries: 6.7%
15 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
Europe PMC: 30297969
[
  • 55,005 cases
  • , 400,308 controls
]
 European NR
GWAS Catalog: GCST008114
Europe PMC: 31049640
 4,347 individuals Sub-Saharan African NR
GWAS Catalog: GCST010118
Europe PMC: 32499647
 433,540 individuals East Asian NR
GWAS Catalog: GCST007515
Europe PMC: 29632382
 298,957 individuals European NR
GWAS Catalog: GCST007515
Europe PMC: 29632382
 153,287 individuals South Asian, East Asian, African American or Afro-Caribbean, Hispanic or Latin American NR
GWAS Catalog: GCST007516
Europe PMC: 29632382
 298,957 individuals European NR
GWAS Catalog: GCST007516
Europe PMC: 29632382
 153,287 individuals South Asian, East Asian, African American or Afro-Caribbean, Hispanic or Latin American NR
Europe PMC: 36653562
[
  • 41,245 cases
  • , 215,160 controls
]
 European
(Finnish)		 FinnGen
GWAS Catalog: GCST90086072
Europe PMC: 33893285
 56,637 individuals European NR
GWAS Catalog: GCST007847
Europe PMC: 30718926
 191,764 individuals East Asian NR
GWAS Catalog: GCST008048
Europe PMC: 31217584
 20,480 individuals Hispanic or Latin American NR
GWAS Catalog: GCST008048
Europe PMC: 31217584
 15,601 individuals African American or Afro-Caribbean NR
GWAS Catalog: GCST008048
Europe PMC: 31217584
 4,576 individuals East Asian, Asian unspecified NR
GWAS Catalog: GCST008048
Europe PMC: 31217584
 3,551 individuals Oceanian NR
GWAS Catalog: GCST008048
Europe PMC: 31217584
 619 individuals Native American NR
GWAS Catalog: GCST008048
Europe PMC: 31217584
 898 individuals Not reported NR
GWAS Catalog: GCST008103
Europe PMC: 31043756
 51,710 individuals European NR
GWAS Catalog: GCST002783
Europe PMC: 25673413
 236,781 individuals European NR
GWAS Catalog: GCST002783
Europe PMC: 25673413
 887 individuals African American or Afro-Caribbean NR
GWAS Catalog: GCST002783
Europe PMC: 25673413
 1,276 individuals Hispanic or Latin American NR
GWAS Catalog: GCST003116
Europe PMC: 26343387
 141,217 individuals European NR
GWAS Catalog: GCST003116
Europe PMC: 26343387
 3,139 individuals African American or Afro-Caribbean NR
GWAS Catalog: GCST003116
Europe PMC: 26343387
 4,095 individuals Hispanic or Latin American NR
GWAS Catalog: GCST003116
Europe PMC: 26343387
 25,557 individuals South Asian NR
GWAS Catalog: GCST003116
Europe PMC: 26343387
 2,268 individuals Greater Middle Eastern (Middle Eastern, North African or Persian) NR
GWAS Catalog: GCST003116
Europe PMC: 26343387
 11,323 individuals East Asian NR
GWAS Catalog: GCST010867
Europe PMC: 33020668
 168,228 individuals East Asian NR
GWAS Catalog: GCST009405
Europe PMC: 31089300
 72,655 individuals East Asian BBJ
GWAS Catalog: GCST007098
Europe PMC: 27841878
 80,792 individuals European NR
GWAS Catalog: GCST007098
Europe PMC: 27841878
 8,231 individuals Hispanic or Latin American NR
GWAS Catalog: GCST007098
Europe PMC: 27841878
 7,243 individuals East Asian NR
GWAS Catalog: GCST007098
Europe PMC: 27841878
 3,058 individuals African American or Afro-Caribbean NR
GWAS Catalog: GCST007098
Europe PMC: 27841878
 461 individuals South Asian NR
GWAS Catalog: GCST003676
Europe PMC: 27225129
 405,072 individuals European NR
GWAS Catalog: GCST90002232
Europe PMC: 34059833
 200,622 individuals European NR
GWAS Catalog: GCST90002244
Europe PMC: 34059833
 146,806 individuals European NR
GWAS Catalog: GCST002223
Europe PMC: 24097068
 94,595 individuals European NR
Europe PMC: 25673412
 213,038 individuals European NR
Europe PMC: 25673412
 211,117 individuals European NR
GWAS Catalog: GCST005180
Europe PMC: 20081858
 36,466 individuals European NR
GWAS Catalog: GCST005179
Europe PMC: 20081858
 37,037 individuals European NR
GWAS Catalog: GCST90002238
Europe PMC: 34059833
 151,013 individuals European NR
GWAS Catalog: GCST002222
Europe PMC: 24097068
 94,595 individuals European NR
GWAS Catalog: GCST90007310
Europe PMC: 32917775
 49,909 individuals European NR
GWAS Catalog: GCST90007322
Europe PMC: 32917775
 49,830 individuals European NR
GWAS Catalog: GCST007095
Europe PMC: 27841878
 80,792 individuals European NR
GWAS Catalog: GCST007095
Europe PMC: 27841878
 8,231 individuals Hispanic or Latin American NR
GWAS Catalog: GCST007095
Europe PMC: 27841878
 7,243 individuals East Asian NR
GWAS Catalog: GCST007095
Europe PMC: 27841878
 3,058 individuals African American or Afro-Caribbean NR
GWAS Catalog: GCST007095
Europe PMC: 27841878
 461 individuals South Asian NR
GWAS Catalog: GCST006803
Europe PMC: 29483656
 105,318 individuals European NR
GWAS Catalog: GCST009403
Europe PMC: 31089300
 165,456 individuals East Asian BBJ
GWAS Catalog: GCST009402
Europe PMC: 31089300
 75,798 individuals East Asian BBJ
GWAS Catalog: GCST009399
Europe PMC: 31089300
 89,638 individuals East Asian BBJ
GWAS Catalog: GCST006906
Europe PMC: 29531354
[
  • 40,585 cases
  • , 406,111 controls
]
 European NR
GWAS Catalog: GCST006910
Europe PMC: 29531354
[
  • 7,193 cases
  • , 355,468 controls
]
 European NR
GWAS Catalog: GCST006908
Europe PMC: 29531354
[
  • 34,217 cases
  • , 406,111 controls
]
 European NR
GWAS Catalog: GCST006907
Europe PMC: 29531354
[
  • 4,373 cases
  • , 297,290 controls
]
 European NR
GWAS Catalog: GCST006909
Europe PMC: 29531354
[
  • 5,386 cases
  • , 343,560 controls
]
 European NR
GWAS Catalog: GCST002221
Europe PMC: 24097068
 94,595 individuals European NR
GWAS Catalog: GCST002216
Europe PMC: 24097068
 94,595 individuals European NR
Europe PMC: 25673412
 232,101 individuals European NR
Europe PMC: 25673412
 231,355 individuals European NR
Europe PMC: 25673412
 212,248 individuals European NR
Europe PMC: 25673412
 210,086 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
—
[
  • 10,304 cases
  • , 120,512 controls
]
,
47.6 % Male samples
 European
(White British)		 UKB 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 Mean = 57.0 years — Ancestry label assigned based on genetic similarity with 1000 Genomes reference panel superpopulations —

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
PPM021432 PSS011747|
European Ancestry|
245,177 individuals
 PGP000656 |
Ritchie SC et al. medRxiv (2024)
|Pre		 Reported Trait: Type 2 diabetes OR: 2.3 [2.26, 2.35] AUROC: 0.777 [0.772, 0.781] — Age at baseline, sex assessment centre (PGS adjusted for 20 PCs prior to model fitting) —
PPM021438 PSS011738|
European Ancestry|
38,941 individuals
 PGP000656 |
Ritchie SC et al. medRxiv (2024)
|Pre		 Reported Trait: Incident type 2 diabetes HR: 2.07 [1.92, 2.23] C-index: 0.774 [0.758, 0.79] — Age at baseline, sex (PGS adjusted for 20 PCs prior to model fitting) —
PPM021460 PSS011746|
European Ancestry|
232,808 individuals
 PGP000656 |
Ritchie SC et al. medRxiv (2024)
|Pre		 Reported Trait: Incident type 2 diabetes HR: 1.8 [1.75, 1.85] C-index: 0.719 [0.713, 0.725] — Age at baseline, sex assessment centre (PGS adjusted for 20 PCs prior to model fitting) —
PPM021467 PSS011735|
African Ancestry|
44,346 individuals
 PGP000656 |
Ritchie SC et al. medRxiv (2024)
|Pre		 Reported Trait: Type 2 diabetes OR: 1.35 [1.31, 1.39] AUROC: 0.725 [0.718, 0.731] — Age at baseline, sex (PGS adjusted for 20 PCs prior to model fitting) —
PPM021491 PSS011736|
Hispanic or Latin American Ancestry|
33,652 individuals
 PGP000656 |
Ritchie SC et al. medRxiv (2024)
|Pre		 Reported Trait: Type 2 diabetes OR: 1.73 [1.67, 1.79] AUROC: 0.777 [0.77, 0.783] — Age at baseline, sex (PGS adjusted for 20 PCs prior to model fitting) —
PPM021515 PSS011740|
East Asian Ancestry|
1,149 individuals
 PGP000656 |
Ritchie SC et al. medRxiv (2024)
|Pre		 Reported Trait: Incident type 2 diabetes OR: 1.37 [1.17, 1.6] AUROC: 0.627 [0.585, 0.669] — Age at baseline, sex (PGS adjusted for 20 PCs prior to model fitting) —
PPM021532 PSS011741|
South Asian Ancestry|
852 individuals
 PGP000656 |
Ritchie SC et al. medRxiv (2024)
|Pre		 Reported Trait: Incident type 2 diabetes OR: 1.69 [1.42, 2.02] AUROC: 0.698 [0.658, 0.737] — Age at baseline, sex (PGS adjusted for 20 PCs prior to model fitting) —
PPM021576 PSS011743|
African Ancestry|
6,871 individuals
 PGP000656 |
Ritchie SC et al. medRxiv (2024)
|Pre		 Reported Trait: Type 2 diabetes OR: 1.41 [1.31, 1.53] AUROC: 0.723 [0.704, 0.742] — Age at baseline, sex assessment centre (PGS adjusted for 20 PCs prior to model fitting) —
PPM021598 PSS011745|
East Asian Ancestry|
1,432 individuals
 PGP000656 |
Ritchie SC et al. medRxiv (2024)
|Pre		 Reported Trait: Type 2 diabetes OR: 1.82 [1.42, 2.37] AUROC: 0.734 [0.678, 0.79] — Age at baseline, sex assessment centre (PGS adjusted for 20 PCs prior to model fitting) —
PPM021621 PSS011749|
South Asian Ancestry|
6,992 individuals
 PGP000656 |
Ritchie SC et al. medRxiv (2024)
|Pre		 Reported Trait: Type 2 diabetes OR: 1.88 [1.75, 2.01] AUROC: 0.742 [0.727, 0.756] — Age at baseline, sex assessment centre (PGS adjusted for 20 PCs prior to model fitting) —
PPM021639 PSS011742|
African Ancestry|
6,019 individuals
 PGP000656 |
Ritchie SC et al. medRxiv (2024)
|Pre		 Reported Trait: Incident type 2 diabetes HR: 1.22 [1.1, 1.34] C-index: 0.649 [0.623, 0.676] — Age at baseline, sex assessment centre (PGS adjusted for 20 PCs prior to model fitting) —
PPM021667 PSS011744|
East Asian Ancestry|
1,350 individuals
 PGP000656 |
Ritchie SC et al. medRxiv (2024)
|Pre		 Reported Trait: Incident type 2 diabetes HR: 1.43 [1.02, 2.01] C-index: 0.696 [0.624, 0.767] — Age at baseline, sex assessment centre (PGS adjusted for 20 PCs prior to model fitting) —
PPM021685 PSS011748|
South Asian Ancestry|
5,685 individuals
 PGP000656 |
Ritchie SC et al. medRxiv (2024)
|Pre		 Reported Trait: Incident type 2 diabetes HR: 1.35 [1.24, 1.48] C-index: 0.629 [0.606, 0.651] — Age at baseline, sex assessment centre (PGS adjusted for 20 PCs prior to model fitting) —
PPM021410 PSS011737|
European Ancestry|
109,021 individuals
 PGP000656 |
Ritchie SC et al. medRxiv (2024)
|Pre		 Reported Trait: Type 2 diabetes OR: 1.92 [1.88, 1.97] AUROC: 0.737 [0.732, 0.742] — Age at baseline, sex (PGS adjusted for 20 PCs prior to model fitting) —
PPM021558 PSS011739|
Additional Asian Ancestries|
870 individuals
 PGP000656 |
Ritchie SC et al. medRxiv (2024)
|Pre		 Reported Trait: Incident type 2 diabetes OR: 1.63 [1.37, 1.96] AUROC: 0.697 [0.655, 0.739] — 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
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 —