Polygenic Score (PGS) ID: PGS002026

Predicted Trait
Reported Trait Type 2 diabetes (T2D)
Mapped Trait(s) type 2 diabetes mellitus (MONDO_0005148)
Additional Trait Information endocrine/metabolic
Released in PGS Catalog: Jan. 10, 2022
Download Score FTP directory
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 portability-ldpred2_250.2
Development Method
Name LDpred2 (bigsnpr)
Parameters LDpred2-auto using HapMap3 variants
Variants
Original Genome Build GRCh37
Number of Variants 830,783
Effect Weight Type beta
PGS Source
PGS Catalog Publication (PGP) ID PGP000263
Citation (link to publication) Privé F et al. Am J Hum Genet (2022)
Ancestry Distribution
Score Development/Training
European: 100%
391,124 individuals (100%)
PGS Evaluation
African: 26.1%
European: 26.1%
East Asian: 17.4%
South Asian: 17.4%
Hispanic or Latin American: 4.3%
Additional Asian Ancestries: 4.3%
Greater Middle Eastern: 4.3%
23 Sample Sets

Development Samples

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
— 391,124 individuals European UKB — — — UK (+ Ireland) —

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
PPM011082 PSS009288|
European Ancestry|
19,931 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: Type 2 diabetes — — Partial Correlation (partial-r): 0.1304 [0.1168, 0.1441] sex, age, birth date, deprivation index, 16 PCs —
PPM011083 PSS009062|
European Ancestry|
4,121 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: Type 2 diabetes — — Partial Correlation (partial-r): 0.0862 [0.0558, 0.1165] sex, age, birth date, deprivation index, 16 PCs —
PPM011084 PSS008616|
European Ancestry|
6,646 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: Type 2 diabetes — — Partial Correlation (partial-r): 0.1134 [0.0896, 0.1371] sex, age, birth date, deprivation index, 16 PCs —
PPM011085 PSS008392|
Greater Middle Eastern Ancestry|
1,197 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: Type 2 diabetes — — Partial Correlation (partial-r): 0.1764 [0.1205, 0.2312] sex, age, birth date, deprivation index, 16 PCs —
PPM011087 PSS007957|
East Asian Ancestry|
1,808 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: Type 2 diabetes — — Partial Correlation (partial-r): 0.0786 [0.0324, 0.1246] sex, age, birth date, deprivation index, 16 PCs —
PPM011088 PSS007738|
African Ancestry|
2,476 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: Type 2 diabetes — — Partial Correlation (partial-r): 0.1001 [0.0607, 0.1391] sex, age, birth date, deprivation index, 16 PCs —
PPM011089 PSS008841|
African Ancestry|
3,896 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: Type 2 diabetes — — Partial Correlation (partial-r): 0.0806 [0.0493, 0.1118] sex, age, birth date, deprivation index, 16 PCs —
PPM011086 PSS008170|
South Asian Ancestry|
6,312 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: Type 2 diabetes — — Partial Correlation (partial-r): 0.158 [0.1338, 0.182] sex, age, birth date, deprivation index, 16 PCs —
PPM020889 PSS011442|
European Ancestry|
564 individuals
 PGP000599 |
Guarischi-Sousa R et al. Circ Genom Precis Med (2023)
|Ext.		 Reported Trait: Raised coronary lesion OR: 0.96 [0.8, 1.16] — — — —
PPM020894 PSS011441|
African Ancestry|
504 individuals
 PGP000599 |
Guarischi-Sousa R et al. Circ Genom Precis Med (2023)
|Ext.		 Reported Trait: Raised coronary lesion OR: 1.1 [0.9, 1.35] — — — —
PPM021418 PSS011737|
European Ancestry|
109,021 individuals
 PGP000656 |
Ritchie SC et al. medRxiv (2024)
|Ext.|Pre		 Reported Trait: Type 2 diabetes OR: 1.67 [1.63, 1.71] AUROC: 0.714 [0.709, 0.719] — Age at baseline, sex (PGS adjusted for 20 PCs prior to model fitting) —
PPM021446 PSS011738|
European Ancestry|
38,941 individuals
 PGP000656 |
Ritchie SC et al. medRxiv (2024)
|Ext.|Pre		 Reported Trait: Incident type 2 diabetes HR: 1.81 [1.68, 1.95] C-index: 0.752 [0.735, 0.769] — Age at baseline, sex (PGS adjusted for 20 PCs prior to model fitting) —
PPM021473 PSS011735|
African Ancestry|
44,346 individuals
 PGP000656 |
Ritchie SC et al. medRxiv (2024)
|Ext.|Pre		 Reported Trait: Type 2 diabetes OR: 1.28 [1.24, 1.32] AUROC: 0.721 [0.714, 0.727] — Age at baseline, sex (PGS adjusted for 20 PCs prior to model fitting) —
PPM021496 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 [0.757, 0.771] — Age at baseline, sex (PGS adjusted for 20 PCs prior to model fitting) —
PPM021538 PSS011741|
South Asian Ancestry|
852 individuals
 PGP000656 |
Ritchie SC et al. medRxiv (2024)
|Ext.|Pre		 Reported Trait: Incident type 2 diabetes OR: 1.43 [1.21, 1.7] AUROC: 0.666 [0.623, 0.708] — Age at baseline, sex (PGS adjusted for 20 PCs prior to model fitting) —
PPM021564 PSS011739|
Additional Asian Ancestries|
870 individuals
 PGP000656 |
Ritchie SC et al. medRxiv (2024)
|Ext.|Pre		 Reported Trait: Incident type 2 diabetes OR: 1.44 [1.22, 1.72] AUROC: 0.685 [0.643, 0.727] — Age at baseline, sex (PGS adjusted for 20 PCs prior to model fitting) —
PPM021582 PSS011743|
African Ancestry|
6,871 individuals
 PGP000656 |
Ritchie SC et al. medRxiv (2024)
|Ext.|Pre		 Reported Trait: Type 2 diabetes OR: 1.35 [1.24, 1.46] AUROC: 0.719 [0.7, 0.737] — Age at baseline, sex assessment centre (PGS adjusted for 20 PCs prior to model fitting) —
PPM021605 PSS011745|
East Asian Ancestry|
1,432 individuals
 PGP000656 |
Ritchie SC et al. medRxiv (2024)
|Ext.|Pre		 Reported Trait: Type 2 diabetes OR: 1.6 [1.26, 2.03] AUROC: 0.722 [0.664, 0.78] — Age at baseline, sex assessment centre (PGS adjusted for 20 PCs prior to model fitting) —
PPM021624 PSS011749|
South Asian Ancestry|
6,992 individuals
 PGP000656 |
Ritchie SC et al. medRxiv (2024)
|Ext.|Pre		 Reported Trait: Type 2 diabetes OR: 1.64 [1.53, 1.75] AUROC: 0.724 [0.709, 0.739] — Age at baseline, sex assessment centre (PGS adjusted for 20 PCs prior to model fitting) —
PPM021651 PSS011742|
African Ancestry|
6,019 individuals
 PGP000656 |
Ritchie SC et al. medRxiv (2024)
|Ext.|Pre		 Reported Trait: Incident type 2 diabetes HR: 1.12 [1.02, 1.24] C-index: 0.643 [0.616, 0.67] — Age at baseline, sex assessment centre (PGS adjusted for 20 PCs prior to model fitting) —
PPM021674 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 [0.92, 1.77] C-index: 0.686 [0.609, 0.763] — Age at baseline, sex assessment centre (PGS adjusted for 20 PCs prior to model fitting) —
PPM021694 PSS011748|
South Asian Ancestry|
5,685 individuals
 PGP000656 |
Ritchie SC et al. medRxiv (2024)
|Ext.|Pre		 Reported Trait: Incident type 2 diabetes HR: 1.23 [1.13, 1.35] C-index: 0.617 [0.595, 0.64] — Age at baseline, sex assessment centre (PGS adjusted for 20 PCs prior to model fitting) —
PPM021516 PSS011740|
East Asian Ancestry|
1,149 individuals
 PGP000656 |
Ritchie SC et al. medRxiv (2024)
|Ext.|Pre		 Reported Trait: Incident type 2 diabetes OR: 1.32 [1.13, 1.54] AUROC: 0.621 [0.579, 0.663] — 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
PSS009288 — — 19,931 individuals — European UK (+ Ireland) UKB —
PSS008392 — — 1,197 individuals — Greater Middle Eastern (Middle Eastern, North African or Persian) Iran (Middle East) UKB —
PSS009062 — — 4,121 individuals — European Poland (NE Europe) UKB —
PSS011442 — —
[
  • 181 cases
  • , 383 controls
]
,
77.0 % Male samples
 Mean = 26.7 years European — PDAY —
PSS011441 — —
[
  • 165 cases
  • , 339 controls
]
,
82.0 % Male samples
 Mean = 27.5 years African unspecified — PDAY —
PSS008170 — — 6,312 individuals — South Asian India (South Asia) 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 —
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 —
PSS008841 — — 3,896 individuals — African unspecified Nigeria (West Africa) UKB —
PSS007957 — — 1,808 individuals — East Asian China (East Asia) UKB —
PSS008616 — — 6,646 individuals — European Italy (South Europe) UKB —
PSS007738 — — 2,476 individuals — African American or Afro-Caribbean Carribean UKB —