Polygenic Score (PGS) ID: PGS003867

Predicted Trait
Reported Trait Type 2 diabetes (T2D)
Mapped Trait(s) type 2 diabetes mellitus (MONDO_0005148)
Released in PGS Catalog: Nov. 1, 2023
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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_PRScs_ARB
Development Method
Name PRS-CS
Parameters a=1,b=0.5,phi=0.0001
Variants
Original Genome Build hg19
Number of Variants 1,068,166
Effect Weight Type beta
PGS Source
PGS Catalog Publication (PGP) ID PGP000501
Citation (link to publication) Shim I et al. Nature Communications (2023)
Ancestry Distribution
Source of Variant
Associations (GWAS)
European: 51.1%
East Asian: 28.4%
South Asian: 8.3%
African: 6.6%
Hispanic or Latin American: 5.6%
492,192 individuals (100%)
PGS Evaluation
European: 25%
African: 12.5%
Hispanic or Latin American: 12.5%
Additional Asian Ancestries: 12.5%
East Asian: 12.5%
Greater Middle Eastern: 12.5%
South Asian: 12.5%
8 Sample Sets

Development Samples

Source of Variant Associations (GWAS)
Study Identifiers Sample Numbers Sample Ancestry Cohort(s)
GWAS Catalog: GCST90132183
Europe PMC: 35551307
 251,740 individuals European NR
GWAS Catalog: GCST90132183
Europe PMC: 35551307
 139,705 individuals East Asian NR
GWAS Catalog: GCST90132183
Europe PMC: 35551307
 40,737 individuals South Asian NR
GWAS Catalog: GCST90132183
Europe PMC: 35551307
 27,417 individuals Hispanic or Latin American NR
GWAS Catalog: GCST90132183
Europe PMC: 35551307
 30,167 individuals African American or Afro-Caribbean NR
GWAS Catalog: GCST90132183
Europe PMC: 35551307
 2,426 individuals Sub-Saharan African NR

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
PPM018759 PSS011097|
Greater Middle Eastern Ancestry|
2,669 individuals
 PGP000501 |
Shim I et al. Nature Communications (2023)
 Reported Trait: Type 2 diabetes OR: 1.83 [1.74, 1.92] AUROC: 0.7384 [0.7194, 0.7574] — age, sex, array version, and the first 10 principal components of ancestry —
PPM021415 PSS011737|
European Ancestry|
109,021 individuals
 PGP000656 |
Ritchie SC et al. medRxiv (2024)
|Ext.|Pre		 Reported Trait: Type 2 diabetes OR: 1.84 [1.8, 1.88] AUROC: 0.73 [0.725, 0.735] — Age at baseline, sex (PGS adjusted for 20 PCs prior to model fitting) —
PPM021443 PSS011738|
European Ancestry|
38,941 individuals
 PGP000656 |
Ritchie SC et al. medRxiv (2024)
|Ext.|Pre		 Reported Trait: Incident type 2 diabetes HR: 1.95 [1.81, 2.1] C-index: 0.766 [0.75, 0.782] — Age at baseline, sex (PGS adjusted for 20 PCs prior to model fitting) —
PPM021466 PSS011735|
African Ancestry|
44,346 individuals
 PGP000656 |
Ritchie SC et al. medRxiv (2024)
|Ext.|Pre		 Reported Trait: Type 2 diabetes OR: 1.37 [1.33, 1.41] AUROC: 0.727 [0.72, 0.733] — Age at baseline, sex (PGS adjusted for 20 PCs prior to model fitting) —
PPM021492 PSS011736|
Hispanic or Latin American Ancestry|
33,652 individuals
 PGP000656 |
Ritchie SC et al. medRxiv (2024)
|Ext.|Pre		 Reported Trait: Type 2 diabetes OR: 1.72 [1.65, 1.78] AUROC: 0.776 [0.769, 0.783] — Age at baseline, sex (PGS adjusted for 20 PCs prior to model fitting) —
PPM021513 PSS011740|
East Asian Ancestry|
1,149 individuals
 PGP000656 |
Ritchie SC et al. medRxiv (2024)
|Ext.|Pre		 Reported Trait: Incident type 2 diabetes OR: 1.42 [1.22, 1.66] AUROC: 0.635 [0.594, 0.676] — Age at baseline, sex (PGS adjusted for 20 PCs prior to model fitting) —
PPM021535 PSS011741|
South Asian Ancestry|
852 individuals
 PGP000656 |
Ritchie SC et al. medRxiv (2024)
|Ext.|Pre		 Reported Trait: Incident type 2 diabetes OR: 1.52 [1.29, 1.81] AUROC: 0.681 [0.641, 0.722] — Age at baseline, sex (PGS adjusted for 20 PCs prior to model fitting) —
PPM021559 PSS011739|
Additional Asian Ancestries|
870 individuals
 PGP000656 |
Ritchie SC et al. medRxiv (2024)
|Ext.|Pre		 Reported Trait: Incident type 2 diabetes OR: 1.64 [1.37, 1.98] AUROC: 0.701 [0.659, 0.742] — 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 —
PSS011097 — — 2,669 individuals — Greater Middle Eastern (Middle Eastern, North African or Persian)
(Arab)		 — NR N total after excluding missing values = 2,553
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 —