Polygenic Score (PGS) ID: PGS003444

Predicted Trait
Reported Trait Type 2 diabetes (T2D)
Mapped Trait(s) type 2 diabetes mellitus (MONDO_0005148)
Released in PGS Catalog: June 1, 2023
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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 PRScsx_T2D_LAT_EASweights
Development Method
Name PRS-CSx
Parameters The polygenicity value that maximized the PRS performance in the score development cohort was 1e-02. To calculate a polygenic risk score in any genotyped individual, please follow the next steps. First, use the ancestry-specific weights (PRScsx_T2D_LAT_EURweights, PRScsx_T2D_LAT_EASweights and PRScsx_T2D_LAT_LATweights) to calculate 3 separate scores for each genotyped individual. Second, standardize each score (mean of zero and standard deviation of 1) and combine the three of them to calculate a single score value: metascore=(zscoreEUR* 0.531117)+(zscoreEAS*0.5690198)+(zscoreLAT*0.1465538). Third, standardize the metascore before applying. Evaluation of each ancestry-specific score separately is not the intended use of this PRS-CSx polygenic score. Note that performance reported is based on the combination of the 3 ancestry-specific scores (PRScsx_T2D_LAT_EURweights,PRScsx_T2D_LAT_EASweights,PRScsx_T2D_LAT_LATweights) as explained above.
Variants
Original Genome Build GRCh37
Number of Variants 1,001,579
Effect Weight Type beta
PGS Source
PGS Catalog Publication (PGP) ID PGP000445
Citation (link to publication) Huerta-Chagoya A et al. Diabetologia (2023)
Ancestry Distribution
Source of Variant
Associations (GWAS)
East Asian: 100%
433,540 individuals (100%)
Score Development/Training
Hispanic or Latin American: 100%
1,730 individuals (100%)
PGS Evaluation
African: 21.4%
East Asian: 21.4%
South Asian: 21.4%
Hispanic or Latin American: 14.3%
European: 14.3%
Additional Asian Ancestries: 7.1%
14 Sample Sets

Development Samples

Source of Variant Associations (GWAS)
Study Identifiers Sample Numbers Sample Ancestry Cohort(s)
GWAS Catalog: GCST010118
Europe PMC: 32499647
 433,540 individuals East Asian AGEN
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
[
  • 409 cases
  • , 1,321 controls
]
 Hispanic or Latin American
(Mexican)		 MXB — — — — —

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
PPM017183 PSS010157|
Hispanic or Latin American Ancestry|
1,484 individuals
 PGP000445 |
Huerta-Chagoya A et al. Diabetologia (2023)
 Reported Trait: type 2 diabetes OR: 1.9 [1.65, 2.19] AUROC: 0.7475 R²: 0.207 sex, age, PCs(1-10), PRScsx_T2D_LAT_EURweights, PRScsx_T2D_LAT_LATweights NOTE: Performance is based on a linear combination of this PGS with PRScsx_T2D_LAT_EASweights and PRScsx_T2D_LAT_LATweights (metascore=(zscoreEUR* 0.531117)+(zscoreEAS*0.5690198)+(zscoreLAT*0.1465538)). See score development details for how to apply
PPM021413 PSS011737|
European Ancestry|
109,021 individuals
 PGP000656 |
Ritchie SC et al. medRxiv (2024)
|Ext.|Pre		 Reported Trait: Type 2 diabetes OR: 1.86 [1.82, 1.9] AUROC: 0.731 [0.726, 0.736] — Age at baseline, sex (PGS adjusted for 20 PCs prior to model fitting) Note: Performance is based on a linear combination of PGS003443 (weight=0.531117), PGS003444 (weight=0.5690198) and PGS003445 (weight=0.1465538). See score development details for more information
PPM021441 PSS011738|
European Ancestry|
38,941 individuals
 PGP000656 |
Ritchie SC et al. medRxiv (2024)
|Ext.|Pre		 Reported Trait: Incident type 2 diabetes HR: 1.98 [1.84, 2.13] C-index: 0.77 [0.754, 0.786] — Age at baseline, sex (PGS adjusted for 20 PCs prior to model fitting) Note: Performance is based on a linear combination of PGS003443 (weight=0.531117), PGS003444 (weight=0.5690198) and PGS003445 (weight=0.1465538). See score development details for more information
PPM021470 PSS011735|
African Ancestry|
44,346 individuals
 PGP000656 |
Ritchie SC et al. medRxiv (2024)
|Ext.|Pre		 Reported Trait: Type 2 diabetes OR: 1.32 [1.28, 1.36] AUROC: 0.723 [0.717, 0.729] — Age at baseline, sex (PGS adjusted for 20 PCs prior to model fitting) Note: Performance is based on a linear combination of PGS003443 (weight=0.531117), PGS003444 (weight=0.5690198) and PGS003445 (weight=0.1465538). See score development details for more information
PPM021489 PSS011736|
Hispanic or Latin American Ancestry|
33,652 individuals
 PGP000656 |
Ritchie SC et al. medRxiv (2024)
|Ext.|Pre		 Reported Trait: Type 2 diabetes OR: 1.77 [1.71, 1.84] AUROC: 0.78 [0.773, 0.786] — Age at baseline, sex (PGS adjusted for 20 PCs prior to model fitting) Note: Performance is based on a linear combination of PGS003443 (weight=0.531117), PGS003444 (weight=0.5690198) and PGS003445 (weight=0.1465538). See score development details for more information
PPM021511 PSS011740|
East Asian Ancestry|
1,149 individuals
 PGP000656 |
Ritchie SC et al. medRxiv (2024)
|Ext.|Pre		 Reported Trait: Incident type 2 diabetes OR: 1.51 [1.29, 1.77] AUROC: 0.648 [0.607, 0.688] — Age at baseline, sex (PGS adjusted for 20 PCs prior to model fitting) Note: Performance is based on a linear combination of PGS003443 (weight=0.531117), PGS003444 (weight=0.5690198) and PGS003445 (weight=0.1465538). See score development details for more information
PPM021541 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: 0.667 [0.626, 0.708] — Age at baseline, sex (PGS adjusted for 20 PCs prior to model fitting) Note: Performance is based on a linear combination of PGS003443 (weight=0.531117), PGS003444 (weight=0.5690198) and PGS003445 (weight=0.1465538). See score development details for more information
PPM021555 PSS011739|
Additional Asian Ancestries|
870 individuals
 PGP000656 |
Ritchie SC et al. medRxiv (2024)
|Ext.|Pre		 Reported Trait: Incident type 2 diabetes OR: 1.71 [1.43, 2.06] AUROC: 0.706 [0.665, 0.746] — Age at baseline, sex (PGS adjusted for 20 PCs prior to model fitting) Note: Performance is based on a linear combination of PGS003443 (weight=0.531117), PGS003444 (weight=0.5690198) and PGS003445 (weight=0.1465538). See score development details for more information
PPM021579 PSS011743|
African Ancestry|
6,871 individuals
 PGP000656 |
Ritchie SC et al. medRxiv (2024)
|Ext.|Pre		 Reported Trait: Type 2 diabetes OR: 1.4 [1.3, 1.52] AUROC: 0.723 [0.705, 0.742] — Age at baseline, sex assessment centre (PGS adjusted for 20 PCs prior to model fitting) Note: Performance is based on a linear combination of PGS003443 (weight=0.531117), PGS003444 (weight=0.5690198) and PGS003445 (weight=0.1465538). See score development details for more information
PPM021619 PSS011749|
South Asian Ancestry|
6,992 individuals
 PGP000656 |
Ritchie SC et al. medRxiv (2024)
|Ext.|Pre		 Reported Trait: Type 2 diabetes OR: 1.91 [1.78, 2.05] AUROC: 0.746 [0.732, 0.761] — Age at baseline, sex assessment centre (PGS adjusted for 20 PCs prior to model fitting) Note: Performance is based on a linear combination of PGS003443 (weight=0.531117), PGS003444 (weight=0.5690198) and PGS003445 (weight=0.1465538). See score development details for more information
PPM021649 PSS011742|
African Ancestry|
6,019 individuals
 PGP000656 |
Ritchie SC et al. medRxiv (2024)
|Ext.|Pre		 Reported Trait: Incident type 2 diabetes HR: 1.13 [1.02, 1.24] C-index: 0.642 [0.616, 0.669] — Age at baseline, sex assessment centre (PGS adjusted for 20 PCs prior to model fitting) Note: Performance is based on a linear combination of PGS003443 (weight=0.531117), PGS003444 (weight=0.5690198) and PGS003445 (weight=0.1465538). See score development details for more information
PPM021665 PSS011744|
East Asian Ancestry|
1,350 individuals
 PGP000656 |
Ritchie SC et al. medRxiv (2024)
|Ext.|Pre		 Reported Trait: Incident type 2 diabetes HR: 1.57 [1.12, 2.21] C-index: 0.689 [0.612, 0.765] — Age at baseline, sex assessment centre (PGS adjusted for 20 PCs prior to model fitting) Note: Performance is based on a linear combination of PGS003443 (weight=0.531117), PGS003444 (weight=0.5690198) and PGS003445 (weight=0.1465538). See score development details for more information
PPM021682 PSS011748|
South Asian Ancestry|
5,685 individuals
 PGP000656 |
Ritchie SC et al. medRxiv (2024)
|Ext.|Pre		 Reported Trait: Incident type 2 diabetes HR: 1.42 [1.3, 1.55] C-index: 0.639 [0.617, 0.662] — Age at baseline, sex assessment centre (PGS adjusted for 20 PCs prior to model fitting) Note: Performance is based on a linear combination of PGS003443 (weight=0.531117), PGS003444 (weight=0.5690198) and PGS003445 (weight=0.1465538). See score development details for more information
PPM021600 PSS011745|
East Asian Ancestry|
1,432 individuals
 PGP000656 |
Ritchie SC et al. medRxiv (2024)
|Ext.|Pre		 Reported Trait: Type 2 diabetes OR: 1.8 [1.4, 2.32] AUROC: 0.738 [0.684, 0.791] — Age at baseline, sex assessment centre (PGS adjusted for 20 PCs prior to model fitting) Note: Performance is based on a linear combination of PGS003443 (weight=0.531117), PGS003444 (weight=0.5690198) and PGS003445 (weight=0.1465538). See score development details for more information

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
PSS010157 — —
[
  • 399 cases
  • , 1,085 controls
]
 Mean = 42.3 years Hispanic or Latin American
(Mexican)		 — METSB —
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 —