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)
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Study Identifiers
Sample Numbers
Sample Ancestry
Cohort(s)
GWAS Catalog: GCST004773
Europe PMC: 28566273
159,208 individualsEuropeanNR
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Score Development/Training
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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—————
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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.

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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
PPM012733PSS009522|
European Ancestry|
258,402 individuals
PGP000271 |
Mars N et al. Cell Genom (2022)
Reported Trait: Type 2 diabetesOR: 1.58 [1.56, 1.6]——age, sex, 10 PCs (+/- dataset-specific technical covariates)—
PPM012737PSS009518|
European Ancestry|
110,597 individuals
PGP000271 |
Mars N et al. Cell Genom (2022)
Reported Trait: Type 2 diabetesOR: 1.55 [1.51, 1.59]——age, sex, 10 PCs (+/- dataset-specific technical covariates)—
PPM012741PSS009514|
East Asian Ancestry|
178,726 individuals
PGP000271 |
Mars N et al. Cell Genom (2022)
Reported Trait: Type 2 diabetesOR: 1.37 [1.36, 1.39]——age, sex, 10 PCs (+/- dataset-specific technical covariates)—
PPM012745PSS009526|
European Ancestry|
69,422 individuals
PGP000271 |
Mars N et al. Cell Genom (2022)
Reported Trait: Type 2 diabetesOR: 1.64 [1.6, 1.69]——birth year, sex, 10 PCs (+/- dataset-specific technical covariates)—
PPM012749PSS009534|
European Ancestry|
25,696 individuals
PGP000271 |
Mars N et al. Cell Genom (2022)
Reported Trait: Type 2 diabetesOR: 1.46 [1.41, 1.51]——age, sex, 10 PCs (+/- dataset-specific technical covariates)—
PPM012753PSS009530|
African Ancestry|
1,535 individuals
PGP000271 |
Mars N et al. Cell Genom (2022)
Reported Trait: Type 2 diabetesOR: 1.24 [1.09, 1.42]——age, sex, 10 PCs (+/- dataset-specific technical covariates)—
PPM012757PSS009542|
European Ancestry|
343,676 individuals
PGP000271 |
Mars N et al. Cell Genom (2022)
Reported Trait: Type 2 diabetesOR: 1.78 [1.75, 1.81]——age, sex, 10 PCs (+/- dataset-specific technical covariates)—
PPM012762PSS009538|
African Ancestry|
7,618 individuals
PGP000271 |
Mars N et al. Cell Genom (2022)
Reported Trait: Type 2 diabetesOR: 1.46 [1.32, 1.62]——age, sex, 10 PCs (+/- dataset-specific technical covariates)—
PPM012767PSS009546|
South Asian Ancestry|
7,628 individuals
PGP000271 |
Mars N et al. Cell Genom (2022)
Reported Trait: Type 2 diabetesOR: 1.66 [1.55, 1.79]——age, sex, 10 PCs (+/- dataset-specific technical covariates)—
PPM021425PSS011737|
European Ancestry|
109,021 individuals
PGP000656 |
Ritchie SC et al. medRxiv (2024)
|Ext.|Pre		Reported Trait: Type 2 diabetesOR: 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)—
PPM021434PSS011747|
European Ancestry|
245,177 individuals
PGP000656 |
Ritchie SC et al. medRxiv (2024)
|Ext.|Pre		Reported Trait: Type 2 diabetesOR: 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)—
PPM021453PSS011738|
European Ancestry|
38,941 individuals
PGP000656 |
Ritchie SC et al. medRxiv (2024)
|Ext.|Pre		Reported Trait: Incident type 2 diabetesHR: 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)—
PPM021462PSS011746|
European Ancestry|
232,808 individuals
PGP000656 |
Ritchie SC et al. medRxiv (2024)
|Ext.|Pre		Reported Trait: Incident type 2 diabetesHR: 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)—
PPM021476PSS011735|
African Ancestry|
44,346 individuals
PGP000656 |
Ritchie SC et al. medRxiv (2024)
|Ext.|Pre		Reported Trait: Type 2 diabetesOR: 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)—
PPM021503PSS011736|
Hispanic or Latin American Ancestry|
33,652 individuals
PGP000656 |
Ritchie SC et al. medRxiv (2024)
|Ext.|Pre		Reported Trait: Type 2 diabetesOR: 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)—
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Evaluated Samples

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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
]
—EuropeanNorwegianHUNT—
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
]
—EuropeanBritishUKB—
PSS009546——
[
  • 1,120 cases
  • , 6,508 controls
]
—South Asian—UKB—
PSS011735T2D cases were ascertained based on a combination of hospital diagnosis codes, prescription medicati... on, 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 analysisShow more—
[
  • 5,663 cases
  • , 38,683 controls
]
—African unspecifiedAncestry label assigned based on genetic similarity with 1000 Genomes reference panel superpopulationsAllofUs—
PSS011736T2D cases were ascertained based on a combination of hospital diagnosis codes, prescription medicati... on, 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 analysisShow more—
[
  • 4,033 cases
  • , 29,619 controls
]
—Hispanic or Latin AmericanAncestry label assigned based on genetic similarity with 1000 Genomes reference panel superpopulationsAllofUs—
PSS011737T2D cases were ascertained based on a combination of hospital diagnosis codes, prescription medicati... on, 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 analysisShow more—
[
  • 10,069 cases
  • , 98,952 controls
]
—EuropeanAncestry label assigned based on genetic similarity with 1000 Genomes reference panel superpopulationsAllofUs—
PSS011738T2D 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 T2DShow more—
[
  • 726 cases
  • , 38,215 controls
]
—EuropeanAncestry label assigned based on genetic similarity with 1000 Genomes reference panel superpopulationsINTERVAL—
PSS011739Incident T2D was ascertained through a combination of linkage to national healthcare records, self-r... eported 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)Show more—
[
  • 187 cases
  • , 683 controls
]
—South East Asian
(Malay Singaporean)		Ancestry label assigned based on Malay being the majority reported ethnicity within the genetic clusterSingaporeMEC—
PSS011740Incident T2D was ascertained through a combination of linkage to national healthcare records, self-r... eported 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)Show more—
[
  • 205 cases
  • , 944 controls
]
—East Asian
(Chinese Singaporean)		Ancestry label assigned based on genetic similarity with 1000 Genomes reference panel superpopulationsSingaporeMEC—
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