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
JSONXMLCSVTXTMS-Excel
Loading, please wait
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 individualsEuropeanUKB———UK (+ Ireland)—
Showing 1 to 1 of 1 rows

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.

JSONXMLCSVTXTMS-Excel
Loading, please wait
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
PPM011082PSS009288|
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—
PPM011083PSS009062|
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—
PPM011084PSS008616|
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—
PPM011085PSS008392|
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—
PPM011086PSS008170|
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—
PPM011087PSS007957|
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—
PPM011088PSS007738|
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—
PPM011089PSS008841|
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—
PPM020889PSS011442|
European Ancestry|
564 individuals
PGP000599 |
Guarischi-Sousa R et al. Circ Genom Precis Med (2023)
|Ext.		Reported Trait: Raised coronary lesionOR: 0.96 [0.8, 1.16]————
PPM020894PSS011441|
African Ancestry|
504 individuals
PGP000599 |
Guarischi-Sousa R et al. Circ Genom Precis Med (2023)
|Ext.		Reported Trait: Raised coronary lesionOR: 1.1 [0.9, 1.35]————
PPM021418PSS011737|
European Ancestry|
109,021 individuals
PGP000656 |
Ritchie SC et al. medRxiv (2024)
|Ext.|Pre		Reported Trait: Type 2 diabetesOR: 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)—
PPM021446PSS011738|
European Ancestry|
38,941 individuals
PGP000656 |
Ritchie SC et al. medRxiv (2024)
|Ext.|Pre		Reported Trait: Incident type 2 diabetesHR: 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)—
PPM021473PSS011735|
African Ancestry|
44,346 individuals
PGP000656 |
Ritchie SC et al. medRxiv (2024)
|Ext.|Pre		Reported Trait: Type 2 diabetesOR: 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)—
PPM021496PSS011736|
Hispanic or Latin American Ancestry|
33,652 individuals
PGP000656 |
Ritchie SC et al. medRxiv (2024)
|Ext.|Pre		Reported Trait: Type 2 diabetesOR: 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)—
PPM021516PSS011740|
East Asian Ancestry|
1,149 individuals
PGP000656 |
Ritchie SC et al. medRxiv (2024)
|Ext.|Pre		Reported Trait: Incident type 2 diabetesOR: 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)—
Showing 1 to 15 of 23 rows
1525All
rows per page

Evaluated Samples

JSONXMLCSVTXTMS-Excel
Loading, please wait
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
PSS007738——2,476 individuals—African American or Afro-CaribbeanCarribeanUKB—
PSS007957——1,808 individuals—East AsianChina (East Asia)UKB—
PSS008170——6,312 individuals—South AsianIndia (South Asia)UKB—
PSS008392——1,197 individuals—Greater Middle Eastern (Middle Eastern, North African or Persian)Iran (Middle East)UKB—
PSS008616——6,646 individuals—EuropeanItaly (South Europe)UKB—
PSS008841——3,896 individuals—African unspecifiedNigeria (West Africa)UKB—
PSS009062——4,121 individuals—EuropeanPoland (NE Europe)UKB—
PSS009288——19,931 individuals—EuropeanUK (+ Ireland)UKB—
PSS011441——
[
  • 165 cases
  • , 339 controls
]
,
82.0 % Male samples
Mean = 27.5 yearsAfrican unspecified—PDAY—
PSS011442——
[
  • 181 cases
  • , 383 controls
]
,
77.0 % Male samples
Mean = 26.7 yearsEuropean—PDAY—
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—
Showing 1 to 15 of 23 rows
1525All
rows per page