Polygenic Score (PGS) ID: PGS002026

Predicted Trait
Reported Trait Type 2 diabetes
Mapped Trait(s) type II diabetes mellitus (EFO_0001360)
Additional Trait Information endocrine/metabolic
Released in PGS Catalog: Jan. 10, 2022
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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
European: 37.5%
African: 25%
East Asian: 12.5%
Greater Middle Eastern: 12.5%
South Asian: 12.5%
8 Sample Sets

Development Samples

Score Development/Training
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
391,124 individuals European UK (+ Ireland) UKB

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

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
PSS009062 4,121 individuals European Poland (NE Europe) UKB
PSS008616 6,646 individuals European Italy (South Europe) UKB
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
PSS008841 3,896 individuals African unspecified Nigeria (West Africa) UKB
PSS008170 6,312 individuals South Asian India (South Asia) UKB
PSS007957 1,808 individuals East Asian China (East Asia) UKB
PSS007738 2,476 individuals African American or Afro-Caribbean Carribean UKB