Predicted Trait | |
Reported Trait | Type 2 diabetes (T2D) |
Mapped Trait(s) | type 2 diabetes mellitus (MONDO_0005148) |
Additional Trait Information | endocrine/metabolic |
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: 40% African: 30% East Asian: 10% Greater Middle Eastern: 10% South Asian: 10% 10 Sample Sets |
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 individuals | European | UKB | — | — | — | UK (+ Ireland) | — |
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 | — |
PPM020889 | PSS011442| European Ancestry| 564 individuals |
PGP000599 | Guarischi-Sousa R et al. Circ Genom Precis Med (2023) |Ext. |
Reported Trait: Raised coronary lesion | OR: 0.96 [0.8, 1.16] | — | — | — | — |
PPM020894 | PSS011441| African Ancestry| 504 individuals |
PGP000599 | Guarischi-Sousa R et al. Circ Genom Precis Med (2023) |Ext. |
Reported Trait: Raised coronary lesion | OR: 1.1 [0.9, 1.35] | — | — | — | — |
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 | — |
PSS011442 | — | — | [ ,
77.0 % Male samples |
Mean = 26.7 years | European | — | PDAY | — |
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 | — |
PSS011441 | — | — | [ ,
82.0 % Male samples |
Mean = 27.5 years | African unspecified | — | PDAY | — |
PSS007957 | — | — | 1,808 individuals | — | East Asian | China (East Asia) | UKB | — |
PSS007738 | — | — | 2,476 individuals | — | African American or Afro-Caribbean | Carribean | UKB | — |