Predicted Trait | |
Reported Trait | Type 2 diabetes |
Mapped Trait(s) | type 2 diabetes mellitus (MONDO_0005148) |
Score Construction | |
PGS Name | gePS_T2D |
Development Method | |
Name | Pruning and Thresholding (P+T) |
Parameters | P < 0.1; r2 < 0.6 |
Variants | |
Original Genome Build | GRCh37 |
Number of Variants | 171,249 |
Effect Weight Type | NR |
PGS Source | |
PGS Catalog Publication (PGP) ID | PGP000023 |
Citation (link to publication) | Mahajan A et al. Nat Genet (2018) |
Ancestry Distribution | |
Source of Variant Associations (GWAS) | |
Score Development/Training | European: 100% 117,946 individuals (100%) |
PGS Evaluation | European: 100% 1 Sample Sets |
Study Identifiers | Sample Numbers | Sample Ancestry | Cohort(s) |
---|---|---|---|
Europe PMC: 29632382 |
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European, African American or Afro-Caribbean, East Asian, Hispanic or Latin American, South Asian | NR |
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 |
---|---|---|---|---|---|---|---|---|
Europe PMC: 31322649 |
[
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European | UKB | Prevalent T2D status was defined using self-reported medical history and medication | — | — | — | — |
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 |
---|---|---|---|---|---|---|---|---|
PPM000080 | PSS000054| European Ancestry| 324,870 individuals |
PGP000024 | Udler MS et al. Endocr Rev (2019) |Ext. |
Reported Trait: Type 2 diabetes | — | AUROC: 0.66 | — | genotyping array, first 6 PCs of ancestry | — |
PPM000081 | PSS000054| European Ancestry| 324,870 individuals |
PGP000024 | Udler MS et al. Endocr Rev (2019) |Ext. |
Reported Trait: Type 2 diabetes | — | AUROC: 0.73 | — | age, sex, genotyping array, first 6 PCs of ancestry | — |
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 |
---|---|---|---|---|---|---|---|---|
PSS000054 | Prevalent T2D status was defined using self-reported medical history and medication | — | [
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— | European | — | UKB | — |