Predicted Trait | |
Reported Trait | Type 2 diabetes (T2D) |
Mapped Trait(s) | type 2 diabetes mellitus (MONDO_0005148) |
Additional Trait Information | Unadjusted weights |
Score Construction | |
PGS Name | T2D |
Development Method | |
Name | snpnet (multi-PRS) |
Parameters | Weighted combination of multiple biomarker PRS. 1,080,968 variants as input (directly genotyped variants, imputed HLA allelotypes, and CNVs) |
Variants | |
Original Genome Build | hg19 |
Number of Variants | 183,830 |
Effect Weight Type | weights.T2D |
PGS Source | |
PGS Catalog Publication (PGP) ID | PGP000128 |
Citation (link to publication) | Sinnott-Armstrong N et al. Nat Genet (2021) |
Ancestry Distribution | |
Score Development/Training | European: 100% 223,327 individuals (100%) |
PGS Evaluation | European: 100% 2 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 |
---|---|---|---|---|---|---|---|---|
Europe PMC: 10.1038/s41588-020-00757-z |
223,327 individuals | European (British) |
UKB | — | — | — | — | Training |
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 |
---|---|---|---|---|---|---|---|---|
PPM001605 | PSS000754| European Ancestry| 87,413 individuals |
PGP000128 | Sinnott-Armstrong N et al. Nat Genet (2021) |
Reported Trait: Type 2 diabetes | — | AUROC: 0.688 | — | Age, sex, PCs(1-10) | — |
PPM001615 | PSS000756| European Ancestry| 135,300 individuals |
PGP000128 | Sinnott-Armstrong N et al. Nat Genet (2021) |
Reported Trait: Type 2 diabetes | HR: 1.49 [1.47, 1.51] | C-index: 0.669 | — | Age as time scale, sex, batch, PCs(1-10) | — |
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 |
---|---|---|---|---|---|---|---|---|
PSS000754 | — | — | 87,413 individuals | — | European | — | UKB | — |
PSS000756 | ICD-10 E11.0 - E11.9 | — | [
|
— | European (Finnish) |
— | FinnGen | — |