Polygenic Score (PGS) ID: PGS001294

Predicted Trait
Reported Trait Non-insulin-dependent diabetes (time-to-event)
Mapped Trait(s) type 2 diabetes mellitus (MONDO_0005148)
Additional Trait Information https://biobankengine.stanford.edu/RIVAS_HG19/snpnet/HC649
Released in PGS Catalog: Oct. 21, 2021
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 GBE_HC649
Development Method
Name snpnet
Parameters NR
Variants
Original Genome Build GRCh37
Number of Variants 3,496
Effect Weight Type NR
PGS Source
PGS Catalog Publication (PGP) ID PGP000244
Citation (link to publication) Tanigawa Y et al. PLoS Genet (2022)
Ancestry Distribution
Score Development/Training
European: 100%
269,704 individuals (100%)
PGS Evaluation
European: 40%
African: 20%
East Asian: 20%
South Asian: 20%
5 Sample Sets

Development Samples

Score Development/Training
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
—
[
  • 16,478 cases
  • , 253,226 controls
]
 European UKB — — — white British ancestry —

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
PPM008968 PSS004575|
African Ancestry|
6,497 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: TTE non-insulin-dependent diabetes mellitus — AUROC: 0.70052 [0.68094, 0.7201] R²: 0.10493
Incremental AUROC (full-covars): 0.00213
PGS R2 (no covariates): 0.00615
PGS AUROC (no covariates): 0.54526 [0.52378, 0.56673]		 age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM008969 PSS004576|
East Asian Ancestry|
1,704 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: TTE non-insulin-dependent diabetes mellitus — AUROC: 0.75536 [0.71488, 0.79584] R²: 0.1242
Incremental AUROC (full-covars): 0.01544
PGS R2 (no covariates): 0.01604
PGS AUROC (no covariates): 0.5808 [0.52621, 0.63538]		 age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM008970 PSS004577|
European Ancestry|
24,905 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: TTE non-insulin-dependent diabetes mellitus — AUROC: 0.72888 [0.71557, 0.7422] R²: 0.10344
Incremental AUROC (full-covars): 0.03534
PGS R2 (no covariates): 0.03413
PGS AUROC (no covariates): 0.63582 [0.62119, 0.65045]		 age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM008971 PSS004578|
South Asian Ancestry|
7,831 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: TTE non-insulin-dependent diabetes mellitus — AUROC: 0.68707 [0.67293, 0.70121] R²: 0.11343
Incremental AUROC (full-covars): 0.01724
PGS R2 (no covariates): 0.02384
PGS AUROC (no covariates): 0.58532 [0.56986, 0.60078]		 age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM008972 PSS004579|
European Ancestry|
67,425 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: TTE non-insulin-dependent diabetes mellitus — AUROC: 0.71038 [0.70256, 0.71821] R²: 0.08854
Incremental AUROC (full-covars): 0.04133
PGS R2 (no covariates): 0.03493
PGS AUROC (no covariates): 0.63323 [0.62453, 0.64194]		 age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method

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
PSS004575 — —
[
  • 806 cases
  • , 5,691 controls
]
 — African unspecified — UKB —
PSS004576 — —
[
  • 106 cases
  • , 1,598 controls
]
 — East Asian — UKB —
PSS004577 — —
[
  • 1,354 cases
  • , 23,551 controls
]
 — European non-white British ancestry UKB —
PSS004578 — —
[
  • 1,637 cases
  • , 6,194 controls
]
 — South Asian — UKB —
PSS004579 — —
[
  • 4,071 cases
  • , 63,354 controls
]
 — European white British ancestry UKB Testing cohort (heldout set)