Polygenic Score (PGS) ID: PGS001329

Predicted Trait
Reported Trait Unspecified diabetes mellitus (time-to-event)
Mapped Trait(s) diabetes mellitus (EFO_0000400)
Additional Trait Information https://biobankengine.stanford.edu/RIVAS_HG19/snpnet/HC652
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_HC652
Development Method
Name snpnet
Parameters NR
Variants
Original Genome Build GRCh37
Number of Variants 2,270
Effect Weight Type NR
PGS Source
PGS Catalog Publication (PGP) ID PGP000244
Citation (link to publication) Tanigawa Y et al. medRxiv (2021) Preprint
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
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
[
  • 11,955 cases
  • , 257,749 controls
]
European white British ancestry 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
PPM009132 PSS004580|
African Ancestry|
6,497 individuals
PGP000244 |
Tanigawa Y et al. medRxiv (2021)
|Pre
Reported Trait: TTE unspecified diabetes mellitus AUROC: 0.69503 [0.67407, 0.716] : 0.08972
Incremental AUROC (full-covars): 0.00332
PGS R2 (no covariates): 0.00713
PGS AUROC (no covariates): 0.55713 [0.53377, 0.58048]
age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM009133 PSS004581|
East Asian Ancestry|
1,704 individuals
PGP000244 |
Tanigawa Y et al. medRxiv (2021)
|Pre
Reported Trait: TTE unspecified diabetes mellitus AUROC: 0.70891 [0.65305, 0.76477] : 0.09058
Incremental AUROC (full-covars): 0.02211
PGS R2 (no covariates): 0.02321
PGS AUROC (no covariates): 0.60847 [0.55016, 0.66678]
age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM009134 PSS004582|
European Ancestry|
24,905 individuals
PGP000244 |
Tanigawa Y et al. medRxiv (2021)
|Pre
Reported Trait: TTE unspecified diabetes mellitus AUROC: 0.72437 [0.70887, 0.73987] : 0.08424
Incremental AUROC (full-covars): 0.03715
PGS R2 (no covariates): 0.02619
PGS AUROC (no covariates): 0.62743 [0.60999, 0.64487]
age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM009135 PSS004583|
South Asian Ancestry|
7,831 individuals
PGP000244 |
Tanigawa Y et al. medRxiv (2021)
|Pre
Reported Trait: TTE unspecified diabetes mellitus AUROC: 0.70359 [0.68854, 0.71865] : 0.11885
Incremental AUROC (full-covars): 0.02262
PGS R2 (no covariates): 0.02671
PGS AUROC (no covariates): 0.59807 [0.58121, 0.61493]
age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM009136 PSS004584|
European Ancestry|
67,425 individuals
PGP000244 |
Tanigawa Y et al. medRxiv (2021)
|Pre
Reported Trait: TTE unspecified diabetes mellitus AUROC: 0.7046 [0.69521, 0.71399] : 0.0749
Incremental AUROC (full-covars): 0.04078
PGS R2 (no covariates): 0.03024
PGS AUROC (no covariates): 0.63102 [0.62084, 0.64119]
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
PSS004580
[
  • 676 cases
  • , 5,821 controls
]
African unspecified UKB
PSS004581
[
  • 85 cases
  • , 1,619 controls
]
East Asian UKB
PSS004582
[
  • 964 cases
  • , 23,941 controls
]
European non-white British ancestry UKB
PSS004583
[
  • 1,284 cases
  • , 6,547 controls
]
South Asian UKB
PSS004584
[
  • 2,899 cases
  • , 64,526 controls
]
European white British ancestry UKB Testing cohort (heldout set)