Polygenic Score (PGS) ID: PGS001296

Predicted Trait
Reported Trait Insulin-dependent diabetes mellitus (time-to-event)
Mapped Trait(s) type I diabetes mellitus (EFO_0001359)
Additional Trait Information https://biobankengine.stanford.edu/RIVAS_HG19/snpnet/HC648
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_HC648
Development Method
Name snpnet
Parameters NR
Variants
Original Genome Build GRCh37
Number of Variants 356
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
[
  • 2,214 cases
  • , 267,490 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
PPM008978 PSS004570|
African Ancestry|
6,497 individuals
PGP000244 |
Tanigawa Y et al. medRxiv (2021)
|Pre
Reported Trait: TTE insulin-dependent diabetes mellitus AUROC: 0.66885 [0.62172, 0.71599] : 0.04054
Incremental AUROC (full-covars): -0.01128
PGS R2 (no covariates): 0.00021
PGS AUROC (no covariates): 0.51906 [0.4689, 0.56923]
age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM008979 PSS004571|
East Asian Ancestry|
1,704 individuals
PGP000244 |
Tanigawa Y et al. medRxiv (2021)
|Pre
Reported Trait: TTE insulin-dependent diabetes mellitus AUROC: 0.89264 [0.80447, 0.98081] : 0.19006
Incremental AUROC (full-covars): -0.01413
PGS R2 (no covariates): 0.00422
PGS AUROC (no covariates): 0.43531 [0.15162, 0.71901]
age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM008980 PSS004572|
European Ancestry|
24,905 individuals
PGP000244 |
Tanigawa Y et al. medRxiv (2021)
|Pre
Reported Trait: TTE insulin-dependent diabetes mellitus AUROC: 0.70536 [0.66494, 0.74577] : 0.0607
Incremental AUROC (full-covars): 0.12077
PGS R2 (no covariates): 0.05496
PGS AUROC (no covariates): 0.68941 [0.64672, 0.73209]
age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM008981 PSS004573|
South Asian Ancestry|
7,831 individuals
PGP000244 |
Tanigawa Y et al. medRxiv (2021)
|Pre
Reported Trait: TTE insulin-dependent diabetes mellitus AUROC: 0.67679 [0.6379, 0.71568] : 0.04266
Incremental AUROC (full-covars): -0.01593
PGS R2 (no covariates): 0.0016
PGS AUROC (no covariates): 0.54249 [0.49552, 0.58946]
age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM008982 PSS004574|
European Ancestry|
67,425 individuals
PGP000244 |
Tanigawa Y et al. medRxiv (2021)
|Pre
Reported Trait: TTE insulin-dependent diabetes mellitus AUROC: 0.65986 [0.63673, 0.68299] : 0.03385
Incremental AUROC (full-covars): 0.06785
PGS R2 (no covariates): 0.02496
PGS AUROC (no covariates): 0.62694 [0.60131, 0.65256]
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
PSS004572
[
  • 186 cases
  • , 24,719 controls
]
European non-white British ancestry UKB
PSS004573
[
  • 153 cases
  • , 7,678 controls
]
South Asian UKB
PSS004574
[
  • 568 cases
  • , 66,857 controls
]
European white British ancestry UKB Testing cohort (heldout set)
PSS004570
[
  • 119 cases
  • , 6,378 controls
]
African unspecified UKB
PSS004571
[
  • 5 cases
  • , 1,699 controls
]
East Asian UKB