Polygenic Score (PGS) ID: PGS001297

Predicted Trait
Reported Trait Type 1 diabetes
Mapped Trait(s) type I diabetes mellitus (EFO_0001359)
Additional Trait Information https://biobankengine.stanford.edu/RIVAS_HG19/snpnet/HC337
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_HC337
Development Method
Name snpnet
Parameters NR
Variants
Original Genome Build GRCh37
Number of Variants 69
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: 50%
African: 25%
South Asian: 25%
4 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
[
  • 286 cases
  • , 269,418 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
PPM008983 PSS004457|
African Ancestry|
6,497 individuals
PGP000244 |
Tanigawa Y et al. medRxiv (2021)
|Pre
Reported Trait: Type 1 diabetes AUROC: 0.78146 [0.64554, 0.91738] : 0.08635
Incremental AUROC (full-covars): -0.05504
PGS R2 (no covariates): 0.00185
PGS AUROC (no covariates): 0.41884 [0.19064, 0.64704]
age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM008984 PSS004458|
European Ancestry|
24,905 individuals
PGP000244 |
Tanigawa Y et al. medRxiv (2021)
|Pre
Reported Trait: Type 1 diabetes AUROC: 0.79737 [0.708, 0.88674] : 0.11683
Incremental AUROC (full-covars): 0.09636
PGS R2 (no covariates): 0.0912
PGS AUROC (no covariates): 0.77118 [0.67108, 0.87128]
age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM008985 PSS004459|
South Asian Ancestry|
7,831 individuals
PGP000244 |
Tanigawa Y et al. medRxiv (2021)
|Pre
Reported Trait: Type 1 diabetes AUROC: 0.81031 [0.66359, 0.95703] : 0.06825
Incremental AUROC (full-covars): -0.01908
PGS R2 (no covariates): 6e-05
PGS AUROC (no covariates): 0.53853 [0.37761, 0.69945]
age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM008986 PSS004460|
European Ancestry|
67,425 individuals
PGP000244 |
Tanigawa Y et al. medRxiv (2021)
|Pre
Reported Trait: Type 1 diabetes AUROC: 0.7643 [0.7041, 0.8245] : 0.06625
Incremental AUROC (full-covars): 0.19149
PGS R2 (no covariates): 0.06103
PGS AUROC (no covariates): 0.76543 [0.70744, 0.82342]
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
PSS004460
[
  • 58 cases
  • , 67,367 controls
]
European white British ancestry UKB Testing cohort (heldout set)
PSS004457
[
  • 9 cases
  • , 6,488 controls
]
African unspecified UKB
PSS004458
[
  • 33 cases
  • , 24,872 controls
]
European non-white British ancestry UKB
PSS004459
[
  • 7 cases
  • , 7,824 controls
]
South Asian UKB