Polygenic Score (PGS) ID: PGS001297

Predicted Trait
Reported Trait Type 1 diabetes (T1D)
Mapped Trait(s) type 1 diabetes mellitus (MONDO_0005147)
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. PLoS Genet (2022)
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
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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
—
[
  • 286 cases
  • , 269,418 controls
]
EuropeanUKB———white British ancestry—
Showing 1 to 1 of 1 rows

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.

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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
PPM008983PSS004457|
African Ancestry|
6,497 individuals
PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
Reported Trait: Type 1 diabetes—AUROC: 0.78146 [0.64554, 0.91738]R²: 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 PCsFull Model & PGS R2 is estimated using Nagelkerke's method
PPM008984PSS004458|
European Ancestry|
24,905 individuals
PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
Reported Trait: Type 1 diabetes—AUROC: 0.79737 [0.708, 0.88674]R²: 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 PCsFull Model & PGS R2 is estimated using Nagelkerke's method
PPM008985PSS004459|
South Asian Ancestry|
7,831 individuals
PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
Reported Trait: Type 1 diabetes—AUROC: 0.81031 [0.66359, 0.95703]R²: 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 PCsFull Model & PGS R2 is estimated using Nagelkerke's method
PPM008986PSS004460|
European Ancestry|
67,425 individuals
PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
Reported Trait: Type 1 diabetes—AUROC: 0.7643 [0.7041, 0.8245]R²: 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 PCsFull Model & PGS R2 is estimated using Nagelkerke's method
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Evaluated Samples

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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
PSS004457——
[
  • 9 cases
  • , 6,488 controls
]
—African unspecified—UKB—
PSS004458——
[
  • 33 cases
  • , 24,872 controls
]
—Europeannon-white British ancestryUKB—
PSS004459——
[
  • 7 cases
  • , 7,824 controls
]
—South Asian—UKB—
PSS004460——
[
  • 58 cases
  • , 67,367 controls
]
—Europeanwhite British ancestryUKBTesting cohort (heldout set)
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