Polygenic Score (PGS) ID: PGS001327

Predicted Trait
Reported Trait Diabetes
Mapped Trait(s) diabetes mellitus (EFO_0000400)
Additional Trait Information https://biobankengine.stanford.edu/RIVAS_HG19/snpnet/HC221
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_HC221
Development Method
Name snpnet
Parameters NR
Variants
Original Genome Build GRCh37
Number of Variants 4,053
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
[
  • 18,583 cases
  • , 251,121 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
PPM009122 PSS004359|
African Ancestry|
6,497 individuals
PGP000244 |
Tanigawa Y et al. medRxiv (2021)
|Pre
Reported Trait: Diabetes AUROC: 0.68586 [0.66802, 0.7037] : 0.09776
Incremental AUROC (full-covars): 0.00638
PGS R2 (no covariates): 0.00926
PGS AUROC (no covariates): 0.55541 [0.53643, 0.5744]
age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM009123 PSS004360|
East Asian Ancestry|
1,704 individuals
PGP000244 |
Tanigawa Y et al. medRxiv (2021)
|Pre
Reported Trait: Diabetes AUROC: 0.69569 [0.64958, 0.7418] : 0.08294
Incremental AUROC (full-covars): 0.01187
PGS R2 (no covariates): 0.01141
PGS AUROC (no covariates): 0.56178 [0.51127, 0.61228]
age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM009124 PSS004361|
European Ancestry|
24,905 individuals
PGP000244 |
Tanigawa Y et al. medRxiv (2021)
|Pre
Reported Trait: Diabetes AUROC: 0.70541 [0.69227, 0.71854] : 0.08595
Incremental AUROC (full-covars): 0.04263
PGS R2 (no covariates): 0.03446
PGS AUROC (no covariates): 0.63125 [0.61738, 0.64511]
age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM009125 PSS004362|
South Asian Ancestry|
7,831 individuals
PGP000244 |
Tanigawa Y et al. medRxiv (2021)
|Pre
Reported Trait: Diabetes AUROC: 0.68746 [0.67395, 0.70097] : 0.11895
Incremental AUROC (full-covars): 0.02618
PGS R2 (no covariates): 0.03527
PGS AUROC (no covariates): 0.60108 [0.5865, 0.61565]
age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM009126 PSS004363|
European Ancestry|
67,425 individuals
PGP000244 |
Tanigawa Y et al. medRxiv (2021)
|Pre
Reported Trait: Diabetes AUROC: 0.69818 [0.69047, 0.70589] : 0.08111
Incremental AUROC (full-covars): 0.04455
PGS R2 (no covariates): 0.03558
PGS AUROC (no covariates): 0.63112 [0.6228, 0.63945]
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
PSS004359
[
  • 1,023 cases
  • , 5,474 controls
]
African unspecified UKB
PSS004360
[
  • 132 cases
  • , 1,572 controls
]
East Asian UKB
PSS004361
[
  • 1,571 cases
  • , 23,334 controls
]
European non-white British ancestry UKB
PSS004362
[
  • 1,878 cases
  • , 5,953 controls
]
South Asian UKB
PSS004363
[
  • 4,540 cases
  • , 62,885 controls
]
European white British ancestry UKB Testing cohort (heldout set)