Polygenic Score (PGS) ID: PGS001117

Predicted Trait
Reported Trait Started insulin within one year diagnosis of diabetes
Mapped Trait(s) insulin use measurement (EFO_0600082)
Additional Trait Information https://biobankengine.stanford.edu/RIVAS_HG19/snpnet/BIN_FC10002986
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_BIN_FC10002986
Development Method
Name snpnet
Parameters NR
Variants
Original Genome Build GRCh37
Number of Variants 68
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%
13,223 individuals (100%)
PGS Evaluation
European: 40%
African: 20%
East Asian: 20%
South Asian: 20%
5 Sample Sets

Development Samples

Score Development/Training
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
—
[
  • 1,532 cases
  • , 11,691 controls
]
 European UKB — — — white British ancestry —

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
PPM008323 PSS003731|
African Ancestry|
705 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: Started insulin within one year diagnosis of diabetes — AUROC: 0.6057 [0.54935, 0.66205] R²: 0.03335
Incremental AUROC (full-covars): 0.01803
PGS R2 (no covariates): 0.00453
PGS AUROC (no covariates): 0.54401 [0.48567, 0.60235]		 age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM008324 PSS003732|
East Asian Ancestry|
86 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: Started insulin within one year diagnosis of diabetes — AUROC: 0.71573 [0.51412, 0.91734] R²: 0.15018
Incremental AUROC (full-covars): -0.09668
PGS R2 (no covariates): 0.11116
PGS AUROC (no covariates): 0.29582 [0.14557, 0.44606]		 age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM008325 PSS003733|
European Ancestry|
1,089 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: Started insulin within one year diagnosis of diabetes — AUROC: 0.80203 [0.75876, 0.8453] R²: 0.28861
Incremental AUROC (full-covars): 0.05722
PGS R2 (no covariates): 0.17586
PGS AUROC (no covariates): 0.72657 [0.67703, 0.77611]		 age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM008326 PSS003734|
South Asian Ancestry|
1,358 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: Started insulin within one year diagnosis of diabetes — AUROC: 0.62878 [0.57833, 0.67923] R²: 0.03294
Incremental AUROC (full-covars): 0.02324
PGS R2 (no covariates): 0.01621
PGS AUROC (no covariates): 0.58662 [0.53076, 0.64248]		 age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM008327 PSS003735|
European Ancestry|
3,243 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: Started insulin within one year diagnosis of diabetes — AUROC: 0.74056 [0.71173, 0.76938] R²: 0.17764
Incremental AUROC (full-covars): 0.0941
PGS R2 (no covariates): 0.12982
PGS AUROC (no covariates): 0.71086 [0.68153, 0.74018]		 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
PSS003731 — —
[
  • 115 cases
  • , 590 controls
]
 — African unspecified — UKB —
PSS003732 — —
[
  • 9 cases
  • , 77 controls
]
 — East Asian — UKB —
PSS003733 — —
[
  • 143 cases
  • , 946 controls
]
 — European non-white British ancestry UKB —
PSS003734 — —
[
  • 120 cases
  • , 1,238 controls
]
 — South Asian — UKB —
PSS003735 — —
[
  • 397 cases
  • , 2,846 controls
]
 — European white British ancestry UKB Testing cohort (heldout set)