Polygenic Score (PGS) ID: PGS001328

Predicted Trait
Reported Trait Family history of diabetes
Mapped Trait(s) family history (EFO_0000493)
Additional Trait Information https://biobankengine.stanford.edu/RIVAS_HG19/snpnet/FH1220
Released in PGS Catalog: Oct. 21, 2021
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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_FH1220
Development Method
Name snpnet
Parameters NR
Variants
Original Genome Build GRCh37
Number of Variants 2,515
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: 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
—
[
  • 63,331 cases
  • , 206,373 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
PPM009127 PSS004054|
African Ancestry|
6,497 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: Diabetes (FH) — AUROC: 0.59818 [0.58435, 0.61201] R²: 0.0372
Incremental AUROC (full-covars): 0.00441
PGS R2 (no covariates): 0.00401
PGS AUROC (no covariates): 0.53127 [0.51708, 0.54547]		 age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM009128 PSS004055|
East Asian Ancestry|
1,704 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: Diabetes (FH) — AUROC: 0.56465 [0.53655, 0.59276] R²: 0.02549
Incremental AUROC (full-covars): 0.0225
PGS R2 (no covariates): 0.00709
PGS AUROC (no covariates): 0.53656 [0.50824, 0.56489]		 age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM009129 PSS004056|
European Ancestry|
24,905 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: Diabetes (FH) — AUROC: 0.58763 [0.57927, 0.59598] R²: 0.02799
Incremental AUROC (full-covars): 0.03336
PGS R2 (no covariates): 0.01623
PGS AUROC (no covariates): 0.56772 [0.55933, 0.57611]		 age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM009130 PSS004057|
South Asian Ancestry|
7,831 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: Diabetes (FH) — AUROC: 0.58336 [0.57075, 0.59597] R²: 0.03022
Incremental AUROC (full-covars): 0.03694
PGS R2 (no covariates): 0.02309
PGS AUROC (no covariates): 0.57176 [0.55908, 0.58443]		 age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM009131 PSS004058|
European Ancestry|
67,425 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: Diabetes (FH) — AUROC: 0.57463 [0.56952, 0.57975] R²: 0.01929
Incremental AUROC (full-covars): 0.05803
PGS R2 (no covariates): 0.01839
PGS AUROC (no covariates): 0.57283 [0.56773, 0.57794]		 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
PSS004054 — —
[
  • 2,779 cases
  • , 3,718 controls
]
 — African unspecified — UKB —
PSS004055 — —
[
  • 612 cases
  • , 1,092 controls
]
 — East Asian — UKB —
PSS004056 — —
[
  • 5,829 cases
  • , 19,076 controls
]
 — European non-white British ancestry UKB —
PSS004057 — —
[
  • 4,226 cases
  • , 3,605 controls
]
 — South Asian — UKB —
PSS004058 — —
[
  • 15,823 cases
  • , 51,602 controls
]
 — European white British ancestry UKB Testing cohort (heldout set)