Polygenic Score (PGS) ID: PGS001371

Predicted Trait
Reported Trait Age diabetes diagnosed
Mapped Trait(s)
Additional Trait Information https://biobankengine.stanford.edu/RIVAS_HG19/snpnet/INI2976
Released in PGS Catalog: Nov. 25, 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_INI2976
Development Method
Name snpnet
Parameters NR
Variants
Original Genome Build GRCh37
Number of Variants 26
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%
13,026 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
13,026 individuals European white British ancestry UKB Training + validation cohort (train_val)

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
PPM007030 PSS006886|
African Ancestry|
673 individuals
PGP000244 |
Tanigawa Y et al. medRxiv (2021)
|Pre
Reported Trait: Age diabetes diagnosed : 0.28398 [0.26544, 0.30253]
Incremental R2 (full-covars): -0.00362
PGS R2 (no covariates): 0.00112 [-0.0005, 0.00275]
age, sex, UKB array type, Genotype PCs
PPM007031 PSS006887|
East Asian Ancestry|
86 individuals
PGP000244 |
Tanigawa Y et al. medRxiv (2021)
|Pre
Reported Trait: Age diabetes diagnosed : 0.31131 [0.27489, 0.34772]
Incremental R2 (full-covars): 0.00576
PGS R2 (no covariates): 0.00203 [-0.00223, 0.00629]
age, sex, UKB array type, Genotype PCs
PPM007032 PSS006888|
European Ancestry|
1,059 individuals
PGP000244 |
Tanigawa Y et al. medRxiv (2021)
|Pre
Reported Trait: Age diabetes diagnosed : 0.37828 [0.36879, 0.38778]
Incremental R2 (full-covars): 0.02371
PGS R2 (no covariates): 0.04728 [0.04214, 0.05243]
age, sex, UKB array type, Genotype PCs
PPM007033 PSS006889|
South Asian Ancestry|
1,335 individuals
PGP000244 |
Tanigawa Y et al. medRxiv (2021)
|Pre
Reported Trait: Age diabetes diagnosed : 0.20384 [0.18792, 0.21975]
Incremental R2 (full-covars): -0.00895
PGS R2 (no covariates): 0.00042 [-0.00049, 0.00133]
age, sex, UKB array type, Genotype PCs
PPM007034 PSS006890|
European Ancestry|
3,195 individuals
PGP000244 |
Tanigawa Y et al. medRxiv (2021)
|Pre
Reported Trait: Age diabetes diagnosed : 0.28031 [0.27455, 0.28606]
Incremental R2 (full-covars): 0.02294
PGS R2 (no covariates): 0.03923 [0.03636, 0.0421]
age, sex, UKB array type, Genotype PCs

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
PSS006886 673 individuals African unspecified UKB
PSS006887 86 individuals East Asian UKB
PSS006888 1,059 individuals European non-white British ancestry UKB
PSS006889 1,335 individuals South Asian UKB
PSS006890 3,195 individuals European white British ancestry UKB Testing cohort (heldout set)