Polygenic Score (PGS) ID: PGS000929

Predicted Trait
Reported Trait All-cause dementia (algorithmically-defined)
Mapped Trait(s) dementia (MONDO_0001627)
Additional Trait Information https://biobankengine.stanford.edu/RIVAS_HG19/snpnet/HC1583
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_HC1583
Development Method
Name snpnet
Parameters NR
Variants
Original Genome Build GRCh37
Number of Variants 6
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
—
[
  • 1,419 cases
  • , 268,285 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
PPM007472 PSS004302|
African Ancestry|
6,497 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: AD all cause dementia — AUROC: 0.87071 [0.81635, 0.92507] R²: 0.20833
Incremental AUROC (full-covars): 0.0113
PGS R2 (no covariates): 0.01979
PGS AUROC (no covariates): 0.61107 [0.52126, 0.70088]		 age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM007473 PSS004303|
East Asian Ancestry|
1,704 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: AD all cause dementia — AUROC: 0.95182 [0.90381, 0.99984] R²: 0.22288
Incremental AUROC (full-covars): 0.00617
PGS R2 (no covariates): 0.01638
PGS AUROC (no covariates): 0.54656 [0.0, 1.0]		 age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM007474 PSS004304|
European Ancestry|
24,905 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: AD all cause dementia — AUROC: 0.81502 [0.78, 0.85005] R²: 0.12968
Incremental AUROC (full-covars): 0.00636
PGS R2 (no covariates): 0.01492
PGS AUROC (no covariates): 0.59229 [0.54215, 0.64242]		 age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM007475 PSS004305|
South Asian Ancestry|
7,831 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: AD all cause dementia — AUROC: 0.82116 [0.74776, 0.89457] R²: 0.1345
Incremental AUROC (full-covars): 0.00919
PGS R2 (no covariates): 0.02074
PGS AUROC (no covariates): 0.56393 [0.44983, 0.67804]		 age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM007476 PSS004306|
European Ancestry|
67,425 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: AD all cause dementia — AUROC: 0.81557 [0.79434, 0.8368] R²: 0.11649
Incremental AUROC (full-covars): 0.02294
PGS R2 (no covariates): 0.02346
PGS AUROC (no covariates): 0.62703 [0.59629, 0.65777]		 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
PSS004302 — —
[
  • 45 cases
  • , 6,452 controls
]
 — African unspecified — UKB —
PSS004303 — —
[
  • 2 cases
  • , 1,702 controls
]
 — East Asian — UKB —
PSS004304 — —
[
  • 141 cases
  • , 24,764 controls
]
 — European non-white British ancestry UKB —
PSS004305 — —
[
  • 34 cases
  • , 7,797 controls
]
 — South Asian — UKB —
PSS004306 — —
[
  • 358 cases
  • , 67,067 controls
]
 — European white British ancestry UKB Testing cohort (heldout set)