Polygenic Score (PGS) ID: PGS000945

Predicted Trait
Reported Trait Dementia in Alzheimer's disease (time-to-event)
Mapped Trait(s)
Additional Trait Information https://biobankengine.stanford.edu/RIVAS_HG19/snpnet/HC710
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_HC710
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. PLoS Genet (2022)
Ancestry Distribution
Score Development/Training
European: 100%
269,704 individuals (100%)
PGS Evaluation
European: 50%
African: 25%
South Asian: 25%
4 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
—
[
  • 324 cases
  • , 269,380 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
PPM007551 PSS004614|
African Ancestry|
6,497 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: TTE dementia in alzheimer's disease — AUROC: 0.98515 [0.97381, 0.9965] R²: 0.33632
Incremental AUROC (full-covars): 0.00807
PGS R2 (no covariates): 0.02667
PGS AUROC (no covariates): 0.7414 [0.59579, 0.88702]		 age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM007552 PSS004615|
European Ancestry|
24,905 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: TTE dementia in alzheimer's disease — AUROC: 0.8807 [0.81377, 0.94763] R²: 0.16889
Incremental AUROC (full-covars): 0.0235
PGS R2 (no covariates): 0.04331
PGS AUROC (no covariates): 0.66609 [0.55451, 0.77766]		 age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM007553 PSS004616|
South Asian Ancestry|
7,831 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: TTE dementia in alzheimer's disease — AUROC: 0.9584 [0.92052, 0.99629] R²: 0.25982
Incremental AUROC (full-covars): 0.0131
PGS R2 (no covariates): 0.0675
PGS AUROC (no covariates): 0.67849 [0.36185, 0.99513]		 age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM007554 PSS004617|
European Ancestry|
67,425 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: TTE dementia in alzheimer's disease — AUROC: 0.8916 [0.86249, 0.9207] R²: 0.16679
Incremental AUROC (full-covars): 0.05458
PGS R2 (no covariates): 0.06543
PGS AUROC (no covariates): 0.75273 [0.69847, 0.80699]		 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
PSS004614 — —
[
  • 5 cases
  • , 6,492 controls
]
 — African unspecified — UKB —
PSS004615 — —
[
  • 27 cases
  • , 24,878 controls
]
 — European non-white British ancestry UKB —
PSS004616 — —
[
  • 6 cases
  • , 7,825 controls
]
 — South Asian — UKB —
PSS004617 — —
[
  • 80 cases
  • , 67,345 controls
]
 — European white British ancestry UKB Testing cohort (heldout set)