Polygenic Score (PGS) ID: PGS000946

Predicted Trait
Reported Trait Unspecified dementia (time-to-event)
Mapped Trait(s) dementia (MONDO_0001627)
Additional Trait Information https://biobankengine.stanford.edu/RIVAS_HG19/snpnet/HC713
Released in PGS Catalog: Oct. 21, 2021
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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_HC713
Development Method
Name snpnet
Parameters NR
Variants
Original Genome Build GRCh37
Number of Variants 9
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
—
[
  • 700 cases
  • , 269,004 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
PPM007555 PSS004622|
African Ancestry|
6,497 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: TTE unspecified dementia — AUROC: 0.82014 [0.73087, 0.90941] R²: 0.13536
Incremental AUROC (full-covars): 0.02407
PGS R2 (no covariates): 0.01431
PGS AUROC (no covariates): 0.57071 [0.42666, 0.71476]		 age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM007556 PSS004624|
European Ancestry|
24,905 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: TTE unspecified dementia — AUROC: 0.82275 [0.77979, 0.86571] R²: 0.12092
Incremental AUROC (full-covars): 0.00342
PGS R2 (no covariates): 0.00838
PGS AUROC (no covariates): 0.57672 [0.50856, 0.64487]		 age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM007557 PSS004625|
South Asian Ancestry|
7,831 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: TTE unspecified dementia — AUROC: 0.90804 [0.86257, 0.9535] R²: 0.20027
Incremental AUROC (full-covars): 0.0061
PGS R2 (no covariates): 0.0151
PGS AUROC (no covariates): 0.56115 [0.41165, 0.71066]		 age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM007558 PSS004626|
European Ancestry|
67,425 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: TTE unspecified dementia — AUROC: 0.83545 [0.80839, 0.8625] R²: 0.11896
Incremental AUROC (full-covars): 0.02339
PGS R2 (no covariates): 0.02543
PGS AUROC (no covariates): 0.64149 [0.59989, 0.68308]		 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
PSS004622 — —
[
  • 24 cases
  • , 6,473 controls
]
 — African unspecified — UKB —
PSS004624 — —
[
  • 80 cases
  • , 24,825 controls
]
 — European non-white British ancestry UKB —
PSS004625 — —
[
  • 21 cases
  • , 7,810 controls
]
 — South Asian — UKB —
PSS004626 — —
[
  • 197 cases
  • , 67,228 controls
]
 — European white British ancestry UKB Testing cohort (heldout set)