Polygenic Score (PGS) ID: PGS001349

Predicted Trait
Reported Trait Alzheimer's disease (time-to-event)
Mapped Trait(s) Alzheimer disease (MONDO_0004975)
Additional Trait Information https://biobankengine.stanford.edu/RIVAS_HG19/snpnet/HC807
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_HC807
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: 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
—
[
  • 601 cases
  • , 269,103 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
PPM009225 PSS004632|
African Ancestry|
6,497 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: TTE alzheimer's disease — AUROC: 0.96248 [0.93046, 0.9945] R²: 0.31063
Incremental AUROC (full-covars): 0.00757
PGS R2 (no covariates): 0.03204
PGS AUROC (no covariates): 0.63583 [0.42385, 0.84781]		 age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM009226 PSS004634|
European Ancestry|
24,905 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: TTE alzheimer's disease — AUROC: 0.86841 [0.82079, 0.91602] R²: 0.16057
Incremental AUROC (full-covars): 0.03323
PGS R2 (no covariates): 0.05188
PGS AUROC (no covariates): 0.67961 [0.58969, 0.76952]		 age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM009227 PSS004635|
South Asian Ancestry|
7,831 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: TTE alzheimer's disease — AUROC: 0.9136 [0.8364, 0.9908] R²: 0.24293
Incremental AUROC (full-covars): 0.00891
PGS R2 (no covariates): 0.01019
PGS AUROC (no covariates): 0.53145 [0.34417, 0.71873]		 age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM009228 PSS004636|
European Ancestry|
67,425 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: TTE alzheimer's disease — AUROC: 0.8666 [0.84246, 0.89075] R²: 0.15418
Incremental AUROC (full-covars): 0.04665
PGS R2 (no covariates): 0.05271
PGS AUROC (no covariates): 0.71238 [0.66844, 0.75632]		 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
PSS004636 — —
[
  • 153 cases
  • , 67,272 controls
]
 — European white British ancestry UKB Testing cohort (heldout set)
PSS004632 — —
[
  • 11 cases
  • , 6,486 controls
]
 — African unspecified — UKB —
PSS004634 — —
[
  • 47 cases
  • , 24,858 controls
]
 — European non-white British ancestry UKB —
PSS004635 — —
[
  • 13 cases
  • , 7,818 controls
]
 — South Asian — UKB —