Polygenic Score (PGS) ID: PGS001348

Predicted Trait
Reported Trait Alzheimer's disease (algorithmically-defined)
Mapped Trait(s) Alzheimer disease (MONDO_0004975)
Additional Trait Information https://biobankengine.stanford.edu/RIVAS_HG19/snpnet/HC1584
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_HC1584
Development Method
Name snpnet
Parameters NR
Variants
Original Genome Build GRCh37
Number of Variants 15
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
—
[
  • 538 cases
  • , 269,166 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
PPM009221 PSS004307|
African Ancestry|
6,497 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: AD alzheimer's disease — AUROC: 0.96694 [0.94819, 0.98568] R²: 0.31464
Incremental AUROC (full-covars): 0.01598
PGS R2 (no covariates): 0.04322
PGS AUROC (no covariates): 0.69389 [0.49462, 0.89316]		 age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM009222 PSS004309|
European Ancestry|
24,905 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: AD alzheimer's disease — AUROC: 0.8626 [0.81314, 0.91206] R²: 0.15552
Incremental AUROC (full-covars): 0.03113
PGS R2 (no covariates): 0.05179
PGS AUROC (no covariates): 0.66389 [0.57085, 0.75693]		 age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM009223 PSS004310|
South Asian Ancestry|
7,831 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: AD alzheimer's disease — AUROC: 0.91522 [0.82612, 1.0] R²: 0.23563
Incremental AUROC (full-covars): 0.0091
PGS R2 (no covariates): 0.01731
PGS AUROC (no covariates): 0.59348 [0.39906, 0.7879]		 age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM009224 PSS004311|
European Ancestry|
67,425 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: AD alzheimer's disease — AUROC: 0.8686 [0.84242, 0.89478] R²: 0.1517
Incremental AUROC (full-covars): 0.05292
PGS R2 (no covariates): 0.05685
PGS AUROC (no covariates): 0.72349 [0.67813, 0.76886]		 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
PSS004309 — —
[
  • 45 cases
  • , 24,860 controls
]
 — European non-white British ancestry UKB —
PSS004310 — —
[
  • 11 cases
  • , 7,820 controls
]
 — South Asian — UKB —
PSS004311 — —
[
  • 134 cases
  • , 67,291 controls
]
 — European white British ancestry UKB Testing cohort (heldout set)
PSS004307 — —
[
  • 11 cases
  • , 6,486 controls
]
 — African unspecified — UKB —