Polygenic Score (PGS) ID: PGS001347

Predicted Trait
Reported Trait Family history of Alzheimer's/dementia
Mapped Trait(s) family history of Alzheimer’s disease (EFO_0009268)
Additional Trait Information https://biobankengine.stanford.edu/RIVAS_HG19/snpnet/FH1263
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_FH1263
Development Method
Name snpnet
Parameters NR
Variants
Original Genome Build GRCh37
Number of Variants 139
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
—
[
  • 41,451 cases
  • , 228,253 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
PPM009216 PSS004059|
African Ancestry|
6,497 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: Alzheimer's/dementia (FH) — AUROC: 0.60815 [0.58401, 0.63228] R²: 0.02957
Incremental AUROC (full-covars): -0.00275
PGS R2 (no covariates): 0.00019
PGS AUROC (no covariates): 0.50162 [0.47638, 0.52686]		 age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM009217 PSS004060|
East Asian Ancestry|
1,704 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: Alzheimer's/dementia (FH) — AUROC: 0.65316 [0.60391, 0.70242] R²: 0.05029
Incremental AUROC (full-covars): 0.01325
PGS R2 (no covariates): 0.00988
PGS AUROC (no covariates): 0.55047 [0.49474, 0.60619]		 age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM009218 PSS004061|
European Ancestry|
24,905 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: Alzheimer's/dementia (FH) — AUROC: 0.60962 [0.60006, 0.61918] R²: 0.03194
Incremental AUROC (full-covars): 0.01629
PGS R2 (no covariates): 0.00825
PGS AUROC (no covariates): 0.55082 [0.5403, 0.56135]		 age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM009219 PSS004062|
South Asian Ancestry|
7,831 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: Alzheimer's/dementia (FH) — AUROC: 0.58721 [0.56379, 0.61063] R²: 0.01634
Incremental AUROC (full-covars): 0.00317
PGS R2 (no covariates): 0.00225
PGS AUROC (no covariates): 0.52129 [0.49619, 0.5464]		 age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM009220 PSS004063|
European Ancestry|
67,425 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: Alzheimer's/dementia (FH) — AUROC: 0.60904 [0.60337, 0.61471] R²: 0.03418
Incremental AUROC (full-covars): 0.02436
PGS R2 (no covariates): 0.01188
PGS AUROC (no covariates): 0.55827 [0.55209, 0.56446]		 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
PSS004060 — —
[
  • 129 cases
  • , 1,575 controls
]
 — East Asian — UKB —
PSS004061 — —
[
  • 3,496 cases
  • , 21,409 controls
]
 — European non-white British ancestry UKB —
PSS004062 — —
[
  • 596 cases
  • , 7,235 controls
]
 — South Asian — UKB —
PSS004063 — —
[
  • 10,334 cases
  • , 57,091 controls
]
 — European white British ancestry UKB Testing cohort (heldout set)
PSS004059 — —
[
  • 561 cases
  • , 5,936 controls
]
 — African unspecified — UKB —