Polygenic Score (PGS) ID: PGS001179

Predicted Trait
Reported Trait Vascular dementia (time-to-event)
Mapped Trait(s) vascular dementia (EFO_0004718)
Additional Trait Information https://biobankengine.stanford.edu/RIVAS_HG19/snpnet/HC711
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_HC711
Development Method
Name snpnet
Parameters NR
Variants
Original Genome Build GRCh37
Number of Variants 7
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
—
[
  • 365 cases
  • , 269,339 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
PPM008585 PSS004618|
African Ancestry|
6,497 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: TTE vascular dementia — AUROC: 0.89609 [0.78011, 1.0] R²: 0.23133
Incremental AUROC (full-covars): -0.00271
PGS R2 (no covariates): 0.00098
PGS AUROC (no covariates): 0.45314 [0.26337, 0.6429]		 age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM008586 PSS004619|
European Ancestry|
24,905 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: TTE vascular dementia — AUROC: 0.86436 [0.80883, 0.91989] R²: 0.14328
Incremental AUROC (full-covars): 0.00289
PGS R2 (no covariates): 0.00776
PGS AUROC (no covariates): 0.59245 [0.49395, 0.69095]		 age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM008587 PSS004620|
South Asian Ancestry|
7,831 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: TTE vascular dementia — AUROC: 0.83842 [0.72824, 0.9486] R²: 0.14604
Incremental AUROC (full-covars): 0.00843
PGS R2 (no covariates): 0.0135
PGS AUROC (no covariates): 0.61894 [0.47358, 0.76431]		 age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM008588 PSS004621|
European Ancestry|
67,425 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: TTE vascular dementia — AUROC: 0.82562 [0.78593, 0.86531] R²: 0.10475
Incremental AUROC (full-covars): 0.00707
PGS R2 (no covariates): 0.01123
PGS AUROC (no covariates): 0.61306 [0.55366, 0.67245]		 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
PSS004620 — —
[
  • 16 cases
  • , 7,815 controls
]
 — South Asian — UKB —
PSS004621 — —
[
  • 97 cases
  • , 67,328 controls
]
 — European white British ancestry UKB Testing cohort (heldout set)
PSS004618 — —
[
  • 12 cases
  • , 6,485 controls
]
 — African unspecified — UKB —
PSS004619 — —
[
  • 36 cases
  • , 24,869 controls
]
 — European non-white British ancestry UKB —