Polygenic Score (PGS) ID: PGS001534

Predicted Trait
Reported Trait Total Volume of white matter hyperintensities (from T1 and T2 FLAIR images)
Mapped Trait(s)
Additional Trait Information https://biobankengine.stanford.edu/RIVAS_HG19/snpnet/INI25781
Released in PGS Catalog: Nov. 25, 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_INI25781
Development Method
Name snpnet
Parameters NR
Variants
Original Genome Build GRCh37
Number of Variants 355
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%
21,575 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
— 21,575 individuals European UKB — — — white British ancestry Training + validation cohort (train_val)

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
PPM006600 PSS006436|
African Ancestry|
189 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: Total vol. of white matter hyperintensities (from T1 and T2 FLAIR images) — — R²: 0.19119 [0.174, 0.20838]
Incremental R2 (full-covars): -0.0148
PGS R2 (no covariates): 0.00168 [-0.00031, 0.00366]		 age, sex, UKB array type, Genotype PCs —
PPM006601 PSS006437|
East Asian Ancestry|
109 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: Total vol. of white matter hyperintensities (from T1 and T2 FLAIR images) — — R²: 0.1477 [0.11666, 0.17874]
Incremental R2 (full-covars): -0.00848
PGS R2 (no covariates): 0.00254 [-0.00222, 0.0073]		 age, sex, UKB array type, Genotype PCs —
PPM006602 PSS006438|
European Ancestry|
1,682 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: Total vol. of white matter hyperintensities (from T1 and T2 FLAIR images) — — R²: 0.16859 [0.16011, 0.17706]
Incremental R2 (full-covars): 0.00942
PGS R2 (no covariates): 0.00723 [0.00514, 0.00933]		 age, sex, UKB array type, Genotype PCs —
PPM006603 PSS006439|
South Asian Ancestry|
306 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: Total vol. of white matter hyperintensities (from T1 and T2 FLAIR images) — — R²: 0.14064 [0.12637, 0.15491]
Incremental R2 (full-covars): 0.0123
PGS R2 (no covariates): 0.01743 [0.01168, 0.02317]		 age, sex, UKB array type, Genotype PCs —
PPM006604 PSS006440|
European Ancestry|
5,254 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: Total vol. of white matter hyperintensities (from T1 and T2 FLAIR images) — — R²: 0.12904 [0.12431, 0.13376]
Incremental R2 (full-covars): 0.00365
PGS R2 (no covariates): 0.00373 [0.00281, 0.00465]		 age, sex, UKB array type, Genotype PCs —

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
PSS006436 — — 189 individuals — African unspecified — UKB —
PSS006437 — — 109 individuals — East Asian — UKB —
PSS006438 — — 1,682 individuals — European non-white British ancestry UKB —
PSS006439 — — 306 individuals — South Asian — UKB —
PSS006440 — — 5,254 individuals — European white British ancestry UKB Testing cohort (heldout set)