Trait: white matter hyperintensity measurement

Experimental Factor Ontology (EFO) Information
Identifier EFO_0005665
Description quantification of white matter hyperintensity, usually measured by MRI
Trait category
Other measurement

Associated Polygenic Score(s)

Filter PGS by Participant Ancestry
Individuals included in:
G - Source of Variant Associations (GWAS)
D - Score Development/Training
E - PGS Evaluation
List of ancestries includes:
Display options:
Ancestry legend
Multi-ancestry (including European)
Multi-ancestry (excluding European)
African
East Asian
South Asian
Additional Asian Ancestries
European
Greater Middle Eastern
Hispanic or Latin American
Additional Diverse Ancestries
Not Reported
Polygenic Score ID & Name PGS Publication ID (PGP) Reported Trait Mapped Trait(s) (Ontology) Number of Variants Ancestry distribution
GWAS
Dev
Eval
 Scoring File (FTP Link)
PGS001534
(GBE_INI25781)
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Total Volume of white matter hyperintensities (from T1 and T2 FLAIR images) neuroimaging measurement,
white matter hyperintensity measurement		 355
-
 https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS001534/ScoringFiles/PGS001534.txt.gz

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) 		Evaluated Score 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 PGS001534
(GBE_INI25781)
 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 PGS001534
(GBE_INI25781)
 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 PGS001534
(GBE_INI25781)
 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 PGS001534
(GBE_INI25781)
 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 PGS001534
(GBE_INI25781)
 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)