Trait: white matter volume measurement

Experimental Factor Ontology (EFO) Information
Identifier EFO_0008320
Description quantification of the volume of white matter in the brain, usually through an MRI scan
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)
PGS001540
(GBE_INI25010)
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Volume of brain, grey+white matter neuroimaging measurement,
grey matter volume measurement,
white matter volume measurement		 1,871
-
 https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS001540/ScoringFiles/PGS001540.txt.gz
PGS001541
(GBE_INI25009)
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Volume of brain, grey+white matter (normalised for head size) neuroimaging measurement,
grey matter volume measurement,
white matter volume measurement		 1,999
-
 https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS001541/ScoringFiles/PGS001541.txt.gz
PGS001640
(GBE_INI25008)
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Volume of white matter neuroimaging measurement,
white matter volume measurement		 1,328
-
 https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS001640/ScoringFiles/PGS001640.txt.gz
PGS001641
(GBE_INI25007)
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Volume of white matter (normalised for head size) neuroimaging measurement,
white matter volume measurement		 1,005
-
 https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS001641/ScoringFiles/PGS001641.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
PPM005395 PGS001540
(GBE_INI25010)
 PSS005231|
African Ancestry|
200 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: Vol. of brain, grey+white matter — — R²: 0.40405 [0.38564, 0.42247]
Incremental R2 (full-covars): -0.0292
PGS R2 (no covariates): 0.02189 [0.01486, 0.02893]		 age, sex, UKB array type, Genotype PCs —
PPM005396 PGS001540
(GBE_INI25010)
 PSS005232|
East Asian Ancestry|
113 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: Vol. of brain, grey+white matter — — R²: 0.38326 [0.34708, 0.41945]
Incremental R2 (full-covars): -0.00215
PGS R2 (no covariates): 0.00409 [-0.00195, 0.01013]		 age, sex, UKB array type, Genotype PCs —
PPM005397 PGS001540
(GBE_INI25010)
 PSS005233|
European Ancestry|
1,739 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: Vol. of brain, grey+white matter — — R²: 0.45229 [0.44314, 0.46144]
Incremental R2 (full-covars): 0.02333
PGS R2 (no covariates): 0.02441 [0.02062, 0.02819]		 age, sex, UKB array type, Genotype PCs —
PPM005398 PGS001540
(GBE_INI25010)
 PSS005234|
South Asian Ancestry|
329 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: Vol. of brain, grey+white matter — — R²: 0.45569 [0.43942, 0.47196]
Incremental R2 (full-covars): 0.03057
PGS R2 (no covariates): 0.03762 [0.02935, 0.04588]		 age, sex, UKB array type, Genotype PCs —
PPM005399 PGS001540
(GBE_INI25010)
 PSS005235|
European Ancestry|
5,445 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: Vol. of brain, grey+white matter — — R²: 0.385 [0.37924, 0.39076]
Incremental R2 (full-covars): 0.03029
PGS R2 (no covariates): 0.03704 [0.03424, 0.03984]		 age, sex, UKB array type, Genotype PCs —
PPM005390 PGS001541
(GBE_INI25009)
 PSS005226|
African Ancestry|
200 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: Vol. of brain, grey+white matter (normalised for head size) — — R²: 0.2789 [0.26039, 0.29741]
Incremental R2 (full-covars): 0.00112
PGS R2 (no covariates): 0.00104 [-0.00053, 0.0026]		 age, sex, UKB array type, Genotype PCs —
PPM005391 PGS001541
(GBE_INI25009)
 PSS005227|
East Asian Ancestry|
113 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: Vol. of brain, grey+white matter (normalised for head size) — — R²: 0.45936 [0.42463, 0.49408]
Incremental R2 (full-covars): 0.03238
PGS R2 (no covariates): 0.01529 [0.00375, 0.02683]		 age, sex, UKB array type, Genotype PCs —
PPM005392 PGS001541
(GBE_INI25009)
 PSS005228|
European Ancestry|
1,739 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: Vol. of brain, grey+white matter (normalised for head size) — — R²: 0.38285 [0.37336, 0.39233]
Incremental R2 (full-covars): 0.01799
PGS R2 (no covariates): 0.02279 [0.01913, 0.02645]		 age, sex, UKB array type, Genotype PCs —
PPM005393 PGS001541
(GBE_INI25009)
 PSS005229|
South Asian Ancestry|
329 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: Vol. of brain, grey+white matter (normalised for head size) — — R²: 0.3165 [0.29947, 0.33353]
Incremental R2 (full-covars): -0.00812
PGS R2 (no covariates): 0.00584 [0.00247, 0.0092]		 age, sex, UKB array type, Genotype PCs —
PPM005394 PGS001541
(GBE_INI25009)
 PSS005230|
European Ancestry|
5,445 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: Vol. of brain, grey+white matter (normalised for head size) — — R²: 0.35045 [0.34464, 0.35625]
Incremental R2 (full-covars): 0.02177
PGS R2 (no covariates): 0.01913 [0.01708, 0.02118]		 age, sex, UKB array type, Genotype PCs —
PPM005385 PGS001640
(GBE_INI25008)
 PSS005221|
African Ancestry|
200 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: Vol. of white matter — — R²: 0.43318 [0.41504, 0.45131]
Incremental R2 (full-covars): -0.011
PGS R2 (no covariates): 0.00301 [0.00035, 0.00566]		 age, sex, UKB array type, Genotype PCs —
PPM005386 PGS001640
(GBE_INI25008)
 PSS005222|
East Asian Ancestry|
113 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: Vol. of white matter — — R²: 0.34622 [0.30976, 0.38267]
Incremental R2 (full-covars): -0.00469
PGS R2 (no covariates): 0.0184 [0.00578, 0.03102]		 age, sex, UKB array type, Genotype PCs —
PPM005387 PGS001640
(GBE_INI25008)
 PSS005223|
European Ancestry|
1,739 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: Vol. of white matter — — R²: 0.42054 [0.4112, 0.42987]
Incremental R2 (full-covars): 0.02476
PGS R2 (no covariates): 0.03298 [0.02862, 0.03734]		 age, sex, UKB array type, Genotype PCs —
PPM005388 PGS001640
(GBE_INI25008)
 PSS005224|
South Asian Ancestry|
329 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: Vol. of white matter — — R²: 0.40545 [0.38868, 0.42221]
Incremental R2 (full-covars): 0.02195
PGS R2 (no covariates): 0.02301 [0.01645, 0.02957]		 age, sex, UKB array type, Genotype PCs —
PPM005389 PGS001640
(GBE_INI25008)
 PSS005225|
European Ancestry|
5,445 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: Vol. of white matter — — R²: 0.3624 [0.35661, 0.36819]
Incremental R2 (full-covars): 0.02639
PGS R2 (no covariates): 0.03437 [0.03167, 0.03707]		 age, sex, UKB array type, Genotype PCs —
PPM005380 PGS001641
(GBE_INI25007)
 PSS005216|
African Ancestry|
200 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: Vol. of white matter (normalised for head size) — — R²: 0.21512 [0.19743, 0.23282]
Incremental R2 (full-covars): -0.0154
PGS R2 (no covariates): 0.0028 [0.00023, 0.00536]		 age, sex, UKB array type, Genotype PCs —
PPM005381 PGS001641
(GBE_INI25007)
 PSS005217|
East Asian Ancestry|
113 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: Vol. of white matter (normalised for head size) — — R²: 0.22502 [0.19018, 0.25986]
Incremental R2 (full-covars): 0.01122
PGS R2 (no covariates): 0.01815 [0.00562, 0.03069]		 age, sex, UKB array type, Genotype PCs —
PPM005382 PGS001641
(GBE_INI25007)
 PSS005218|
European Ancestry|
1,739 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: Vol. of white matter (normalised for head size) — — R²: 0.16789 [0.15943, 0.17636]
Incremental R2 (full-covars): 0.02175
PGS R2 (no covariates): 0.02403 [0.02027, 0.02779]		 age, sex, UKB array type, Genotype PCs —
PPM005383 PGS001641
(GBE_INI25007)
 PSS005219|
South Asian Ancestry|
329 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: Vol. of white matter (normalised for head size) — — R²: 0.16364 [0.14866, 0.17861]
Incremental R2 (full-covars): 0.00858
PGS R2 (no covariates): 0.02028 [0.0141, 0.02646]		 age, sex, UKB array type, Genotype PCs —
PPM005384 PGS001641
(GBE_INI25007)
 PSS005220|
European Ancestry|
5,445 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: Vol. of white matter (normalised for head size) — — R²: 0.12086 [0.11624, 0.12547]
Incremental R2 (full-covars): 0.02406
PGS R2 (no covariates): 0.02556 [0.02321, 0.02791]		 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
PSS005216 — — 200 individuals — African unspecified — UKB —
PSS005217 — — 113 individuals — East Asian — UKB —
PSS005218 — — 1,739 individuals — European non-white British ancestry UKB —
PSS005219 — — 329 individuals — South Asian — UKB —
PSS005220 — — 5,445 individuals — European white British ancestry UKB Testing cohort (heldout set)
PSS005221 — — 200 individuals — African unspecified — UKB —
PSS005222 — — 113 individuals — East Asian — UKB —
PSS005223 — — 1,739 individuals — European non-white British ancestry UKB —
PSS005224 — — 329 individuals — South Asian — UKB —
PSS005225 — — 5,445 individuals — European white British ancestry UKB Testing cohort (heldout set)
PSS005226 — — 200 individuals — African unspecified — UKB —
PSS005227 — — 113 individuals — East Asian — UKB —
PSS005228 — — 1,739 individuals — European non-white British ancestry UKB —
PSS005229 — — 329 individuals — South Asian — UKB —
PSS005230 — — 5,445 individuals — European white British ancestry UKB Testing cohort (heldout set)
PSS005231 — — 200 individuals — African unspecified — UKB —
PSS005232 — — 113 individuals — East Asian — UKB —
PSS005233 — — 1,739 individuals — European non-white British ancestry UKB —
PSS005234 — — 329 individuals — South Asian — UKB —
PSS005235 — — 5,445 individuals — European white British ancestry UKB Testing cohort (heldout set)