Trait: caudate nucleus volume

Experimental Factor Ontology (EFO) Information
Identifier EFO_0004830
Description The volume of the caudate nucleus, a brain structure implicated in many common neurological and psychiatric disorders
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)
PGS001542
(GBE_INI25013)
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Volume of caudate (L) neuroimaging measurement,
caudate nucleus volume		 1,055
-
 https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS001542/ScoringFiles/PGS001542.txt.gz
PGS001543
(GBE_INI25014)
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Volume of caudate (R) neuroimaging measurement,
caudate nucleus volume		 1,910
-
 https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS001543/ScoringFiles/PGS001543.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
PPM005414 PGS001542
(GBE_INI25013)
 PSS005250|
European Ancestry|
5,443 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: Vol. of caudate (L) — — R²: 0.14115 [0.13628, 0.14602]
Incremental R2 (full-covars): 0.02462
PGS R2 (no covariates): 0.02936 [0.02685, 0.03187]		 age, sex, UKB array type, Genotype PCs —
PPM005410 PGS001542
(GBE_INI25013)
 PSS005246|
African Ancestry|
200 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: Vol. of caudate (L) — — R²: 0.23943 [0.22134, 0.25752]
Incremental R2 (full-covars): 0.0134
PGS R2 (no covariates): 0.00696 [0.00293, 0.01099]		 age, sex, UKB array type, Genotype PCs —
PPM005411 PGS001542
(GBE_INI25013)
 PSS005247|
East Asian Ancestry|
113 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: Vol. of caudate (L) — — R²: 0.13126 [0.10143, 0.16108]
Incremental R2 (full-covars): -0.03076
PGS R2 (no covariates): 0.00028 [-0.00131, 0.00188]		 age, sex, UKB array type, Genotype PCs —
PPM005412 PGS001542
(GBE_INI25013)
 PSS005248|
European Ancestry|
1,739 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: Vol. of caudate (L) — — R²: 0.1889 [0.18014, 0.19765]
Incremental R2 (full-covars): 0.03091
PGS R2 (no covariates): 0.03563 [0.03111, 0.04015]		 age, sex, UKB array type, Genotype PCs —
PPM005413 PGS001542
(GBE_INI25013)
 PSS005249|
South Asian Ancestry|
328 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: Vol. of caudate (L) — — R²: 0.2434 [0.22687, 0.25993]
Incremental R2 (full-covars): 0.01478
PGS R2 (no covariates): 0.00711 [0.0034, 0.01081]		 age, sex, UKB array type, Genotype PCs —
PPM005415 PGS001543
(GBE_INI25014)
 PSS005251|
African Ancestry|
200 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: Vol. of caudate (R) — — R²: 0.22602 [0.20813, 0.24391]
Incremental R2 (full-covars): 0.00503
PGS R2 (no covariates): 0.00505 [0.00162, 0.00849]		 age, sex, UKB array type, Genotype PCs —
PPM005416 PGS001543
(GBE_INI25014)
 PSS005252|
East Asian Ancestry|
113 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: Vol. of caudate (R) — — R²: 0.15452 [0.12303, 0.18602]
Incremental R2 (full-covars): -0.02257
PGS R2 (no covariates): 0.00857 [-0.00013, 0.01726]		 age, sex, UKB array type, Genotype PCs —
PPM005417 PGS001543
(GBE_INI25014)
 PSS005253|
European Ancestry|
1,739 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: Vol. of caudate (R) — — R²: 0.19467 [0.18584, 0.20349]
Incremental R2 (full-covars): 0.04031
PGS R2 (no covariates): 0.04548 [0.04042, 0.05053]		 age, sex, UKB array type, Genotype PCs —
PPM005418 PGS001543
(GBE_INI25014)
 PSS005254|
South Asian Ancestry|
328 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: Vol. of caudate (R) — — R²: 0.24337 [0.22685, 0.2599]
Incremental R2 (full-covars): 0.01477
PGS R2 (no covariates): 0.00986 [0.00551, 0.01421]		 age, sex, UKB array type, Genotype PCs —
PPM005419 PGS001543
(GBE_INI25014)
 PSS005255|
European Ancestry|
5,443 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: Vol. of caudate (R) — — R²: 0.14561 [0.14069, 0.15053]
Incremental R2 (full-covars): 0.03457
PGS R2 (no covariates): 0.03729 [0.03448, 0.04009]		 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
PSS005246 — — 200 individuals — African unspecified — UKB —
PSS005247 — — 113 individuals — East Asian — UKB —
PSS005248 — — 1,739 individuals — European non-white British ancestry UKB —
PSS005249 — — 328 individuals — South Asian — UKB —
PSS005250 — — 5,443 individuals — European white British ancestry UKB Testing cohort (heldout set)
PSS005251 — — 200 individuals — African unspecified — UKB —
PSS005252 — — 113 individuals — East Asian — UKB —
PSS005253 — — 1,739 individuals — European non-white British ancestry UKB —
PSS005254 — — 328 individuals — South Asian — UKB —
PSS005255 — — 5,443 individuals — European white British ancestry UKB Testing cohort (heldout set)