Trait: pallidum volume

Experimental Factor Ontology (EFO) Information
Identifier EFO_0006933
Description quantification of the volume of the pallidum or globus pallidus, a sub-cortical structure of the brain that is part of the telencephalon
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)
PGS001631
(GBE_INI25017)
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Volume of pallidum (L) neuroimaging measurement,
pallidum volume		 1,405
-
 https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS001631/ScoringFiles/PGS001631.txt.gz
PGS001632
(GBE_INI25018)
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Volume of pallidum (R) neuroimaging measurement,
pallidum volume		 303
-
 https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS001632/ScoringFiles/PGS001632.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
PPM005431 PGS001631
(GBE_INI25017)
 PSS005267|
East Asian Ancestry|
113 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: Vol. of pallidum (L) — — R²: 0.07632 [0.05214, 0.1005]
Incremental R2 (full-covars): -0.01186
PGS R2 (no covariates): 0.00144 [-0.00215, 0.00504]		 age, sex, UKB array type, Genotype PCs —
PPM005430 PGS001631
(GBE_INI25017)
 PSS005266|
African Ancestry|
200 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: Vol. of pallidum (L) — — R²: 0.12265 [0.10771, 0.13758]
Incremental R2 (full-covars): 0.00421
PGS R2 (no covariates): 0.00624 [0.00242, 0.01005]		 age, sex, UKB array type, Genotype PCs —
PPM005432 PGS001631
(GBE_INI25017)
 PSS005268|
European Ancestry|
1,739 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: Vol. of pallidum (L) — — R²: 0.13481 [0.12692, 0.1427]
Incremental R2 (full-covars): 0.0246
PGS R2 (no covariates): 0.02469 [0.02088, 0.02849]		 age, sex, UKB array type, Genotype PCs —
PPM005433 PGS001631
(GBE_INI25017)
 PSS005269|
South Asian Ancestry|
328 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: Vol. of pallidum (L) — — R²: 0.19628 [0.18051, 0.21204]
Incremental R2 (full-covars): 0.0148
PGS R2 (no covariates): 0.00627 [0.00278, 0.00975]		 age, sex, UKB array type, Genotype PCs —
PPM005434 PGS001631
(GBE_INI25017)
 PSS005270|
European Ancestry|
5,443 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: Vol. of pallidum (L) — — R²: 0.12713 [0.12243, 0.13183]
Incremental R2 (full-covars): 0.01655
PGS R2 (no covariates): 0.0196 [0.01753, 0.02167]		 age, sex, UKB array type, Genotype PCs —
PPM005435 PGS001632
(GBE_INI25018)
 PSS005271|
African Ancestry|
200 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: Vol. of pallidum (R) — — R²: 0.18922 [0.17207, 0.20636]
Incremental R2 (full-covars): 0.00945
PGS R2 (no covariates): 0.01528 [0.00936, 0.0212]		 age, sex, UKB array type, Genotype PCs —
PPM005436 PGS001632
(GBE_INI25018)
 PSS005272|
East Asian Ancestry|
113 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: Vol. of pallidum (R) — — R²: 0.07787 [0.05348, 0.10225]
Incremental R2 (full-covars): 0.016
PGS R2 (no covariates): 0.02811 [0.01267, 0.04356]		 age, sex, UKB array type, Genotype PCs —
PPM005437 PGS001632
(GBE_INI25018)
 PSS005273|
European Ancestry|
1,739 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: Vol. of pallidum (R) — — R²: 0.15735 [0.14905, 0.16565]
Incremental R2 (full-covars): 0.01102
PGS R2 (no covariates): 0.0135 [0.01065, 0.01634]		 age, sex, UKB array type, Genotype PCs —
PPM005438 PGS001632
(GBE_INI25018)
 PSS005274|
South Asian Ancestry|
328 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: Vol. of pallidum (R) — — R²: 0.22398 [0.20772, 0.24024]
Incremental R2 (full-covars): 0.01069
PGS R2 (no covariates): 0.00504 [0.00191, 0.00816]		 age, sex, UKB array type, Genotype PCs —
PPM005439 PGS001632
(GBE_INI25018)
 PSS005275|
European Ancestry|
5,443 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: Vol. of pallidum (R) — — R²: 0.13349 [0.12871, 0.13827]
Incremental R2 (full-covars): 0.01438
PGS R2 (no covariates): 0.01851 [0.01649, 0.02052]		 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
PSS005266 — — 200 individuals — African unspecified — UKB —
PSS005267 — — 113 individuals — East Asian — UKB —
PSS005268 — — 1,739 individuals — European non-white British ancestry UKB —
PSS005269 — — 328 individuals — South Asian — UKB —
PSS005270 — — 5,443 individuals — European white British ancestry UKB Testing cohort (heldout set)
PSS005271 — — 200 individuals — African unspecified — UKB —
PSS005272 — — 113 individuals — East Asian — UKB —
PSS005273 — — 1,739 individuals — European non-white British ancestry UKB —
PSS005274 — — 328 individuals — South Asian — UKB —
PSS005275 — — 5,443 individuals — European white British ancestry UKB Testing cohort (heldout set)