Trait: brain stem volume measurement

Experimental Factor Ontology (EFO) Information
Identifier EFO_0010605
Description Quantification of the volume of the brainstem.
Trait category
Other measurement
Mapped term PMID: 31636452

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)
PGS001539
(GBE_INI25025)
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Volume of brain stem + 4th ventricle neuroimaging measurement,
fourth ventricle volume measurement,
brain stem volume measurement		 1,183
-
 https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS001539/ScoringFiles/PGS001539.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
PPM005455 PGS001539
(GBE_INI25025)
 PSS005291|
African Ancestry|
200 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: Vol. of brain stem + 4th ventricle — — R²: 0.2926 [0.274, 0.31119]
Incremental R2 (full-covars): 0.01256
PGS R2 (no covariates): 0.00642 [0.00255, 0.01029]		 age, sex, UKB array type, Genotype PCs —
PPM005456 PGS001539
(GBE_INI25025)
 PSS005292|
East Asian Ancestry|
113 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: Vol. of brain stem + 4th ventricle — — R²: 0.19093 [0.15743, 0.22443]
Incremental R2 (full-covars): 0.01554
PGS R2 (no covariates): 0.01543 [0.00384, 0.02701]		 age, sex, UKB array type, Genotype PCs —
PPM005457 PGS001539
(GBE_INI25025)
 PSS005293|
European Ancestry|
1,739 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: Vol. of brain stem + 4th ventricle — — R²: 0.25836 [0.249, 0.26772]
Incremental R2 (full-covars): 0.0229
PGS R2 (no covariates): 0.02689 [0.02293, 0.03085]		 age, sex, UKB array type, Genotype PCs —
PPM005458 PGS001539
(GBE_INI25025)
 PSS005294|
South Asian Ancestry|
328 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: Vol. of brain stem + 4th ventricle — — R²: 0.29818 [0.28121, 0.31514]
Incremental R2 (full-covars): 0.02021
PGS R2 (no covariates): 0.0085 [0.00446, 0.01255]		 age, sex, UKB array type, Genotype PCs —
PPM005459 PGS001539
(GBE_INI25025)
 PSS005295|
European Ancestry|
5,443 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: Vol. of brain stem + 4th ventricle — — R²: 0.23487 [0.22927, 0.24047]
Incremental R2 (full-covars): 0.02596
PGS R2 (no covariates): 0.02874 [0.02625, 0.03122]		 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
PSS005291 — — 200 individuals — African unspecified — UKB —
PSS005292 — — 113 individuals — East Asian — UKB —
PSS005293 — — 1,739 individuals — European non-white British ancestry UKB —
PSS005294 — — 328 individuals — South Asian — UKB —
PSS005295 — — 5,443 individuals — European white British ancestry UKB Testing cohort (heldout set)