Polygenic Score (PGS) ID: PGS001539

Predicted Trait
Reported Trait Volume of brain stem + 4th ventricle
Mapped Trait(s)
Additional Trait Information https://biobankengine.stanford.edu/RIVAS_HG19/snpnet/INI25025
Released in PGS Catalog: Nov. 25, 2021
Download Score FTP directory
Terms and Licenses
PGS obtained from the Catalog should be cited appropriately, and used in accordance with any licensing restrictions set by the authors. See EBI Terms of Use (https://www.ebi.ac.uk/about/terms-of-use/) for additional details.

Score Details

Score Construction
PGS Name GBE_INI25025
Development Method
Name snpnet
Parameters NR
Variants
Original Genome Build GRCh37
Number of Variants 1,183
Effect Weight Type NR
PGS Source
PGS Catalog Publication (PGP) ID PGP000244
Citation (link to publication) Tanigawa Y et al. PLoS Genet (2022)
Ancestry Distribution
Score Development/Training
European: 100%
22,312 individuals (100%)
PGS Evaluation
European: 40%
African: 20%
East Asian: 20%
South Asian: 20%
5 Sample Sets

Development Samples

Score Development/Training
Study Identifiers Sample Numbers Sample Ancestry Cohort(s) Phenotype Definitions & Methods Age of Study Participants Participant Follow-up Time Additional Ancestry Description Additional Sample/Cohort Information
— 22,312 individuals European UKB — — — white British ancestry Training + validation cohort (train_val)

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) 		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 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 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 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 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 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)