Polygenic Score (PGS) ID: PGS001541

Predicted Trait
Reported Trait Volume of brain, grey+white matter (normalised for head size)
Mapped Trait(s)
Additional Trait Information https://biobankengine.stanford.edu/RIVAS_HG19/snpnet/INI25009
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_INI25009
Development Method
Name snpnet
Parameters NR
Variants
Original Genome Build GRCh37
Number of Variants 1,999
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%
22,323 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
22,323 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
PPM005390 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) : 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 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) : 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 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) : 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 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) : 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 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) : 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

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
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)