Polygenic Score (PGS) ID: PGS001509

Predicted Trait
Reported Trait Median T2star in pallidum (L)
Mapped Trait(s) neuroimaging measurement (EFO_0004346)
Additional Trait Information https://biobankengine.stanford.edu/RIVAS_HG19/snpnet/INI25032
Released in PGS Catalog: Nov. 25, 2021
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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_INI25032
Development Method
Name snpnet
Parameters NR
Variants
Original Genome Build GRCh37
Number of Variants 942
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%
20,228 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
— 20,228 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
PPM005485 PSS005321|
African Ancestry|
177 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: Median T2star in pallidum (L) — — R²: 0.1042 [0.09015, 0.11826]
Incremental R2 (full-covars): 0.00954
PGS R2 (no covariates): 0.01123 [0.00614, 0.01632]		 age, sex, UKB array type, Genotype PCs —
PPM005486 PSS005322|
East Asian Ancestry|
103 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: Median T2star in pallidum (L) — — R²: 0.11852 [0.08977, 0.14728]
Incremental R2 (full-covars): 0.06825
PGS R2 (no covariates): 0.0829 [0.05787, 0.10792]		 age, sex, UKB array type, Genotype PCs —
PPM005487 PSS005323|
European Ancestry|
1,543 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: Median T2star in pallidum (L) — — R²: 0.08374 [0.07715, 0.09032]
Incremental R2 (full-covars): 0.07536
PGS R2 (no covariates): 0.0774 [0.07102, 0.08377]		 age, sex, UKB array type, Genotype PCs —
PPM005488 PSS005324|
South Asian Ancestry|
293 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: Median T2star in pallidum (L) — — R²: 0.10933 [0.09629, 0.12237]
Incremental R2 (full-covars): 0.0589
PGS R2 (no covariates): 0.07995 [0.06844, 0.09147]		 age, sex, UKB array type, Genotype PCs —
PPM005489 PSS005325|
European Ancestry|
4,942 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: Median T2star in pallidum (L) — — R²: 0.0947 [0.0905, 0.09891]
Incremental R2 (full-covars): 0.08949
PGS R2 (no covariates): 0.09078 [0.08664, 0.09491]		 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
PSS005321 — — 177 individuals — African unspecified — UKB —
PSS005322 — — 103 individuals — East Asian — UKB —
PSS005323 — — 1,543 individuals — European non-white British ancestry UKB —
PSS005324 — — 293 individuals — South Asian — UKB —
PSS005325 — — 4,942 individuals — European white British ancestry UKB Testing cohort (heldout set)