PGS Catalog - PGS001507 / Median T2star in caudate (L) (Polygenic Score)

Polygenic Score (PGS) ID: PGS001507

Predicted Trait
Reported Trait	Median T2star in caudate (L)
Mapped Trait(s)	neuroimaging measurement (EFO_0004346)
Additional Trait Information	https://biobankengine.stanford.edu/RIVAS_HG19/snpnet/INI25028

Released in PGS Catalog: Nov. 25, 2021

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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_INI25028
Development Method
Name	snpnet
Parameters	NR
Variants
Original Genome Build	GRCh37
Number of Variants	1,009
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
PPM005465	PSS005301\| African Ancestry\| 177 individuals	PGP000244 \| Tanigawa Y et al. PLoS Genet (2022)	Reported Trait: Median T2star in caudate (L)	—	—	R²: 0.18535 [0.1683, 0.2024] Incremental R2 (full-covars): -0.00024 PGS R2 (no covariates): 0.00163 [-0.00033, 0.00359]	age, sex, UKB array type, Genotype PCs	—
PPM005466	PSS005302\| East Asian Ancestry\| 103 individuals	PGP000244 \| Tanigawa Y et al. PLoS Genet (2022)	Reported Trait: Median T2star in caudate (L)	—	—	R²: 0.12277 [0.09364, 0.1519] Incremental R2 (full-covars): 0.0064 PGS R2 (no covariates): 0.01704 [0.00488, 0.0292]	age, sex, UKB array type, Genotype PCs	—
PPM005467	PSS005303\| European Ancestry\| 1,543 individuals	PGP000244 \| Tanigawa Y et al. PLoS Genet (2022)	Reported Trait: Median T2star in caudate (L)	—	—	R²: 0.0983 [0.09127, 0.10532] Incremental R2 (full-covars): 0.0566 PGS R2 (no covariates): 0.06093 [0.05518, 0.06669]	age, sex, UKB array type, Genotype PCs	—
PPM005468	PSS005304\| South Asian Ancestry\| 293 individuals	PGP000244 \| Tanigawa Y et al. PLoS Genet (2022)	Reported Trait: Median T2star in caudate (L)	—	—	R²: 0.13605 [0.12194, 0.15016] Incremental R2 (full-covars): 0.03811 PGS R2 (no covariates): 0.03132 [0.02373, 0.03891]	age, sex, UKB array type, Genotype PCs	—
PPM005469	PSS005305\| European Ancestry\| 4,942 individuals	PGP000244 \| Tanigawa Y et al. PLoS Genet (2022)	Reported Trait: Median T2star in caudate (L)	—	—	R²: 0.09505 [0.09083, 0.09926] Incremental R2 (full-covars): 0.06213 PGS R2 (no covariates): 0.06423 [0.06065, 0.06781]	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
PSS005301	—	—	177 individuals	—	African unspecified	—	UKB	—
PSS005302	—	—	103 individuals	—	East Asian	—	UKB	—
PSS005303	—	—	1,543 individuals	—	European	non-white British ancestry	UKB	—
PSS005304	—	—	293 individuals	—	South Asian	—	UKB	—
PSS005305	—	—	4,942 individuals	—	European	white British ancestry	UKB	Testing cohort (heldout set)