PGS Catalog - PGS001602 / Volume of grey matter in Supracalcarine Cortex (R) (Polygenic Score)

Polygenic Score (PGS) ID: PGS001602

Predicted Trait
Reported Trait	Volume of grey matter in Supracalcarine Cortex (R)
Mapped Trait(s)	neuroimaging measurement (EFO_0004346) grey matter volume measurement (EFO_0005420)
Additional Trait Information	https://biobankengine.stanford.edu/RIVAS_HG19/snpnet/INI25875

Released in PGS Catalog: Nov. 25, 2021

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Score Details

Score Construction
PGS Name	GBE_INI25875
Development Method
Name	snpnet
Parameters	NR
Variants
Original Genome Build	GRCh37
Number of Variants	527
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% 22,320 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
—	22,320 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
PPM006840	PSS006686\| African Ancestry\| 200 individuals	PGP000244 \| Tanigawa Y et al. PLoS Genet (2022)	Reported Trait: Vol. of grey matter in Supracalcarine Cortex (R)	—	—	R²: 0.15718 [0.14094, 0.17342] Incremental R2 (full-covars): 0.0142 PGS R2 (no covariates): 0.01358 [0.00799, 0.01917]	age, sex, UKB array type, Genotype PCs	—
PPM006841	PSS006687\| East Asian Ancestry\| 113 individuals	PGP000244 \| Tanigawa Y et al. PLoS Genet (2022)	Reported Trait: Vol. of grey matter in Supracalcarine Cortex (R)	—	—	R²: 0.1448 [0.11396, 0.17563] Incremental R2 (full-covars): -0.01922 PGS R2 (no covariates): 0.01943 [0.00648, 0.03238]	age, sex, UKB array type, Genotype PCs	—
PPM006842	PSS006688\| European Ancestry\| 1,739 individuals	PGP000244 \| Tanigawa Y et al. PLoS Genet (2022)	Reported Trait: Vol. of grey matter in Supracalcarine Cortex (R)	—	—	R²: 0.15399 [0.14575, 0.16224] Incremental R2 (full-covars): -0.00041 PGS R2 (no covariates): 0.00128 [0.00039, 0.00216]	age, sex, UKB array type, Genotype PCs	—
PPM006843	PSS006689\| South Asian Ancestry\| 329 individuals	PGP000244 \| Tanigawa Y et al. PLoS Genet (2022)	Reported Trait: Vol. of grey matter in Supracalcarine Cortex (R)	—	—	R²: 0.14505 [0.13063, 0.15946] Incremental R2 (full-covars): 0.01122 PGS R2 (no covariates): 0.01255 [0.00765, 0.01744]	age, sex, UKB array type, Genotype PCs	—
PPM006844	PSS006690\| European Ancestry\| 5,443 individuals	PGP000244 \| Tanigawa Y et al. PLoS Genet (2022)	Reported Trait: Vol. of grey matter in Supracalcarine Cortex (R)	—	—	R²: 0.08449 [0.08047, 0.0885] Incremental R2 (full-covars): 0.01016 PGS R2 (no covariates): 0.01074 [0.00919, 0.01228]	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
PSS006686	—	—	200 individuals	—	African unspecified	—	UKB	—
PSS006687	—	—	113 individuals	—	East Asian	—	UKB	—
PSS006688	—	—	1,739 individuals	—	European	non-white British ancestry	UKB	—
PSS006689	—	—	329 individuals	—	South Asian	—	UKB	—
PSS006690	—	—	5,443 individuals	—	European	white British ancestry	UKB	Testing cohort (heldout set)