PGS Catalog - PGS001465 / Mean ICVF in fornix on FA skeleton (Polygenic Score)

Polygenic Score (PGS) ID: PGS001465

Predicted Trait
Reported Trait	Mean ICVF in fornix on FA skeleton
Mapped Trait(s)	neuroimaging measurement (EFO_0004346) brain volume measurement (EFO_0006930)
Additional Trait Information	https://biobankengine.stanford.edu/RIVAS_HG19/snpnet/INI25349

Released in PGS Catalog: Nov. 25, 2021

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Score Details

Score Construction
PGS Name	GBE_INI25349
Development Method
Name	snpnet
Parameters	NR
Variants
Original Genome Build	GRCh37
Number of Variants	188
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% 21,080 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
—	21,080 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
PPM005685	PSS005521\| African Ancestry\| 182 individuals	PGP000244 \| Tanigawa Y et al. PLoS Genet (2022)	Reported Trait: Mean ICVF in fornix on FA skeleton	—	—	R²: 0.10875 [0.09446, 0.12304] Incremental R2 (full-covars): -0.00305 PGS R2 (no covariates): 0.00011 [-0.0004, 0.00063]	age, sex, UKB array type, Genotype PCs	—
PPM005686	PSS005522\| East Asian Ancestry\| 106 individuals	PGP000244 \| Tanigawa Y et al. PLoS Genet (2022)	Reported Trait: Mean ICVF in fornix on FA skeleton	—	—	R²: 0.07272 [0.04902, 0.09641] Incremental R2 (full-covars): -0.00139 PGS R2 (no covariates): 0.00024 [-0.00123, 0.00172]	age, sex, UKB array type, Genotype PCs	—
PPM005687	PSS005523\| European Ancestry\| 1,651 individuals	PGP000244 \| Tanigawa Y et al. PLoS Genet (2022)	Reported Trait: Mean ICVF in fornix on FA skeleton	—	—	R²: 0.06811 [0.06207, 0.07415] Incremental R2 (full-covars): 0.00582 PGS R2 (no covariates): 0.00481 [0.0031, 0.00653]	age, sex, UKB array type, Genotype PCs	—
PPM005688	PSS005524\| South Asian Ancestry\| 299 individuals	PGP000244 \| Tanigawa Y et al. PLoS Genet (2022)	Reported Trait: Mean ICVF in fornix on FA skeleton	—	—	R²: 0.14317 [0.12882, 0.15753] Incremental R2 (full-covars): 0.00998 PGS R2 (no covariates): 0.01486 [0.00954, 0.02018]	age, sex, UKB array type, Genotype PCs	—
PPM005689	PSS005525\| European Ancestry\| 5,120 individuals	PGP000244 \| Tanigawa Y et al. PLoS Genet (2022)	Reported Trait: Mean ICVF in fornix on FA skeleton	—	—	R²: 0.04937 [0.04618, 0.05255] Incremental R2 (full-covars): 0.00787 PGS R2 (no covariates): 0.0081 [0.00675, 0.00944]	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
PSS005521	—	—	182 individuals	—	African unspecified	—	UKB	—
PSS005522	—	—	106 individuals	—	East Asian	—	UKB	—
PSS005523	—	—	1,651 individuals	—	European	non-white British ancestry	UKB	—
PSS005524	—	—	299 individuals	—	South Asian	—	UKB	—
PSS005525	—	—	5,120 individuals	—	European	white British ancestry	UKB	Testing cohort (heldout set)