Polygenic Score (PGS) ID: PGS001456

Predicted Trait
Reported Trait Mean ICVF in cerebral peduncle on FA skeleton (R)
Mapped Trait(s)
Additional Trait Information https://biobankengine.stanford.edu/RIVAS_HG19/snpnet/INI25358
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_INI25358
Development Method
Name snpnet
Parameters NR
Variants
Original Genome Build GRCh37
Number of Variants 1,501
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
PPM005720 PSS005556|
African Ancestry|
182 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: Mean ICVF in cerebral peduncle on FA skeleton (R) — — R²: 0.09 [0.07673, 0.10327]
Incremental R2 (full-covars): 0.00054
PGS R2 (no covariates): 0.00752 [0.00334, 0.01171]		 age, sex, UKB array type, Genotype PCs —
PPM005721 PSS005557|
East Asian Ancestry|
106 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: Mean ICVF in cerebral peduncle on FA skeleton (R) — — R²: 0.09328 [0.06704, 0.11952]
Incremental R2 (full-covars): -0.01462
PGS R2 (no covariates): 0.00513 [-0.00162, 0.01188]		 age, sex, UKB array type, Genotype PCs —
PPM005722 PSS005558|
European Ancestry|
1,651 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: Mean ICVF in cerebral peduncle on FA skeleton (R) — — R²: 0.10095 [0.09386, 0.10805]
Incremental R2 (full-covars): 0.04385
PGS R2 (no covariates): 0.04365 [0.03868, 0.04861]		 age, sex, UKB array type, Genotype PCs —
PPM005723 PSS005559|
South Asian Ancestry|
299 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: Mean ICVF in cerebral peduncle on FA skeleton (R) — — R²: 0.07997 [0.06845, 0.09149]
Incremental R2 (full-covars): 0.03617
PGS R2 (no covariates): 0.03394 [0.02606, 0.04182]		 age, sex, UKB array type, Genotype PCs —
PPM005724 PSS005560|
European Ancestry|
5,120 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: Mean ICVF in cerebral peduncle on FA skeleton (R) — — R²: 0.0692 [0.06551, 0.0729]
Incremental R2 (full-covars): 0.03131
PGS R2 (no covariates): 0.03321 [0.03055, 0.03587]		 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
PSS005556 — — 182 individuals — African unspecified — UKB —
PSS005557 — — 106 individuals — East Asian — UKB —
PSS005558 — — 1,651 individuals — European non-white British ancestry UKB —
PSS005559 — — 299 individuals — South Asian — UKB —
PSS005560 — — 5,120 individuals — European white British ancestry UKB Testing cohort (heldout set)