Polygenic Score (PGS) ID: PGS001737

Predicted Trait
Reported Trait WA L3 in tract inferior longitudinal fasciculus (L)
Mapped Trait(s)
Additional Trait Information https://biobankengine.stanford.edu/RIVAS_HG19/snpnet/INI25637
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_INI25637
Development Method
Name snpnet
Parameters NR
Variants
Original Genome Build GRCh37
Number of Variants 919
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%
19,818 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
— 19,818 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
PPM006320 PSS006156|
African Ancestry|
166 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: WA L3 in tract inferior longitudinal fasciculus (L) — — R²: 0.16423 [0.14722, 0.18124]
Incremental R2 (full-covars): 0.00926
PGS R2 (no covariates): 0.00642 [0.00242, 0.01042]		 age, sex, UKB array type, Genotype PCs —
PPM006321 PSS006157|
East Asian Ancestry|
98 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: WA L3 in tract inferior longitudinal fasciculus (L) — — R²: 0.15937 [0.12658, 0.19215]
Incremental R2 (full-covars): 0.0253
PGS R2 (no covariates): 0.03762 [0.01938, 0.05585]		 age, sex, UKB array type, Genotype PCs —
PPM006322 PSS006158|
European Ancestry|
1,547 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: WA L3 in tract inferior longitudinal fasciculus (L) — — R²: 0.18611 [0.1771, 0.19512]
Incremental R2 (full-covars): 0.0276
PGS R2 (no covariates): 0.02428 [0.02038, 0.02818]		 age, sex, UKB array type, Genotype PCs —
PPM006323 PSS006159|
South Asian Ancestry|
283 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: WA L3 in tract inferior longitudinal fasciculus (L) — — R²: 0.08628 [0.074, 0.09856]
Incremental R2 (full-covars): -0.0015
PGS R2 (no covariates): 0.00458 [0.0015, 0.00766]		 age, sex, UKB array type, Genotype PCs —
PPM006324 PSS006160|
European Ancestry|
4,801 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: WA L3 in tract inferior longitudinal fasciculus (L) — — R²: 0.13759 [0.13261, 0.14258]
Incremental R2 (full-covars): 0.023
PGS R2 (no covariates): 0.02254 [0.02025, 0.02482]		 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
PSS006156 — — 166 individuals — African unspecified — UKB —
PSS006157 — — 98 individuals — East Asian — UKB —
PSS006158 — — 1,547 individuals — European non-white British ancestry UKB —
PSS006159 — — 283 individuals — South Asian — UKB —
PSS006160 — — 4,801 individuals — European white British ancestry UKB Testing cohort (heldout set)