Polygenic Score (PGS) ID: PGS001740

Predicted Trait
Reported Trait WA L3 in tract superior thalamic radiation (L)
Mapped Trait(s)
Additional Trait Information https://biobankengine.stanford.edu/RIVAS_HG19/snpnet/INI25646
Released in PGS Catalog: Nov. 25, 2021
Download Score FTP directory
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_INI25646
Development Method
Name snpnet
Parameters NR
Variants
Original Genome Build GRCh37
Number of Variants 855
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%
21,081 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
— 21,081 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
PPM006335 PSS006171|
African Ancestry|
182 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: WA L3 in tract superior thalamic radiation (L) — — R²: 0.17589 [0.15909, 0.19269]
Incremental R2 (full-covars): -0.01636
PGS R2 (no covariates): 0.001 [-0.00054, 0.00254]		 age, sex, UKB array type, Genotype PCs —
PPM006336 PSS006172|
East Asian Ancestry|
106 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: WA L3 in tract superior thalamic radiation (L) — — R²: 0.15935 [0.12754, 0.19115]
Incremental R2 (full-covars): 0.01182
PGS R2 (no covariates): 0.02343 [0.00926, 0.03759]		 age, sex, UKB array type, Genotype PCs —
PPM006337 PSS006173|
European Ancestry|
1,651 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: WA L3 in tract superior thalamic radiation (L) — — R²: 0.14901 [0.14086, 0.15717]
Incremental R2 (full-covars): 0.00488
PGS R2 (no covariates): 0.00723 [0.00513, 0.00932]		 age, sex, UKB array type, Genotype PCs —
PPM006338 PSS006174|
South Asian Ancestry|
299 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: WA L3 in tract superior thalamic radiation (L) — — R²: 0.07527 [0.06403, 0.0865]
Incremental R2 (full-covars): 0.01049
PGS R2 (no covariates): 0.01193 [0.00715, 0.0167]		 age, sex, UKB array type, Genotype PCs —
PPM006339 PSS006175|
European Ancestry|
5,120 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: WA L3 in tract superior thalamic radiation (L) — — R²: 0.12986 [0.12512, 0.13459]
Incremental R2 (full-covars): 0.01453
PGS R2 (no covariates): 0.01538 [0.01354, 0.01722]		 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
PSS006172 — — 106 individuals — East Asian — UKB —
PSS006173 — — 1,651 individuals — European non-white British ancestry UKB —
PSS006174 — — 299 individuals — South Asian — UKB —
PSS006175 — — 5,120 individuals — European white British ancestry UKB Testing cohort (heldout set)
PSS006171 — — 182 individuals — African unspecified — UKB —